Recent News

Recent News

Identification of NTRK3 Fusions in Childhood Melanocytic Neoplasms

Spitzoid neoplasms are a distinct group of melanocytic tumors. Genetically, they lack mutations in common melanoma-associated oncogenes. Recent studies have shown that spitzoid tumors may contain a variety of kinase fusions, including ROS1, NTRK1, ALK, BRAF, and RET fusions. We report herein the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms with spitzoid and/or atypical features, based on genome-wide copy number analysis by single-nucleotide polymorphism array, which showed intragenic copy number changes in NTRK3.

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A One-Step PCR-Based Assay to Evaluate the Efficiency and Precision of Genomic DNA-Editing Tools

Despite rapid progress, many problems and limitations persist and limit the applicability of gene-editing techniques. Making use of meganucleases, TALENs, or CRISPR/Cas9-based tools requires an initial step of pre-screening to determine the efficiency and specificity of the designed tools. This step remains time consuming and material consuming. Here we propose a simple, cheap, reliable, time-saving, and highly sensitive method to evaluate a given gene-editing tool based on its capacity to induce chromosomal translocations when combined with a reference engineered nuclease.

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Partial tetrasomy 11q resulting from an intrachromosomal triplication of a 22 Mb region of chromosome 11

Intrachromosomal triplications are complex chromosomal rearrangements which arise during meiosis or mitosis and lead to a tetrasomic dose of the affected genomic regions. We describe a female patient harboring an intrachromosomal triplication who presented to the Genetics clinic with dysmorphic features, including telecanthus, flat facial profile, and prognathism, short stature, widely spaced nipples, multiple allergy complaints, loose bowel movements, and mild speech delay. Microarray analysis showed a copy number gain of a 22.37 Mb region of chromosome 11 between bands 11q14.1 and 11q22.1. This region contains 95 genes and seven microRNAs, none of which have been implicated in a disease resulting from increased gene dosage.

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Proteasome Ubiquitin Receptor PSMD4 is an Amplification Target in Breast Cancer and May Predict Sensitivity to PARPi

Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair under investigation as a chemotherapeutic target. Current randomized phase 3 trials of PARPi in metastatic breast cancer are limited to patients with documented BRCA1/2 mutations and no biomarker of PARPi beyond BRCA status is available. In an effort to identify novel biomarkers for PARP inihibition, we created a cell line (HCC1187/TALRES) resistant to the PARP1 inhibitor talazoparib. Herein we show by array-CGH that HCC1187/TALRES has a selective loss of the proteasome ubiquitin receptor PSMD4 amplicon resulting in significant down-regulation of PSMD4.

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Engineering of systematic elimination of a targeted chromosome in human cells

Embryonic trisomy leads to abortion or congenital genetic disorders in humans. The most common autosomal chromosome abnormalities are trisomy of chromosome 13, 18, and 21. Although alteration of gene dosage is thought to contribute to disorders caused by extra copies of chromosomes, genes associated with specific disease phenotypes remains unclear. To generate a normal cell from a trisomic cell as a means of etiological analysis or candidate therapy for trisomy syndromes, we developed a system to eliminate a targeted chromosome from human cells. Chromosome 21 was targeted by integration of a DNA cassette in HeLa cells that harbored three copies of chromosome 21. The DNA cassette included two inverted loxP sites and a herpes simplex virus thymidine kinase (HSV-tk) gene. This system causes mis-segregation of chromosome 21 after expression of Cre recombinase and subsequently, enables the selection of cells lacking the chromosome by culturing in a medium that includes ganciclovir (GCV). Cells harboring only two copies of chromosome 21 were efficiently induced by transfection of a Cre expression vector, indicating that this approach is useful for eliminating a targeted chromosome.

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Expression and trafficking of placental microRNAs at the feto-maternal interface

During pregnancy, placental trophoblasts at the feto-maternal interface produce a broad repertoire of microRNA (miRNA) species. These species include miRNA from the primate-specific chromosome 19 miRNA cluster (C19MC), which is expressed nearly exclusively in the placenta. Trafficking of these miRNAs among the maternal, placental, and fetal compartments is unknown. To determine miRNA expression and trafficking patterns during pregnancy, we sequenced miRNAs in triads of human placenta and of maternal and fetal blood and found large subject-to-subject variability, with C19MC exhibiting compartment-specific expression.

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CANT1 lncRNA triggers efficient therapeutic efficacy by correcting aberrant lncing cascade in malignant uveal melanoma

Uveal melanoma (UM) is an intraocular malignant tumor with high mortality rate.Recent studies have shown the functions of long non-coding RNAs (lncRNAs) in tumorigenesis, thus, targeting tumor-specific lncRNA abnormalities has become an attractive approach for developing therapeutics to treat uveal melanoma. In this study, we identified a novel nuclear CANT1 lncRNA (CASC15-New-Transcript 1) and acts as a necessary UM suppressor. CANT1 significantly reduced the tumor metastatic capacity and tumor formation, either in cell culture or in animals harboring tumor xenograft. Intriguingly, XIST lncRNA serves as a potential target of CANT1, and JPX or FTX lncRNA subsequently plays a contextual hinge to activate a novel CANT1-JPX/FTX-XIST long non-coding (lncing) pathway in UM. Moreover, CANT1 triggers the expression of JPX or FTX by directly binding to their promoters and promoting H3K4 methylation. These observations delineate a novel lncing cascade in which lncRNAs directly build a long non-coding cascade without coding genes that aims to modulate UM tumorigenesis, thereby specifying a novel lncing-cascade renewal anti-tumor therapeutic strategy by correcting aberrant lncing cascade in uveal melanoma.

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FANCD2 Binds Human Papillomavirus Genomes and Associates with a Distinct Set of DNA Repair Proteins to Regulate Viral Replication

The life cycle of human papillomavirus (HPV) is dependent on the differentiation state of its host cell. HPV genomes are maintained as low-copy episomes in basal epithelial cells and amplified to thousands of copies per cell in differentiated layers. Replication of high-risk HPVs requires the activation of the ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR) DNA repair pathways. The Fanconi anemia (FA) pathway is a part of the DNA damage response and mediates cross talk between the ATM and ATR pathways. Our studies show that HPV activates the FA pathway, leading to the accumulation of a key regulatory protein, FANCD2, in large nuclear foci. These HPV-dependent foci colocalize with a distinct population of DNA repair proteins, including ATM components ?H2AX and BRCA1, but infrequently with p-SMC1, which is required for viral genome amplification in differentiated cells. Furthermore, FANCD2 is found at viral replication foci, where it is preferentially recruited to viral genomes compared to cellular chromosomes and is required for maintenance of HPV episomes in undifferentiated cells. These findings identify FANCD2 as an important regulator of HPV replication and provide insight into the role of the DNA damage response in the differentiation-dependent life cycle of HPV.

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Impact of an alternative chromosome 17 probe and the 2013 American Society of Clinical Oncology and College of American Pathologists guidelines on fluorescence in situ hybridization for the determination of HER2 gene amplification in breast cancer

The dual-probe fluorescence in situ hybridization (FISH) assay for human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer provides an HER2:CEP17 (centromere enumeration probe for chromosome 17) ratio. Copy number alteration (CNA) in CEP17 may skew this ratio. The authors analyzed the impact of the 2013 American Society of Oncology/College of American Pathologists (ASCO/CAP) guidelines and an alternative chromosome 17 probe on HER2 status in tumor specimens with CEP17 CNA.

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A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica

An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.

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Centrosome Amplification Is Sufficient to Promote Spontaneous Tumorigenesis in Mammals

Centrosome amplification is a common feature of human tumors, but whether this is a cause or a consequence of cancer remains unclear. Here, we test the consequence of centrosome amplification by creating mice in which centrosome number can be chronically increased in the absence of additional genetic defects. We show that increasing centrosome number elevated tumor initiation in a mouse model of intestinal neoplasia. Most importantly, we demonstrate that supernumerary centrosomes are sufficient to drive aneuploidy and the development of spontaneous tumors in multiple tissues. Tumors arising from centrosome amplification exhibit frequent mitotic errors and possess complex karyotypes, recapitulating a common feature of human cancer. Together, our data support a direct causal relationship among centrosome amplification, genomic instability, and tumor development.

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Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis

Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal epithelial but not stroma cells, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.

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Incidence, clinicopathologic features, and fusion transcript landscape of translocation renal cell carcinomas

Aims
Translocation renal cell carcinoma (tRCC) is a rare subtype of kidney tumour characterized by translocations involving the transcription factor TFE3 or TFEB. tRCC was introduced into the World Health Organization classification in 2004, but much is still unknown about the natural history, clinicopathologic features, and outcomes of the disease. The aim of this study was to describe the landscape of fusion transcript in a large single-institution series of FISH confirmed tRCCs and then to confront it to morphological and clinical data.

Methods and results
Paired-end RNA sequencing was performed within a prospective database of the Department of Pathology, Centre Hospitalier Rional Universitaire (Lille, France). The diagnosis of tRCC was confirmed by fluorescence in situ hybridization. Among a total of 1,130 identified renal cell carcinomas, 21 cases (1.9%) showed rearrangement of the TFE3 (n=20) or TFEB (n=1) gene. Median patient age was 31 years (range 15 to 47), and the female-to-male ratio was 6:1. Five different TFE3 fusion transcripts were identified, the most frequent TFE3 partners were PRCC (n=4) and SFPQ (n=4). The other partners involved were ASPCR1 (n=1) and MED15 (n=1) genes as well as a novel TFE3 partner, GRIPAP1.

Conclusions
We identified a new fusion partner, GRIPAP1. The prognostic role of transcript type could not be determined because our number of cases was too small. Four patients (19%) died of the disease, all of which presented with a lymph node involvement at diagnosis. We confirm that tRCC can be an aggressive tumour, especially those of advanced clinical stage.

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Exome and genome sequencing of nasopharynx cancer identifies NF-κB pathway activating mutations

Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression and rational therapy design. Here we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-κB pathway, including CYLD, TRAF3, NFKBIA and NLRC5, in a total of 41% of cases. Functional analysis confirmed inactivating CYLD mutations as drivers for NPC cell growth. The EBV oncoprotein latent membrane protein 1 (LMP1) functions to constitutively activate NF-κB signalling, and we observed mutual exclusivity among tumours with somatic NF-κB pathway aberrations and LMP1-overexpression, suggesting that NF-κB activation is selected for by both somatic and viral events during NPC pathogenesis.

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Native Oligodendrocytes in Astrocytomas Might Inhibit Tumor Proliferation by WIF1 Expression

Malignant astrocytoma remains incurable and rapidly fatal despite multimodal therapy. In particular, accelerated tumor cell heterogeneity often overcomes therapeutic effects of molecular protein targeting. This study aimed at identifying a gene with therapeutic potential that was consistently downregulated with astrocytoma progression. Analysis of the Rembrandt gene expression data revealed Wnt inhibitory factor 1 (WIF1) gene as the most promising candidate with tumor suppressor function. Consequently, 288 randomly selected tissue regions of astrocytoma specimens were investigated immunohistochemically with the aid of image analysis. This in situ approach identified tumor areas with numerous single cells strongly expressing Wif-1. In diffuse and anaplastic astrocytoma, the proliferation index was independent of the generally weak Wif-1 expression in tumor cells but was significantly correlated with the density of Wif-1-expressing single cells, subsequently characterized as native and non-neoplastic oligodendrocytes. Because these cells may contribute to inhibition of tumor cell proliferation by paracrine signaling, the endogenous protein Wif-1 may represent a promising therapeutic agent with expected minimal side effects. Moreover, we suggest that immunohistochemistry for Wif might be useful for discriminating between astrocytic tumors and reactive changes.

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Human Papillomavirus-related Carcinoma with Adenoid Cystic-like Features of the Sinonasal Tract: Clinical and Morphological Characterization of 6 New Cases

Human Papillomavirus (HPV) is known as causative for squamous cell carcinoma (SCC) of the oropharynx, but is also not infrequently found in carcinomas of the sinonasal tract. Recently, a subset of these carcinomas was recognized to harbour HPV33 and have a significant morphological overlap with adenoid cystic carcinoma (ACC), a rare and aggressive carcinoma originating in the minor salivary glands. Termed HPV-related carcinoma with ACC-like features, only 9 cases have been reported. To clarify the occurrence of these tumours we screened a large material for presence of HPV-related ACC-like carcinoma. The identified tumours were characterized immunohistochemically and with fluorescence in situ hybridization and clinicopathologic information for all cases is presented.

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Gene-edited pseudogene resurrection corrects p47phox-deficient chronic granulomatous disease

Pseudogenes are duplicated genes with mutations rendering them nonfunctional. For single-gene disorders with homologous pseudogenes, the pseudogene might be a target for genetic correction. Autosomal-recessive p47phox-deficient chronic granulomatous disease (p47-CGD) is a life-threatening immune deficiency caused by mutations in NCF1, a gene with 2 pseudogenes, NCF1B and NCF1C. The most common NCF1 mutation, a GT deletion (ΔGT) at the start of exon 2 (>90% of alleles), is constitutive to NCF1B and NCF1C. NCF1 ΔGT results in premature termination, undetectable protein expression, and defective production of antimicrobial superoxide in neutrophils. We examined strategies for p47-CGD gene correction using engineered zinc-finger nucleases targeting the exon 2 ΔGT in induced pluripotent stem cells or CD34+ hematopoietic stem cells derived from p47-CGD patients. Correction of ΔGT in NCF1 pseudogenes restores oxidase function in p47-CGD, providing the first demonstration that targeted restoration of pseudogene function can correct a monogenic disorder.

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Comprehensive Screening for MED12 Mutations in Gynecological Mesenchymal Tumors Identified Morphologically Distinctive Mixed Epithelial and Stromal Tumors

MED12 exon 2 mutations have been identified in most uterine leiomyomas and mammary fibroepithelial tumors. MED12 has not been genotyped in most other gynecological mesenchymal tumors.

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Concomitant AID Expression and BCL7A Loss Associates With Accelerated Phase Progression and Imatinib Resistance in Chronic Myeloid Leukemia

The mechanisms involved in chronic myeloid leukemia (CML) progression from the chronic phase (CP) to an accelerated phase (AP) or blast crisis (BC) remain largely undetermined, but generally involve additional molecular changes besides the Philadelphia chromosome [1]. Evidence suggests that secondary BCR (breakpoint cluster region)-ABL1 (Abelson murine leukemia viral oncogene homolog 1)-dependent/independent genetic events play a critical role in blast transformation [2]. Besides BCR-ABL1 point mutations, deletions and/or rearrangements of other cancer-related genes have been associated with CML-BC [2]. Recent studies have demonstrated that aberrant activation-induced cytidine deaminase (AID) expression promotes genetic instability, eventually leading to progression and drug resistance in CML

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Fibrosis in Chronic Hepatitis C: Correlation between Immunohistochemically-Assessed Virus Load with Steatosis and Cellular Iron Content

AIM: We aimed study impact of hepatocytic viral load, steatosis, and iron load on fibrosis in chronic hepatitis C and role of VEGF and VEGFR overexpression in cirrhotic cases in evolving HCC.
MATERIAL AND METHODS: Total of 120 cases were included from TBRI and Beaujon Hospital as chronic hepatitis C (CHC), post-hepatitis C cirrhosis, and HCC. Cases of CHC were stained for Sirius red, Prussian blue and immunohistochemically (IHC) for HCV-NS3/NS4. HCC were stained IHC for VEGF and by FISH.
RESULTS: Stage of fibrosis was significantly correlated with inflammation in CHC (P < 0.01). Noticed iron load did not correlate with fibrosis. Steatosis was associated with higher inflammation and fibrosis. The cellular viral load did not correlate with inflammation, steatosis or fibrosis. VEGF by IHC was significantly higher in cases of HCC when compared to cirrhotic group (P < 0.001). Amplification of VEGFR2 was confirmed in 40% of cases of HCC. Scoring of VEGF by IHC was the good indicator of VEGFR2 amplification by FISH (P < 0.005).
CONCLUSION: Grade of inflammation is the factor affecting fibrosis in CHC. The degree of liver damage is not related to cellular viral load or iron load. Steatosis is associated with higher inflammation and fibrosis. VEGF by IHC is correlated with overexpression of VEGFR2 by FISH.

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HRG/HER2/HER3 signaling promotes AhR-mediated Memo-1 expression and migration in colorectal cancer

Colorectal cancer (CRC) is a complex disease with still unsatisfactory prognosis even in western societies, although substantial progress has been made in pre-screening programs, surgical techniques and targeted therapy options. Mediator of motility-1 (Memo-1) was previously recognized as an important effector of cell migration downstream of receptor tyrosine kinase signaling in breast cancer. This study identified Memo-1 as frequently overexpressed in CRC and established a close link between extracellular HER2 activation, AhR/ARNT transcriptional activity and Memo-1 expression. Dissection of the hMemo-1 gene promoter using reporter assays and chromatin IP techniques revealed recruitment of Aryl hydrocarbon receptor (AhR)/Aryl hydrocarbon receptor nuclear-translocator (ARNT) complex, which positively influenced Memo-1 expression in cancer cells. We found that Memo-1 depletion negatively influenced the cellular actin network and that its expression is required for HER2-mediated cell migration and invasion. Moreover, analyses of Memo-1 expression in primary CRC revealed correlation with clinical parameters that point to Memo-1 as a new prognostic factor of aggressive disease in CRC patients. Altogether, these observations demonstrate that Memo-1 is an important downstream regulator of HER2-driven CRC cell migration and invasion through connecting extracellular signals from membrane to the cytoskeletal actin network.

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TLR10 Is a B Cell Intrinsic Suppressor of Adaptive Immune Responses

Toll-like receptors play a central role in the initiation of adaptive immune responses with several TLR agonists acting as known B cell mitogens. Despite thousands of publications on TLRs, the function of TLR10 remains unknown. We have found that Ab-mediated engagement of TLR10 on primary human B cells suppresses B cell proliferation, cytokine production, and signal transduction. When challenged with either a T independent or T dependent Ag, TLR10 transgenic mice exhibit diminished Ab responses. Adoptive transfer of splenic B cells into B celldeficient mice revealed that the suppressive effects on Ag-specific humoral immune responses are entirely B cell intrinsic. Our results demonstrate that TLR10 has a functional role within the B cell lineage that is distinct from that of other TLR family members and may provide a potential therapeutic target for diseases characterized by dysregulated B cell activity.

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CELL PREPARATIONS AND CELL SUPPORTS AND THEIR USE IN THERANOSIS

A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

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Heterogeneous leukemia stem cells in myeloid blast phase chronic myeloid leukemia

Chronic myeloid leukemia (CML) is an excellent model of the multistep processes in cancer. Initiating BCR-ABL mutations are required for the initial phase of the disease (chronic phase, CP-CML). Some CP-CML patients acquire additional mutation(s) that transforms CP-CML to poor prognosis, hard to treat, acute myeloid or lymphoid leukemia or blast phase CML (BP-CML). It is unclear where in the hemopoietic hierarchy additional mutations are acquired in BP-CML, how the hemopoietic hierarchy is altered as a consequence, and the cellular identity of the resulting leukemia-propagating stem cell (LSC) populations.

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A Female Patient with FMR1 Premutation and Mosaic X Chromosome Aneuploidy and Two Sons with Intellectual Disability

In this report, we describe a molecular cytogenetic study of a family burdened with intellectual disability (ID) and suicide. Our study revealed that the mother has a heterozygous premutation in the FMR1 gene and supernumerary X chromosomes as well as X-derived marker chromosomes. Both of her sons have ID and a normal chromosome number. One of the sons has fragile X syndrome, and the other has ID of an unclear nature.

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Cytoplasmic Immunoglobulin Light Chain Revelation and Interphase Fluorescence In Situ Hybridization in Myeloma

The cytogenetic analysis of plasma cell myeloma (PCM) allows stratification of patients so that prognosis may be determined and appropriate therapeutic options can be discussed. Owing to the patchy nature of the disease in the bone marrow (BM), the low proliferative activity of plasma cells and the cryptic nature of some PCM-associated cytogenetic changes, karyotypic analysis in this disease should be augmented with targeted interphase fluorescence in situ hybridization (FISH). Immunofluorescent revelation of cytoplasmic immunoglobulin light chains, together with interphase FISH (cIg-FISH), allows the identification of plasma cells within a sample so that they may be scored preferentially. This is particularly useful in situations where there are only a small percentage of plasma cells in a sample. Where an underlying myeloid disease is suspected the cIg-FISH-negative cells can be scored separately. Two methods are provided in this chapter: the technique for cIg-FISH in fresh PCM BM samples and a procedure for use in fixed cytogenetics preparations.

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Gold nanoparticle-filled biodegradable photopolymer scaffolds induced muscle remodeling: in vitro and in vivo findings

Therapeutic stem cell transplantation bears the promise of new directions in organ and tissue replacement, but a number of its difficulties and perils are also well known. Our goal was to develop a method of transplantation by which the transplanted cells remain confined to the transplantation site and induce favorable processes. With the help of mask-projection excimer laser stereolithography, 3D hybrid nanoscaffolds were fabricated from biodegradable, photocurable PPF:DEF resin with incorporated gold nanoparticles (Au NPs). The scaffolds were tested in vitro and in vivo in order to find out about their biocompatibility and fitness for our purposes.

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Heterogeneous leukemia stem cells in myeloid blast phase chronic myeloid leukemia

Chronic myeloid leukemia (CML) is an excellent model of the multistep processes in cancer. Initiating BCR-ABL mutations are required for the initial phase of the disease (chronic phase, CP-CML). Some CP-CML patients acquire additional mutation(s) that transforms CP-CML to poor prognosis, hard to treat, acute myeloid or lymphoid leukemia or blast phase CML (BP-CML). It is unclear where in the hemopoietic hierarchy additional mutations are acquired in BP-CML, how the hemopoietic hierarchy is altered as a consequence, and the cellular identity of the resulting leukemia-propagating stem cell (LSC) populations. Here, we show that myeloid BP-CML is associated with expanded populations that have the immunophenotype of normal progenitor populations that vary between patients. Serial transplantation in immunodeficient mice demonstrated functional LSCs reside in multiple populations with the immunophenotype of normal progenitor as well as stem cells. Multicolor fluorescence in situ hybridization detected serial acquisition of cytogenetic abnormalities of chromosome 17, associated with transformation to BP-CML, that is detected with equal frequency in all functional LSC compartments. New effective myeloid BP-CML therapies will likely have to target all these LSC populations.

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Performance Testing of RREB1, MYB, and CCND1 Fluorescence In Situ Hybridization in Spindle-Cell and Desmoplastic Melanoma Argues for a Two-Step Test Algorithm

Diagnostic confirmation of spindle-cell melanoma (SM) or desmoplastic melanoma (DM) as a melanoma can be challenging. In conventional melanoma (CM), a recently established fluorescence in situ hybridization (FISH) assay for RREB1, MYB, CCND1 can be helpful. Here, we determined the presence of RREB1, MYB, and CCND1 abnormalities in an SM/DM/mixed cohort.

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Hepatocellular carcinomas with intracellular hyaline bodies have a poor prognosis

Mallory-Denk-bodies (MDB) and intracellular hyaline bodies (IHB) are cytoplasmic inclusions found in a subset of hepatocellular carcinoma (HCC). MDB are mainly composed of the intermediate filament proteins keratin (K) 8 and K18, the cellular stress- and adapter-protein sequestosome 1/p62 (p62) and ubiquitin, whereas IHB consist of p62 and/or ubiquitin. Of note, cytoplasmic inclusions containing p62 can serve as markers of suppressed autophagy which in turn has been associated with poor prognosis. The aim of this study was to evaluate the prognostic significance of p62-containing MDB and IHB in patients with HCC.

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Detection of the ASPL-TFE3 and PRCC-TFE3 gene fusion in paraffin-embedded Xp11 translocation renal cell carcinomas

Xp11 translocation renal cell carcinomas (RCCs) are uncommon renal tumors, characterized by several different translocations involving the TFE3 gene. In these diseases, the TFE3 gene is fused by translocation to 1 of several other genes, including ASPL, PRCC, NONO (p54nrb), CLTC, PSF, LUC7L3, KHSRP, PARP14 and unknown genes on chromosomes 10. Tumors with different specific gene fusions may have slightly different clinical manifestations and morphologic features. In this study, we developed a FISH assay to detect the TFE3 gene rearrangement for the presence of the 2 most common fusion genes ASPL-TFE3 and PRCC-TFE3 inroutinely processed archival materials. 10 Xp11 translocation RCCs were detected TFE3 fusion genes. Cases 1-6 displayed fusion signals of ASPL-TFE3 and cases 7-10 demonstrated fusion signals of PRCC-TFE3. All cases contained a high percentage of cells displaying fusion signals for ASPL-TFE3 (mean, 45%; range, 35% to 60%) and for PRCC-TFE3 (mean, 45%; range, 35% to 60%). The sensitivity and specificity were both 100%. The interphase fluorescencein situ hybridization (FISH) assays should enable a more definitive identification of the ASPL-TFE3 and PRCC-TFE3 fusion gene in archival material and allow more meaningful clinicopathologic associations to be drawn.

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Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues

A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendmentsapproved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection. FFPE-based classification demonstrated overall high concordance (83%) with the matched frozen specimens, on removal of cases with low confidence scores, showing sensitivity and specificity in predicting type B classification (poor outcome) of 43% and 98%, respectively. Concordance between research and clinical methods increased to 87% on removal of low confidence cases. Median survival times in the validation cohort were 18 and 7 months in type A and type B cases, respectively (P = 0.002). Multivariate classification adding pathologic staging information to the gene expression score resulted in significant stratification of risk groups. The median survival times were 52 and 14 months in the low-risk (class 1) and intermediate-risk (class 2) groups, respectively. The prognostic molecular test for mesothelioma can be performed on FFPE tissues to predict survival, and can provide an orthogonal tool, in combination with established pathologic parameters, for risk evaluation.

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Ossifying Fibromyxoid Tumor: a study of 6 cases of atypical and malignant variants

Ossifying Fibromyxoid Tumors (OFMT) of soft parts are rare, slow growing tumors that have potential for local recurrence and may metastasize. While OFMT originally was considered benign, several cases of malignant OFMT have been documented. There is no universally accepted risk stratification, although this study emphasizes the importance of utilizing histology, immunohistochemistry and FISH in establishing the diagnosis. Herein, we describe six cases of atypical and malignant OFMT with differences in morphologic features, 5 of which display the proposed morphological criteria for malignancy. The patients were mostly male (M?=?5, F?=?1) with an age range of 3369 years. The tumors arose from the extremities (3 cases), the shoulder (1 case), the head and neck area (1 case), and the paraspinal area (1 case). One tumor had high grade and overtly sarcomatous changes, while another invaded the underlying clavicle. Two cases showed cytological atypia and necrosis. Fluorescence in situ hybridization (FISH) detected rearrangement of the PHF1 gene in 5 cases. All cases were positive for EAAT4 and actin by immunohistochemistry, while negative for desmin. Three tumors were immunoreactive for S100 protein. INI-1 immunohistochemical staining was conserved in all but 2 cases in which a mosaic loss of expression was noted. All but two patients are currently alive and free of disease.

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Empire CEO, Anthony Johnson, to speak at the Companion Diagnostics Symposium 2016

Empires own CEO, Anthony Johnson, will be speaking at the 2016 Companion Diagnostic (CDx) Symposium. His session is titled, Developing a Companion Dx in Oncology: From Academic Research Project to Companion Trial.

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Solitary fibrous tumour of the genitourinary tract: a clinicopathological study of 11 cases and their association with the NAB2-STAT6 fusion gene

A subset of solitary fibrous tumours of the genitourinary tract behaved aggressively. Using a break-apart FISH probe cocktail, we found the NAB2-STAT6 gene fusion in 64% of cases. However, the NAB2-STAT6 fusion status was not correlated with STAT6 expression or useful in discriminating between low-risk or high-risk tumours and subsequent clinical outcomes.

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Re-evaluation of MAML2 fusion - negative mucoepidermoid carcinoma: a subgroup being actually hyalinizing clear cell carcinoma of the salivary gland with EWSR1 translocation

Hyalinizing clear cell carcinoma (HCCC) is a rare salivary gland tumor with a specific EWSR1-ATF1 fusion gene and can have mucin production. Mucoepidermoid carcinoma (MEC) with a clear cell component is its morphologic mimic. Using MAML2 fluorescence in situ hybridization (FISH), a total of 49 MEC cases were separated into MAML2 fusionpositive (32 cases) and MAML2 fusionnegative groups (17 cases). This study used EWSR1 FISH to investigate MAML2 fusionnegative cases to identify previously unrecognized HCCC. Among 17 MAML2 fusionnegative cases, 3 had rearrangement of the EWSR1 gene and were reclassified as HCCC. Including 5 previously diagnosed HCCC cases, these 8 HCCC cases had a male-to-female ratio of 1:7, and most (7/8) tumors arose from oral minor salivary glands in the oral cavity (tongue base and palate). EWSR1-ATF1 fusion was confirmed by FISH in all 8 HCCC cases. The histologic features between genetically confirmed HCCC and MEC were compared. HCCC was significantly associated with minor salivary gland involvement, a discrepancy between low-grade cytology and intermediate- to high-grade histology using the MEC grading system, and absence of both epidermoid cells with abundant cytoplasm and goblet cells lining cysts or forming clusters. Clear cells and a hyalinized stroma were not specific for HCCC. HCCC may be erroneously classified as MEC as clear cells may be a minor histologic component and mucin production is not uncommon. Previously diagnosed MEC cases should be reevaluated, especially those arising from minor salivary glands or without MAML2 fusion. Careful histologic evaluation with supporting molecular testing can facilitate pathologic diagnoses.

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A novel t(11;14)(q13;q32) translocation involving Pellino3 links innate immune and inflammatory signaling to a myeloproliferative neoplasm

oll-like receptor (TLR)/interleukin-1 receptor (IL-1R) plays a central role in innate immune response and
inflammation. Pellino3 is an E3 ubiquitin ligase which has important regulatory functions in TLR signaling. We identified a novel t(11;14)(q13;q32) translocation in a patient with JAK2 positive myeloproliferative neoplasm who later developed acute myeloid leukemia. FISH analysis revealed no CCND1-IGH fusion. By sequential FISH using a series of bacterial artificial clone (BAC) probes, we demonstrated that the translocation involved Pellino3, resulting in its translocation to der(14) and overexpression of Pellino3 protein. This is the first report linking the Pellino3 signaling to myeloproliferative neoplasm.

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Join Us for AMP 2016 in Charlotte!

Empire Genomics is proud to be exhibiting at the upcoming Association for Molecular Pathology 2015 Annual Meeting in Charlotte, NC, November 10 - 12. We invite you to visit us at Booth #224

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Donor and host photoreceptors engage in material transfer following transplantation of post-mitotic photoreceptor precursors

Photoreceptor replacement by transplantation is proposed as a treatment for blindness. Transplantation of healthy photoreceptor precursor cells into diseased murine eyes leads to the presence of functional photoreceptors within host retinae that express an array of donor-specific proteins. The resulting improvement in visual function was understood to be due to donor cells integrating within host retinae. Here, however, we show that while integration occurs the majority of donor-reporter-labelled cells in the host arises as a result of material transfer between donor and host photoreceptors. Material transfer does not involve permanent donorhost nuclear or cellcell fusion, or the uptake of free protein or nucleic acid from the extracellular environment. Instead, RNA and/or protein are exchanged between donor and host cells in vivo. These data require a re-evaluation of the mechanisms underlying rescue by photoreceptor transplantation and raise the possibility of material transfer as a strategy for the treatment of retinal disorders.

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Comprehensive functional analysis of the tousled-like kinase 2 frequently amplified in aggressive luminal breast cancers

More aggressive and therapy-resistant oestrogen receptor (ER)-positive breast cancers remain a great clinical challenge. Here our integrative genomic analysis identifies tousled-like kinase 2 (TLK2) as a candidate kinase target frequently amplified in ?10.5% of ER-positive breast tumours. The resulting overexpression of TLK2 is more significant in aggressive and advanced tumours, and correlates with worse clinical outcome regardless of endocrine therapy. Ectopic expression of TLK2 leads to enhanced aggressiveness in breast cancer cells, which may involve the EGFR/SRC/FAK signalling. Conversely, TLK2 inhibition selectively inhibits the growth of TLK2-high breast cancer cells, downregulates ER?, BCL2 and SKP2, impairs G1/S cell cycle progression, induces apoptosis and significantly improves progression-free survival in vivo. We identify two potential TLK2 inhibitors that could serve as backbones for future drug development. Together, amplification of the cell cycle kinase TLK2 presents an attractive genomic target for aggressive ER-positive breast cancers.

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Divergent Expression and Metabolic Functions of Human Glucuronosyltransferases through Alternative Splicing

Maintenance of cellular homeostasis and xenobiotic detoxification is mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by ten genes that comprise the glucuronidation pathway. Deep RNA sequencing of major metabolic organs exposes a substantial expansion of the UGT transcriptome by alternative splicing, with variants representing 20% to 60% of canonical transcript expression. Nearly a fifth of expressed variants comprise in-frame sequences that may create distinct structural and functional features. Follow-up cell-based assays reveal biological functions for these alternative UGT proteins. Some isoforms were found to inhibit or induce inactivation of drugs and steroids in addition to perturbing global cell metabolism (energy, amino acids, nucleotides), cell adhesion, and proliferation. This work highlights the biological relevance of alternative UGT expression, which we propose increases protein diversity through the evolution of metabolic regulators from specific enzymes.

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MIIP haploinsufficiency induces chromosomal instability and promotes tumour progression in colorectal cancer

The gene encoding Migration and Invasion Inhibitory Protein (MIIP), located on 1p36.22, is a potential tumour suppressor gene in glioma. In this study, we aimed to explore the role and mechanism of action of MIIP in colorectal cancer (CRC).

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Characterization of a novel acquired der(1)del(1)(p13p31)t(1;15)(q42;q15) in a high risk t(12;21)-positive acute lymphoblastic leukemia

he t(12;21)(p13;q22) with ETV6-RUNX1 fusion occurs in 25% of cases of B-cell precursor acute lymphoblastic leukemia (BCP-ALL); and is generally associated with favorable prognosis. However, 1520% of the t(12;21)-positive cases are associated with high-risk disease due to for example slow early responses to therapy. It is well-known that development of overt leukemia in t(12;21)-positive ALL requires secondary chromosomal aberrations although the full spectrum of these cytogenetic alterations is yet unsettled, and also, how they may be associated with disease outcome. This report describes the case of an adolescent male with t(12;21)-positive ALL who displayed a G-banded karyotype initially interpreted as del(1)(p22p13) and del(15)(q15). The patient was treated according to NOPHO standard risk protocol at diagnosis, but had minimal residual disease (MRD) at 6,4% on day 29 as determined by flowcytometric immunophenotyping. Because of MRD level > 0.1% he was then assigned as a high risk patient and received intensified chemotherapy accordingly.

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Clinical relevance of small copy-number variants in chromosomal microarray clinical testing

The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (<500 kb) has not been well established in a clinical setting.

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Mammary analog secretory carcinoma of thyroid: A case report

Mammary analog secretory carcinoma (MASC) is a recently described rare neoplasm that was first reported in the salivary gland with an associated ETV6-NTRK3 fusion. We present a case of MASC involving and presumably arising in the thyroid, which was originally diagnosed as papillary thyroid carcinoma on fine needle aspiration and surgical resection. The later correct diagnosis of MASC was confirmed by immunohistochemistry and molecular studies. The cytopathological features of MASC in the salivary gland are previously described; however, we present the first cytopathological description of MASC arising in the thyroid with the unique feature of prominent nuclear grooves. Differentiating MASC from overlapping features of cytopathologic mimics such as papillary thyroid carcinoma may carry crucial therapeutic implications.

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Tandemly Integrated HPV16 Can Form a Brd4-Dependent Super-Enhancer-Like Element That Drives Transcription of Viral Oncogenes

In cancer cells associated with human papillomavirus (HPV) infections, the viral genome is very often found integrated into the cellular genome. The viral oncogenes E6 and E7 are transcribed from the viral promoter, and integration events that alter transcriptional regulation of this promoter contribute to carcinogenic progression. In this study, we detected highly enriched binding of the super-enhancer markers Brd4, MED1, and H3K27ac, visible as a prominent nuclear focus by immunofluorescence, at the tandemly integrated copies of HPV16 in cells of the cervical neoplasia cell line W12 subclone 20861. Tumor cells are often addicted to super-enhancer-driven oncogenes and are particularly sensitive to disruption of transcription factor binding to the enhancers. Treatment of 20861 cells with bromodomain inhibitors displaced Brd4 from the HPV integration site, greatly decreased E6/E7 transcription, and inhibited cellular proliferation. Thus, Brd4 activates viral transcription at this integration site, and strong selection for E6/E7 expression can drive the formation of a super-enhancer-like element to promote oncogenesis

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An Impediment to Personalized Medicine Commercialization is the Lack of Understanding of the Value of the Testing

Over the past 20 years there have been tremendous advancements in technology in areas such as imaging, medicinal chemistry, data integration, the digitization of medical records, computing power and yet the medical delivery model is largely unchanged. The healthcare community now has a treasure chest of new tools that should permit it to be much more proactive, effective and thus produce improved outcomes at lower costs. Personalized medicine (PM), also called Precision Medicine by some, is the category in which all of these new tools can be grouped. While there are a myriad of reasons such as legacy infrastructure, lack of incentives, costs of adopting new technologies, one of the major reasons, is the lack of understanding of the value of such testing by payers. Moving to a value based pricing model for diagnostic testing will increase adoption rate of PM, raise reimbursement rates for PM testing and improve quality of care at a lower cost for patients. The end result of this will be tests that have a demonstrated benefit in PM business models and result in the acceleration of commercialization.

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Myeloid Neoplasms with t(5;12) and ETV6-ACSL6 Gene Fusion, Potential Mimickers of Myeloid Neoplasm with PDGFRB Rearrangement: Case Report with Imatinib Therapy and Review of the Literature

We report the second case of ETV6-ACSL6 associated myeloproliferative neoplasm that has received a full course of imatinib therapy. The patient was a 51-year-old previously healthy man who presented with three months of worsening dyspnea and was found to have a white count of 216,000/cmm, of which 84% were eosinophil lineage. Cytogenetic analysis revealed a t(5;12)(q31?33;p13). FISH was negative for PDGFRB rearrangement but additional FISH testing demonstrated an ACSL6 rearrangement. ETV6-ACSL6 gene fusion is a rare abnormality that most often presents as a myeloproliferative-type disorder with prominent eosinophilia or basophilia. Review of the literature yielded a total of 11 previous cases.This gene fusion results in a t(5;12)(q31?33;p13) that mimics the t(5;12) found in ETV6-PDGFRB neoplasms. Identification of the fusion genes involved in t(5;12) in eosinophilia-associated myeloproliferative disorders is crucial to direct an effective treatment plan. In particular, while tyrosine kinase inhibitor therapy is effective in patients with PDGFRB rearrangement, there is little information on imatinib efficacy in patients with ETV6-ACSL6 gene fusion. Our patient was found to be nonresponsive to imatinib therapy.

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CTCF-Mediated and Pax6-Associated Gene Expression in Corneal Epithelial Cell-Specific Differentiation

The purpose of the study is to elicit the epigenetic mechanism involving CCCTC binding factor (CTCF)-mediated chromatin remodeling that regulates PAX6 gene interaction with differentiation-associated genes to control corneal epithelial differentiation.

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Preclinical Efficacy of the Auristatin-Based Antibody Drug Conjugate BAY 1187982 for the Treatment of FGFR2-Positive Solid Tumors

The fibroblast growth factor receptor FGFR2 is overexpressed in a variety of solid tumors, including breast, gastric, and ovarian tumors, where it offers a potential therapeutic target. In this study, we present evidence of the preclinical efficacy of BAY 1187982, a novel antibodydrug conjugate (ADC). It consists of a fully human FGFR2 monoclonal antibody (mAb BAY 1179470), which binds to the FGFR2 isoforms FGFR2-IIIb and FGFR2-IIIc, conjugated through a noncleavable linker to a novel derivative of the microtubule-disrupting cytotoxic drug auristatin (FGFR2-ADC). In FGFR2-expressing cancer cell lines, this FGFR2-ADC exhibited potency in the low nanomolar to subnanomolar range and was more than 100-fold selective against FGFR2-negative cell lines. High expression levels of FGFR2 in cells correlated with efficient internalization, efficacy, and cytotoxic effects in vitro. Pharmacokinetic analyses in mice bearing FGFR2-positive NCIH716 tumors indicated that the toxophore metabolite of FGFR2- ADC was enriched more than 30-fold in tumors compared with healthy tissues. Efficacy studies demonstrated that FGFR2-ADC treatment leads to a significant tumor growth inhibition or tumor regression of cell linebased or patient-derived xenograft models of human gastric or breast cancer. Furthermore, FGFR2 amplification or mRNA overexpression predicted high efficacy in both of these types of in vivo model systems. Taken together, our results strongly support the clinical evaluation of BAY 1187982 in cancer patients and a phase I study (NCT02368951) has been initiated.

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Long-Term Consumption of High-Fat Diet in Rats: Effects on Microglial and Astrocytic Morphology and Neuronal Nitric Oxide Synthase Expression

Obesity in humans is associated with cognitive decline and elevated risk of neurodegenerative diseases of old age. Variations of high-fat diet are often used to model these effects in animal studies. However, we previously reported improvements in markers of memory and learning, as well as larger hippocampi and higher metabolite concentrations in Wistar rats fed high-fat, high-carbohydrate diet (HFCD, 60 % energy from fat, 28 % from carbohydrates) for 1 year; this diet leads to mild ketonemia (Setkowicz et al. in PLoS One 10:e0139987, 2015). In the present study, we follow up on this cohort to assess glial morphology and expression of markers related to gliosis. Twenty-five male Wistar rats were kept on HFCD and twenty-five on normal chow. At 12 months of age, the animals were sacrificed and processed for immunohistochemical staining for astrocytic (glial fibrillary acidic protein), microglial (Iba1), and neuronal (neuronal nitric oxide synthetase, nNOS) markers in the hippocampus. We have found changes in immunopositive area fraction and cellular complexity, as studied by a simplified Sholl procedure. To our knowledge, this study is the first to apply this methodology to the study of glial cells in HFCD animals. GFAP and Iba1 immunoreactive area fraction in the hippocampi of HFCD-fed rats were decreased, while the mean number of intersections (an indirect measure of cell complexity) was decreased in GFAP-positive astrocytes, but not in Iba1-expressing microglia. At the same time, nNOS expression was lowered after HFCD in both the cortex and the hippocampus.

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Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

Long noncoding RNAs (lncRNAs) represent an attractive class of candidates to mediate cancer risk. Through integrative analysis of the lncRNA transcriptome with genomic data and SNP data from prostate cancer genome-wide association studies (GWAS), we identified 45 candidate lncRNAs associated with risk to prostate cancer. We further evaluated the mechanism underlying the top hit, PCAT1, and found that a risk-associated variant at rs7463708 increases binding of ONECUT2, a novel androgen receptor (AR)-interacting transcription factor, at a distal enhancer that loops to the PCAT1 promoter, resulting in upregulation of PCAT1 upon prolonged androgen treatment. In addition, PCAT1 interacts with AR and LSD1 and is required for their recruitment to the enhancers of GNMT and DHCR24, two androgen late-response genes implicated in prostate cancer development and progression. PCAT1 promotes prostate cancer cell proliferation and tumor growth in vitro and in vivo. These findings suggest that modulating lncRNA expression is an important mechanism for risk-associated SNPs in promoting prostate transformation.

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Evidence of a dual histogenetic pathway of sacrococcygeal teratomas

Sacrococcygeal teratomas are rare tumors that occur most frequently in neonates, although adult cases also occur. Molecular pathogenesis of these tumors and their long-term prognosis is uncertain.

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Cytogenetics and FISH Technologist

The technologist has the primary responsibility of assuring the provision of quality and safe services through other technologists within the assigned laboratory. The lead technologist assures that employees are performing their work consistent with organizational expectations and policies and procedures conforming to regulatory standards. The lead tech is responsible for the daily clinical, administrative and operational success of the laboratory. Under the general direction of the Team leader/Supervisor and/or Director, manages laboratory sections, and employs a results oriented approach to leadership.

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FGFR3 preferentially colocalizes with IGH in the interphase nucleus of multiple myeloma patient B-cells when FGFR3 is located outside of CT4

Many B-cell malignancies are characterized by chromosomal translocations involving IGH and a proto-oncogene. For translocations to occur, spatial proximity of translocation-prone genes is necessary. Currently, it is not known how such genes are brought into proximity with one another. Although decondensed chromosomes occupy definitive, non-random spaces in the interphase nucleus known as chromosome territories (CTs), chromatin at the edges of CTs can intermingle, and specific genomic regions from some chromosomes have been shown to loop out of their respective CTs. This extra-territorial positioning of specific genomic regions may provide a mechanism whereby translocation-prone genes are brought together in the interphase nucleus. FGFR3 and MAF recurrently participate in translocations with IGH at different frequencies. Using 3D, 4-color FISH, and 3D analysis software, we show frequent extra-territorial positioning of FGFR3 and significantly less frequent extra-territorial positioning of MAF. Frequent extra-territorial positioning may be characteristic of FGFR3 in B-cells from healthy adult donors and non-malignant B-cells from patients, but not in hematopoietic stem cells from patients with translocations. The frequency of extra-territorial positioning of FGFR3 and MAF in B-cells correlates with the frequency of translocations in the patient population. Most importantly, in patient B-cells, we demonstrate a significant proportion of extra-territorial FGFR3 participating in close loci pairs and/or colocalizing with IGH. This preliminary work suggests that in patient B-cells, extra-territorial positioning of FGFR3 may provide a mechanism for forming close loci pairs and/or colocalization with IGH; indirectly facilitating translocation events involving these two genes.

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Empire Genomics building a global network

The Buffalo-based global molecular diagnostics company, which specializes in oncology products and clinical services, sells and ships directly to customers worldwide. Distributors provide detailed knowledge of local dynamics and logistics needs. The company now has distributors that span 29 companies in 23 countries.

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Nivolumab for classical Hodgkin's lymphoma after failure of both autologous stem-cell transplantation and brentuximab vedotin: a multicentre, multicohort, single-arm phase 2 trial

Malignant cells of classical Hodgkin's lymphoma are characterised by genetic alterations at the 9p24.1 locus, leading to overexpression of PD-1 ligands and evasion of immune surveillance. In a phase 1b study, nivolumab, a PD-1-blocking antibody, produced a high response in patients with relapsed and refractory classical Hodgkin's lymphoma, with an acceptable safety profile. We aimed to assess the clinical benefit and safety of nivolumab monotherapy in patients with classical Hodgkin's lymphoma after failure of both autologous stem-cell transplantation and brentuximab vedotin.

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TFE3-positive renal cell carcinomas are not always Xp11 translocation carcinomas: Report of a case with TPM3-ALK translocation

Translocation-associated renal cell carcinoma (RCC) is a distinct subtype of RCC with gene rearrangements of the TFE3 or TFEB loci. The TFE3 gene is located at Xp11 and can fuse to a number of translocation partners, resulting in high nuclear expression of TFE3 protein. TFE3 immunostaining is often used as a surrogate marker for a TFE3 translocation. We report a case of an RCC that expressed TFE3 but showed only gain of TFE3 rather than a translocation. Moreover, this case had a t(1;2) translocation fusing ALK and TMP3, identical to that seen in inflammatory myofibroblastic tumour.

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Buffalo's new STEM high school program will enroll 40 students this fall; future sites considered

About 40 incoming freshman in the Buffalo City School District have signed up for a new high-school program that will aim to prepare them for a career in a STEM field.

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Liquid biopsy and therapeutic response: Circulating tumor cell cultures for evaluation of anticancer treatment

The lack of a robust anticancer drug screening system to monitor patients during treatment delays realization of personalized treatment. We demonstrate an efficient approach to evaluate drug response using patient-derived circulating tumor cell (CTC) cultures obtained from liquid biopsy. Custom microfabricated tapered microwells were integrated with microfluidics to allow robust formation of CTC clusters without pre-enrichment and subsequent drug screening in situ. Rapid feedback after 2 weeks promotes immediate intervention upon detection of drug resistance or tolerance. The procedure was clinically validated with blood samples (n = 73) from 55 patients with early-stage, newly diagnosed, locally advanced, or refractory metastatic breast cancer. Twenty-four of these samples were used for drug evaluation. Cluster formation potential correlated inversely with increased drug concentration and therapeutic treatment. This new and robust liquid biopsy technique can potentially evaluate patient prognosis with CTC clusters during treatment and provide a noninvasive and inexpensive assessment that can guide drug discovery development or therapeutic choices for personalized treatment.

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Empire Genomics CEO Selected Fellow as Health Care Innovator for Aspen Institute

Anthony Johnson, Empire Genomics Chief Executive Officer and President, is one of twenty-one health care leaders selected to participate in the Aspen Institutes Health Care Innovators Fellowship Program.

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Subsets of salivary duct carcinoma defined by morphologic evidence of pleomorphic adenoma, PLAG1 or HMGA2 rearrangements, and common genetic alterations

The authors hypothesized that histogenetic classification of salivary duct carcinoma (SDC) could account for de novo tumors and those with morphologic or molecular evidence (pleomorphic adenoma gene 1 [PLAG1], high-mobility group AT hook 2 [HMGA2] rearrangement, amplification) of pleomorphic adenoma (PA).

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Play Golf & Make A Difference In Local Students' Futures In Science

Empire Genomics is hosting an Inaugural Golf Benefit, Tee it Up for STEM, which will be funding scholarships awarded to local students pursuing college careers in Science, Technology, Engineering, and Math (STEM).

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Mesenchymal Stromal/Stem Cells Do Not Ameliorate Experimental Autoimmune Encephalomyelitis and Are Not Detectable in the Central Nervous System of Transplanted Mice

Mesenchymal stromal/stem cells (MSCs) constitute progenitor cells that can be isolated from different tissues. Based on their immunomodulatory and neuroprotective functions, MSC-based cell-therapy approaches have been suggested to antagonize inflammatory activity and neuronal damage associated with autoimmune disease of the central nervous system (CNS), e.g. multiple sclerosis (MS). Intravenous MSC transplantation was reported to ameliorate experimental autoimmune encephalomyelitis (EAE), the murine model of MS, within days after transplantation. However, systemic distribution patterns and fate of MSCs after administration, especially their potential to migrate into inflammatory lesions within the CNS, remain to be elucidated. This question has of recent become particularly important, since therapeutic infusion of MSCs is now being tested in clinical trials with MS-affected patients. Here we made use of the established EAE mouse model to investigate migration and therapeutic efficacy of murine bone-marrow derived MSCs. Applying a variety of techniques, including magnetic-resonance imaging, immunohistochemistry, fluorescence in-situ hybridization, and quantitative PCR we found no evidence for immediate migration of infused MSC into the CNS of treated mice. Moreover, in contrast to other studies, transplanted MSCs did not ameliorate EAE. In conclusion, our data does not provide substantiation for a relevant migration of infused MSCs into the CNS of EAE mice supporting the hypothesis that potential therapeutic efficacy could be based on systemic effects. Evaluation of possible mechanisms underlying the observed discrepancies in MSC-treatment outcomes between different EAE models demands further studies.

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Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as Regulatory Communities. We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures.

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Epigenetic Regulation of SMARCB1 by miR-206, -381 and -671-5p is Evident in a Variety of SMARCB1 Immunonegative Soft Tissue Sarcomas, while miR-765 Appears Specific for Epithelioid Sarcoma. A miRNA Study of 223 Soft Tissue Sarcomas

Complete/partial loss of SMARCB1 nuclear-immunopositivity is characteristic of a certain subset of soft tissue sarcomas. Our previous work showed that oncomiRs-206,-381, and 671-5p could silence the SMARCB1 mRNA and protein expression and that they display significant overexpression in epithelioid sarcomas (ESs). MiR-765 was overexpressed too, but functionally was inactive in the silencing. In the current work, using quantitative PCR, we conducted a miRNA study of 51 ESs, 20 rhabdoid tumors (RTs), 20 synovial sarcomas (SSs), 15 malignant peripheral nerve sheath tumors (MPNSTs), 11 myoepithelial carcinomas (MECs), and 10 extraskeletal myxoid chondrosarcomas (EMCSs) with complete/partial loss of SMARCB1 nuclear immunostain, in contrast to controls (SMARCB1-immunopositive) of 96 STSs, 13 melanomas and 10 sarcomatoid carcinomas. The SMARCB1 genetic status of ESs was determined by MLPA and FISH. A subset of ESs (5/51) showed biallelic deletion of SMARCB1 with no overexpression of any miRNA, suggesting these tumors could be the counterpart of pediatric RT, at least genetically. Another subset (5/51) was genetically either intact or monoallelic deleted with at least threefold overexpression of one of miR-206,-381,-671-5p, suggesting epigenetic regulation only. 39/51 ESs had biallelic deletion (>20% by FISH and/or by MLPA) but with overexpressed miR-206,-381, and 671-5p, suggesting intratumoral heterogeneity, i.e., both genetic and epigenetic regulation. At least threefold overexpression of one of miR-206,-381, and 671-5p was detected in all MPNSTs, EMCSs, SSs and 7 MCs. Except for ESs, four SSs and one MPNST, there was no event above threefold overexpression of miR-765 among all 195 tested tumors. Our results suggest a general role of miR-206,-381, and 671-5p in SMARCB1 gene silencing of ES, MC, EMCS, MPNST and SS. In the future, miR-765 could possibly be a diagnostic tool for ES because of its 97% specificity and 80% sensitivity. This article is protected by copyright. All rights reserved.

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Empire Genomics Gains $1.75M in Venture Capital

Empire Genomics has closed a $1.75 million follow-on financing round, the company and investor Rand Capital said yesterday.

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Meet Us in Toronto at the 54th Annual Great Lakes Cytogenomics Conference!

Held this year in Toronto from May 19-20, conference attendees from all over Canada and the USA will share and discuss their experiences in the field of Clinical Laboratory Genetics and Cytogenomics.

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New York State Grants Clinical Lab Permit to Empire Genomics

Cancer diagnostics company Empire Genomics announced today that it has received approval from New York State to offer molecular and cellular tumor marker testing through the state's Clinical Laboratory Evaluation Program (CLEP).

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Copy number alterations of EGFR and FGFR1 in pulmonary carcinosarcoma

Carcinosarcoma may develop through sarcomatoid changes in a carcinoma, known as epithelial-mesenchymal transition, or may develop from a single cancer stem cell and subsequently diverge into morphologically dissimilar carcinomatous and sarcomatous components. Thus, we tried to elucidate the histogenesis of pulmonary carcinosarcoma, which has not been thoroughly examined. A key approach to the investigation was use of fluorescence in situ hybridization analysis of EGFR and FGFR1, because the carcinomatous component of the carcinosarcoma of the available sample was a squamous cell carcinoma, which tends to harbor copy number gain in EGFR and FGFR1. Consequently, it was postulated that the carcinosarcoma originated from cancer stem cells polysomic for EGFR, and only the carcinomatous component received FGFR1 amplification during divergence into carcinomatous and sarcomatous components.

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CIC-DUX4 Fusion-Positive Round Cell Sarcomas of soft tissue and bone: a single institution morphologic and molecular analysis of 7 cases

Round cell sarcomas lacking specific translocations represent a diagnostic challenge. The aim of this study is to describe seven cases of CIC-DUX4 positive sarcomas, including the first reported example arising primarily in bone.

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A Case of Primary Mammary Analog Secretory Carcinoma (MASC) of the Thyroid Masquerading as Papillary Thyroid Carcinoma: Potentially More than a One Off

We present the second reported mammary analog secretory carcinoma (MASC) apparently arising in the thyroid and propose a potential close relationship to ETV6-NTRK3 fusion papillary thyroid carcinoma. The patient, a 36 year old woman, presented with a neck mass of 1 years duration. Imaging studies showed a tumor involving most of the thyroid with enlarged regional lymph nodes. FNA biopsy yielded a diagnosis of papillary thyroid carcinoma.

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Visit us downtown at the Research Laboratory of Life Sciences & Bioinformatics High School Open House!

Join us for the Research Laboratory for Bioinformatics and Life Sciences High School Open House. Find out how Empire Genomics is partnering with Buffalo's latest addition to the public school system.

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A Subset of Ectomesenchymal Chondromyxoid Tumors of the Tongue shows EWSR1 Rearrangements and is Genetically Linked to Soft Tissue Myoepithelial Neoplasms: A study of 11 cases

Ectomesenchymal chondromyxoid tumor (ECT) is a rare, benign intraoral neoplasm showing predilection for the anterior dorsum of the tongue. The World Health Organization (W.H.O.) includes ECT in the pathologic spectrum of soft tissue myoepithelioma. EWSR1 rearrangement is identified in 45% of cutaneous, soft tissue and bone myoepithelial neoplasms, while PLAG1 aberrations are found in 37% of EWSR1-negative soft tissue myoepitheliomas. The aim of this study was to evaluate the presence of EWSR1 and PLAG1 rearrangements in ECTs.

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Orchard Park High School Honors Empire Genomics!

Empire Genomics, an active member of their local community, participated in Orchard Park High School's annual Career Shadow Day Program. Students toured the facility, met skilled scientists and staff members, and immersed themselves in a hands on experience inside Empire's diagnostics lab. Orchard Park High School thanked Empire with a Certificate of Acknowledgement!

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Empire Genomics Partners with Buffalo's Research Laboratory of Life Sciences and Bioinformatics High School!

A new high school program from the Buffalo City School District will debut this fall with 60 incoming freshman in the former Triangle Academy building in South Buffalo. The school is motivated by the growth of the Buffalo Niagara Medical Campus and the strength of the health-care industry in Western New York, and the eventual goal is to move its 120 upperclassmen to a full-time site somewhere in that medical corridor. Both Empire Genomics -- a growing diagnostics company -- and the University at Buffalo have signed on as partners to help guide curriculum and foster connections in the medical community.

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Isolated Follicles Enriched for Centroblasts and Lacking t(14;18)/BCL2 in Lymphoid Tissue: Diagnostic and Clinical Implications

Type I Interferon (IFN-α/Β) plays a critical role in suppressing viral replication by driving the transcription of hundreds of interferon sensitive genes (ISGs). While many ISGs are transcriptionally activated by the ISGF3 complex, the significance of other signaling intermediates in IFN-α/Β-mediated gene regulation remains elusive, particularly in rare cases of gene silencing. In human Th2 cells, IFN-α/Β signaling suppressed IL5 and IL13 mRNA expression during recall responses to T cell receptor (TCR) activation. This suppression occurred through a rapid reduction in the rate of nascent transcription, independent of de novo expression of ISGs. Further, IFN-α/Β-mediated STAT4 activation was required for repressing the human IL5 gene, and disrupting STAT4 dimerization reversed this effect. This is the first demonstration of STAT4 acting as a transcriptional repressor in response to IFN-α/Β signaling and highlights the unique activity of this cytokine to acutely block the expression of an inflammatory cytokine in human T cells.

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CSO, Dr. Norma Nowak, speaks at UB's Spring Clinical Day 2016 and Scholarly Exchange Day

Celebrate UB Jacobs School of Medicine and Biomedical Sciences during Alumni weekend April 29th - 30th. Join alumni, faculty, residents, scientists and students for a weekend full of networking, education, touring, research and information!

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Rapid determination of recent cocaine use with magnetic particles-based enzyme immunoassays in serum, saliva, and urine fluids

Cocaine is one of the most worldwide used illicit drugs. We report a magnetic particles-based enzyme-linked immunoassay (mpEIA) method for the rapid and sensitive determination of cocaine (COC) in saliva, urine and serum samples. Under optimized conditions, the limits of detections were 0.09 ng mL-1 (urine), 0.15 ng mL-1 (saliva), and 0.06 ng mL-1 COC (human serum). Sensitivities were in the range EC50 = 0.6-2.5 ng mL-1 COC. The cross-reactivity with the principal metabolite benzoylecgonine (BZE) was only 1.6%. Recovering percentages of doped samples (0, 10, 50, and 100 ng mL-1 of COC) ranged from about 86 to 111%. Some advantages of the developed mpEIA over conventional ELISA kits are faster incubations, improved reproducibility, and consumption of lower amounts of antibody and enzyme conjugates due to the use of magnetic beads. The reported method was validated following the guidelines on bioanalytical methods of the European Medicines Agency (2011). Unmetabolized COC detection has a great interest in pharmacological, pharmacokinetics, and toxicokinetics studies, and can be used to detect a very recent COC use (1-6 h.).

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Does Buffalo have enough biotech workers to fill need?

Experienced industry veterans can be harder to find locally, said Anthony Johnson, president and CEO of Empire Genomics, but he said those workers can be persuaded to move here when they see the energy and growth in the downtown medical corridor.

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Dr. Norma Nowak, Featured Speaker at Upcoming Innovation Lecture Series!

Listen, learn, and network with bioinformatics and life science professionals at the NYS Center of Excellence in Bioinformatics and Life Sciences, upcoming Innovation Lecture Series.

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Empires own, Dr. Norma Nowak, is the keynote speaker at The Friends of Crystal Peoples 6th Annual Women's Luncheon!

Join us and be inspired by Dr. Norma Nowak's Keynote Speech at The Friends of Crystal Peoples 6th Annual Women's Luncheon!

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Learn from Empire's COO, Dr. John Rushton, the tips and tricks of networking within the life sciences industry!

Join us to see Empire's own COO, John Rushton, discuss the ins and outs of networking within the life science industry!

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Reorganization of chromosome architecture in replicative cellular senescence

Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.

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Fibroblast growth factor family aberrations as a putative driver of head and neck squamous cell carcinoma in an epidemiologically low-risk patient as defined by targeted sequencing

Targeted sequencing of patients with epidemiologically low-risk (ELR) head and neck squamous cell carcinoma (HNSCC) could help identify novel drivers or lost suppressors leading to precision medicine protocols and improved survival rates.

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Transplantation of Immortalized CD34+ and CD34- Adipose-Derived Stem Cells Improve Cardiac Function and Mitigate Systemic Pro-Inflammatory Responses

Adipose-derived stem cells (ADSCs) have the potential to differentiate into various cell lineages and they are easily obtainable from patients, which makes them a promising candidate for cell therapy. However, a drawback is their limited life span during in vitro culture.

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Medical Biller II

Initially part time with transition to full time position. Accurately analyze and process paper billing sheets and electronic billing into management system for timely processing of claims and revenue recognition for all submissions. Review for appropriate ICD coding. Verify/update and obtain patient demographic information for submission of claims. Assist in recovery of self-pay patients. Perform eligibility checking for all necessary claims Process overpayments and refunds in efficient manner. Perform extensive follow up, denials and collections of claims with multiple insurance carriers. Maintain confidentiality of billing information in accordance with HIPAA guidelines.

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Congenital Hydrocephalus and Hemivertebrae Associated with De Novo Partial Monosomy 6q (6q25.3 ~>qter)

This study was conducted to describe a prenatal case of congenital hydrocephalus and hemivertebrae with a 6q terminal deletion and to investigate the possible correlation between the genotype and phenotype of the proband. We performed an array-based comparative genomic hybridization (aCGH) analysis on a fetus diagnosed with congenital hydrocephalus and hemivertebrae. The deletion, spanning 10.06 Mb from 6q25.3 to 6qter, was detected in this fetus. The results of aCGH, karyotype and fluorescent in situ hybridization (FISH) analyses in the healthy parents were normal, which confirmed that the probands copy-number variant (CNV) was de novo. This deleted region encompassed 97 genes, including 28 OMIM genes. We discussed four genes (TBP, PSMB1, QKI and Pacrg) that may be responsible for hydrocephalus while the T gene may have a role in hemivertebra. We speculate that five genes in the 6q terminal deletion region were potentially associated with hemivertebrae and hydrocephalus in the proband.

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Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

Long noncoding RNAs (lncRNAs) have emerged as regulators of diverse biological processes. Here, we describe the initial functional analysis of a poorly characterized human lncRNA (LINC00657) that is induced after DNA damage, which we termed noncoding RNA activated by DNA damage, or NORAD. NORAD is highly conserved and abundant, with expression levels of approximately 5001,000 copies per cell. Remarkably, inactivation of NORAD triggers dramatic aneuploidy in previously karyotypically stable cell lines. NORAD maintains genomic stability by sequestering PUMILIO proteins, which repress the stability and translation of mRNAs to which they bind. In the absence of NORAD, PUMILIO proteins drive chromosomal instability by hyperactively repressing mitotic, DNA repair, and DNA replication factors. These findings introduce a mechanism that regulates the activity of a deeply conserved and highly dosage-sensitive family of RNA binding proteins and reveal unanticipated roles for a lncRNA and PUMILIO proteins in the maintenance of genomic stability.

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Transient PLK4 Overexpression Accelerates Tumorigenesis in P53-Deficient Epidermis

Aneuploidy is found in most solid tumours, but it remains unclear whether it is the cause or the consequence of tumorigenesis. Using PLK4 overexpression (PLK4OE) during epidermal development, we assess the impact of centrosome amplification and aneuploidy on skin development and tumorigenesis. PLK4OE in the developing epidermis induced centrosome amplification and multipolar divisions, leading to p53 stabilization and apoptosis of epidermal progenitors. The resulting delayed epidermal stratification led to skin barrier defects. Plk4 transgene expression was shut down postnatally in the surviving mice and PLK4OE mice never developed skin tumours. Concomitant PLK4OE and p53 deletion (PLK4OE/p53cKO) rescued the differentiation defects, but did not prevent the apoptosis of PLK4OE cells. Remarkably, the short-term presence of cells with supernumerary centrosomes in PLK4OE/p53cKO mice was sufficient to generate aneuploidy in the adult epidermis and triggered spontaneous skin cancers with complete penetrance. These results reveal that aneuploidy induced by transient centrosome amplification can accelerate tumorigenesis in p53-deficient cells.

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Empire Genomics Obtains CE Marking

Empire Genomics has announced that it has received CE Mark designation for a number of its molecular diagnostic products. This is an important designation for the European Economic Area (EEA) and is a demonstration of the companys commitment to providing the highest level of quality products.

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Clinical Lab Scientist - Molecular

This position is responsible for pre-analytical, analytical, and post-analytical processes associated with specimen processing, test performance and reporting test results. Perform isolation of DNA and RNA from human blood, bone marrow and FFPE specimens using manual and automated techniques. Will set-up molecular assays and perform analysis of data; operate and maintain laboratory equipment needed to perform daily duties; increase productivity and maintain proficiency in the wet lab and analysis sections; continue to gain knowledge of hematological and solid tumor diseases and recognition of specific abnormalities; adhere to laboratory policies for safety, conduct, and performance.

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Enhancer Scanning to Locate Regulatory Regions in Genomic Loci

This protocol provides a rapid, streamlined and scalable strategy to systematically scan genomic regions for the presence of transcriptional regulatory regions that are active in a specific cell type. It creates genomic tiles spanning a region of interest that are subsequently cloned by recombination into a luciferase reporter vector containing the simian virus 40 promoter. Tiling clones are transfected into specific cell types to test for the presence of transcriptional regulatory regions. The protocol includes testing of different single-nucleotide polymorphism (SNP) alleles to determine their effect on regulatory activity. This procedure provides a systematic framework for identifying candidate functional SNPs within a locus during functional analysis of genome-wide association studies. This protocol adapts and combines previous well-established molecular biology methods to provide a streamlined strategy, based on automated primer design and recombinational cloning, allowing one to rapidly go from a genomic locus to a set of candidate functional SNPs in 8 weeks.

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Palisading and Verocay body-prominent dermatofibrosarcoma protuberans: a case report

Dermatofibrosarcoma protuberans (DFSP) is a rare cutaneous sarcoma with a tendency for local recurrence, which commonly presents as a slowly growing flesh-colored skin lesion without epidermal invasion but with intracutaneous and subcutaneous spread. Pathologically, the tumor generally presents with an infiltrating dermal mass containing closely packed fibroblasts arranged in a storiform pattern. Several uncommon growth patterns have been described, including sclerosing, atrophic, myxoid, pigmented, giant cell-rich, granular cell, herringbone pattern and palisading/Verocay body-prominent forms. To our knowledge, only five cases of DFSP with nuclear palisading/Verocay body formation have been reported in the literature, and no t(17:22) translocation study has been done on these cases. In this report we describe such a case with negative t(17:22) translocation.

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Empire Genomics is collaborating

Empire Genomics, a Buffalo-based life sciences company that provides clinical services and develops high-tech tests for cancer, is collaborating with Memorial Sloan Kettering Cancer Center in Manhattan and five other hospitals in a partnership meant to standardize how prostate cancer is tested and reported.

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Empire Genomics Announces Agreement with Cancer Centers for the Standardization of Prostate Diagnostics

Empire Genomics, LLC (www.empiregenomics.com), a leading provider of oncology molecular diagnostics products and services, which enable precision medicine has announced a strategic collaboration with Memorial Sloan Kettering Cancer Center (MSK) to support their DOD Transformative Impact Award: Toward the Practice of Precision Medicine: A Biomarker Validation Coordinating Center.

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Identification of Prognostically Relevant Chromosomal Abnormalities in Routine Diagnostics of Multiple Myeloma Using Genomic Profiling

The combination of serum Β2-microglubulin and albumin levels is highly prognostic in multiple myeloma (MM), defined as the International Staging System (ISS). Recurrent genomic abnormalities present in myeloma cells also have a strong prognostic power. This study aimed to assess, in a routine diagnostic setting, whether genomic aberrations can be used to identify sub-groups in ISS staging, as this system does not incorporate intrinsic myeloma cell variability at the molecular level. Materials and Methods: A prospective population-based study of 123 patients newly diagnosed with MM with ISS staging were included for karyotyping, interphase nuclei fluorescence in situ hybridization (iFISH) and oligo-based array comparative genomic hybridization (oaCGH) analyses. Results: Clonal abnormalities were identified in 27% of analyses by karyotyping, in 83% by iFISH, and in 99% by oaCGH analysis. ISS staging combined with oaCGH aberrations identified ISS sub-groups. Conclusion: oaCGH analysis is a valuable asset in detecting prognostically relevant genomic abnormalities. The combination of oaCGH data with ISS staging might help define new sub-groups in MM.

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Replication factor C-40 (RFC40/RFC2) as a prognostic marker and target in estrogen positive and negative and triple negative breast cancer

The present disclosure relates generally to cancer and particularly to breast cancer including estrogen sensitive, estrogen resistant and triple negative breast cancer (TNBC), and to methods of diagnosis and prognosis thereof and therapeutic intervention involving replication factor C 40 (RFC40). Methods and assays for evaluating breast cancer are provided. The disclosure also relates to inhibition or modulation of RFC40 in treatment or alleviation of cancer, including breast cancer. RFC40 inhibitors, including siRNAs and miRNAs, which specifically affect cancer cells, particularly breast cancer cells, are provided.

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Transient PLK4 overexpression accelerates tumorigenesis in p53-deficient epidermis

Aneuploidy is found in most solid tumours, but it remains unclear whether it is the cause or the consequence of tumorigenesis. Using Plk4 overexpression (PLK4OE) during epidermal development, we assess the impact of centrosome amplification and aneuploidy on skin development and tumorigenesis. PLK4OE in the developing epidermis induced centrosome amplification and multipolar divisions, leading to p53 stabilization and apoptosis of epidermal progenitors. The resulting delayed epidermal stratification led to skin barrier defects. Plk4 transgene expression was shut down postnatally in the surviving mice and PLK4OE mice never developed skin tumours. Concomitant PLK4OE and p53 deletion (PLK4OE/p53cKO) rescued the differentiation defects, but did not prevent the apoptosis of PLK4OE cells. Remarkably, the short-term presence of cells with supernumerary centrosomes in PLK4OE/p53cKO mice was sufficient to generate aneuploidy in the adult epidermis and triggered spontaneous skin cancers with complete penetrance. These results reveal that aneuploidy induced by transient centrosome amplification can accelerate tumorigenesis in p53-deficient cells

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NUP160 - SLC43A3 Is a Novel Recurrent Fusion Oncogene in Angiosarcoma

Angiosarcoma is a malignant vascular tumor originating from endothelial cells of blood vessels or lymphatic vessels. The specific driver mutations in angiosarcoma remain unknown. In this study, we investigated this issue by transcriptome sequencing of patient-derived angiosarcoma cells (ISO-HAS), identifying a novel fusion gene NUP160SLC43A3 found to be expressed in 9 of 25 human angiosarcoma specimens that were examined. In tumors harboring the fusion gene, the duration between the onset of symptoms and the first hospital visit was significantly shorter, suggesting more rapid tumor progression. Stable expression of the fusion gene in nontransformed human dermal microvascular endothelial cells elicited a gene-expression pattern mimicking ISO-HAS cells and increased cell proliferation, an effect traced in part to NUP160 truncation. Conversely, RNAi-mediated attenuation of NUP160 in ISO-HAS cells decreased cell number. Confirming the oncogenic effects of the fusion protein, subcutaneous implantation of NUP160SLC43A3-expressing fibroblasts induced tumors resembling human angiosarcoma. Collectively, our findings advance knowledge concerning the genetic causes of angiosarcoma, with potential implications for new diagnostic and therapeutic approaches.

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AMP 2015 | November 5 - 7 | Austin, TX | Booth #224

Empire Genomics is proud to be exhibiting at the upcoming Association for Molecular Pathology 2015 Annual Meeting in Austin, Texas, November 5 - 7. We invite you to visit us at Booth #224 to learn more.

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EG's own Lacarya Scott is a Celebrity Judge at 43North!

For the second year in a row, eleven startups are coming to Buffalo to vie for $1M, $500K or $250K to grow their businesses. That's $5 million in prizes and eleven new companies in Buffalo for at least one year. All of the startups are already considered winners - finalists out of more than 11,000 applicants.

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Primary Cutaneous Follicle Center Lymphoma Associated With an Extracutaneous Dissemination A Cytogenetic Finding of Potential Prognostic Value

Cytogenetic studies on cutaneous lymphomas are rare, and very little is known about their prognostic value. We present a rare case of primary cutaneous follicle center lymphoma (PCFCL) with a complex translocation presenting with cutaneous and extracutaneous dissemination in the lymph node.

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A further inv dup/del 9p de novo rearrangement. Reappraisal of 25 instances

Over 20 patients with an inv dup/del 9p de novo rearrangement have been described. We report on a similar der(9) found in a mildly affected girl and summarize the cytogenetic findings in 25 patients. The patient's G-banded karyotype was 46,XX,add(9)(p23) de novo with the extra segment being interpreted as a 9p23 ? p13 inverted duplication. FISH assays revealed that the rearranged chromosome was entirely painted by a WCP probe, lacked 9p subtelomeric repeats, and had two BAC RP11-795C14 (mapping at 9p13) signals, one proximal and one terminal. aCGH using a 4x180K Microarray Kit from Agilent confirmed a terminal deletion of ~ 12.5 Mb in 9p24.3p23 (204,193-12,455,192)x1 and an immediately adjacent duplication of ~ 21.3 Mb involving 9p13.3p23 (12,490,471-33,777,844)x3. The inverted duplication disclosed by the BAC probe and the absence of an intercalary single copy region between both imbalances, are consistent with an intrachromosomal U-type reunion. Moreover, the imbalances' size falls within the observed ranges in 20 previous patients. The rea(9) was always de novo (n = 23 parental couples) and involved either the paternal (3 cases) or the maternal (2 cases) homolog.

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NUT Carcinoma of the Thorax: Case report and review of the literature

NUT (nuclear protein in testis) carcinomas are exceedingly rare neoplasms with specific molecular alterations and often follow a devastating course. Thus, a precise early diagnosis is of utmost importance. Known from the sinonasal region for years, the new 2015 WHO classification now also recognizes the existence of this entity in the thorax, specifically the lungs and the mediastinum. However, yet available data on this entity are sparse

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Empire Genomics Names Dr. John J. Rushton as Chief Operating Officer

Empire Genomics announces today it has appointed Dr. John J. Rushton as Chief Operating Officer. As COO, Dr. Rushton will be responsible for overseeing day-to-day operations and ensuring company alignment with corporate strategies to enhance service delivery to Empire Genomics customers worldwide. He brings a wealth of experience having worked at both large and rapidly growing molecular diagnostic firms. He will provide operational, scientific, technical, and leadership support as Empire Genomics expands its footprint and testing options.

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Showcasing Empire Genomics to Steve Case on the Rise of the Rest Tour

Empire Genomics hosted Steve Case and the Revolution Team for the Rise of the Rest Tour at its location in Buffalo, New York on September 30, 2015. Mr. Case discussed with company executives the healthcare innovations taking place at their facility, and how it serves as a driver for economic development in the local community. The company was chosen out of many other worthy firms in the area, and was the only biotech organization toured.

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Development, Characterization And Application Of A Novel Mouse Line Humanized For The Intestinal Peptide Transporter PepT1

The proton-coupled oligopeptide transporter PepT1 is abundantly expressed on the apical side of small intestinal enterocytes and has major responsibility for the intestinal absorption of nutritional nitrogen, peptides and peptide-like drugs. However, there is growing evidence that a significant species difference exists in the affinity and capacity of substrates for PepT1. Therefore, a humanized PepT1 mouse model (huPepT1) was established by introducing hPepT1 genomic DNA into animals previously nulled for mouse PepT1. The mRNA and protein expression profiles indicated that huPepT1 mice had substantial but lower levels than wildtype animals in their expression of PepT1 in small intestine. However, colonic expression of PepT1 was greater in huPepT1 mice than wildtype mice, where the expression of PepT1 was quite low. In situ intestinal perfusion studies revealed that the permeability of glycylsarcosine (GlySar) and cefadroxil were similar, but lower, in the small intestine of huPepT1 mice as compared to wildtype animals. However, in colon, the permeability was greater in huPepT1 mice.

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Adenomyoepithelioma with carcinoma of the breast: A report of two cases and a review of literatures

We herein described two cases of adenomyoepithelioma (AME) with carcinoma of the breast. Both of them were Japanese women, and they presented with a mass in their breast. Post-operative specimens revealed encapsulated and well-circumscribed tumors with local invasion, necrosis, cytological atypia, and a high mitotic rate. On Immunohistochemistry, coincidentally with the loose adhesion pattern of myoepithelial cells in both cases, the intensities of E-cadherin and beta-catenin were much weaker in myoepithelial than luminal epithelial cells., with almost negative finding of beta-catenin in one case. We first found deletion of CDH1 and polysomy of CEP16 in myoepithelial cells by double color-fluorescence in situ hybridization. The two cases have been followed up for 5 to 8 years, and both remained free from local recurrence and distant metastases. We also presented an overview of 47 cases of AME with carcinoma on English-language literature.

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NOTCH, ASCL1, p53 and RB alterations define an alternative pathway driving neuroendocrine and small cell lung carcinomas

Small cell lung cancers (SCLCs) and extrapulmonary small cell cancers (SCCs) are very aggressive tumors arising de novo as primary small cell cancer with characteristic genetic lesions in RB1 and TP53. Based on murine models, neuroendocrine stem cells of the terminal bronchioli have been postulated as the cellular origin of primary SCLC. However, both in lung and many other organs, combined small cell/non-small cell tumors and secondary transitions from non-small cell carcinomas upon cancer therapy to neuroendocrine and small cell tumors occur.

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High-Throughput siRNA Screening to Reveal GATA-2 Upstream Transcriptional Mechanisms in Hematopoietic Cells

Hematopoietic stem cells can self-renew and differentiate into all blood cell types. The transcription factor GATA-2 is expressed in both hematopoietic stem and progenitor cells and is essential for cell proliferation, survival, and differentiation. Recently, evidence from studies of aplastic anemia, MonoMAC syndrome, and lung cancer has demonstrated a mechanistic link between GATA-2 and human pathophysiology. GATA-2-dependent disease processes have been extensively analyzed; however, the transcriptional mechanisms upstream of GATA-2 remain less understood. Here, we conducted high-throughput small-interfering-RNA (siRNA) library screening and showed that YN-1, a human erythroleukemia cell line, expressed high levels of GATA-2 following the activation of the hematopoietic-specific 1S promoter. As transient luciferase reporter assay in YN-1 cells revealed the highest promoter activity in the 1S promoter fused with GATA-2 intronic enhancer (+9.9 kb/1S); therefore, we established a cell line capable of stably expressing +9.9 kb/1S-Luciferase. Subsequently, we screened 995 transcription factor genes and revealed that CITED2 acts as a GATA-2 activator in human hematopoietic cells. These results provide novel insights into and further identify the regulatory mechanism of GATA-2.

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Adipose-derived stromal cells mediate in vivo adipogenesis, angiogenesis and inflammation in decellularized adipose tissue bioscaffolds

Decellularized adipose tissue (DAT) has shown promise as an adipogenic bioscaffold for soft tissue augmentation and reconstruction. The objective of the current study was to investigate the effects of allogeneic adipose-derived stem/stromal cells (ASCs) on in vivo fat regeneration in DAT bioscaffolds using an immunocompetent rat model. ASC seeding significantly enhanced angiogenesis and adipogenesis, with cell tracking studies indicating that the newly-forming tissues were host-derived. Incorporating ASCs also mediated the inflammatory response and promoted a more constructive macrophage phenotype. A fraction of the CD163+ macrophages in the implants expressed adipogenic markers, with higher levels of this adipocyte-like phenotype in proximity to the developing adipose tissues. Our results indicate that the combination of ASCs and adipose extracellular matrix (ECM) provides an inductive microenvironment for adipose regeneration mediated by infiltrating host cell populations. The DAT scaffolds are a useful tissue-specific model system for investigating the mechanisms of in vivo adipogenesis that may help to develop a better understanding of this complex process in the context of both regeneration and disease. Overall, combining adipose-derived matrices with ASCs is a highly promising approach for the in situ regeneration of host-derived adipose tissue.

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Correction of Down syndrome and Edwards syndrome aneuploidies in human cell cultures

Aneuploidy, an abnormal number of chromosomes, has previously been considered irremediable. Here, we report findings that euploid cells increased among cultured aneuploid cells after exposure to the protein ZSCAN4, encoded by a mammalian-specific gene that is ordinarily expressed in preimplantation embryos and occasionally in stem cells. For footprint-free delivery of ZSCAN4 to cells, we developed ZSCAN4 synthetic mRNAs and Sendai virus vectors that encode human ZSCAN4. Applying the ZSCAN4 biologics to established cultures of mouse embryonic stem cells, most of which had become aneuploid and polyploid, dramatically increased the number of euploid cells within a few days. We then tested the biologics on non-immortalized primary human fibroblast cells derived from four individuals with Down syndromethe most frequent autosomal trisomy of chromosome 21. Within weeks after ZSCAN4 application to the cells in culture, fluorescent in situ hybridization with a chromosome 21-specific probe detected the emergence of up to 24% of cells with only two rather than three copies. High-resolution G-banded chromosomes further showed up to 40% of cells with a normal karyotype. These findings were confirmed by whole-exome sequencing. Similar results were obtained for cells with the trisomy 18 of Edwards syndrome. Thus a direct, efficient correction of aneuploidy in human fibroblast cells seems possible in vitro using human ZSCAN4.

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Evidence for chromosome fragility at the frataxin locus in Friedreich ataxia

Friedreich ataxia (FRDA) is a member of the Repeat Expansion Diseases, a group of genetic conditions resulting from an increase/expansion in the size of a specific tandem array. FRDA results from expansion of a GAA/TTC-tract in the first intron of the frataxin gene (FXN). The disease-associated tandem repeats all form secondary structures that are thought to contribute to the propensity of the repeat to expand. The subset of these diseases that result from a CGG/CCG-repeat expansion, such as Fragile X syndrome, also express a folate-sensitive fragile site coincident with the repeat on the affected chromosome. This chromosome fragility involves the generation of chromosome/chromatid gaps or breaks, or the high frequency loss of one or both copies of the affected gene when cells are grown under folate stress or as we showed previously, in the presence of an inhibitor of the ATM checkpoint kinase. Whether Repeat Expansion Disease loci containing different repeats form similar fragile sites was not known. We show here that the region of chromosome 9 that contains the FXN locus is intrinsically prone to breakage in vivo even in control cells. However, like FXS alleles, FRDA alleles show significantly elevated levels of chromosome abnormalities in the presence of an ATM inhibitor, consistent with the formation of a fragile site.

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Setleis syndrome due to inheritance of the 1p36.22p36.21 duplication: evidence for lack of penetrance

Setleis syndrome, focal facial dermal dysplasia type III (FFDD3, MIM #227260), is characterized by scar-like bitemporal lesions and other ocular and facial dysmorphic features. The syndrome results from recessive mutations in the TWIST2 gene, encoding a basic helix-loop-helix transcription factor or de novo genomic duplication or triplication, which include 1.3Mb at 1p36.22p36.21, or other yet undefined lesions, emphasizing the syndromes genetic heterogeneity. Recently, three patients were reported with 1p36.22p36.21 duplications/triplication that had the characteristic FFDD3 features and developmental delay or intellectual disabilities. Here, we describe a male with this microduplication, and the typical FFDD3 phenotype, but normal intelligence. Notably, his duplication was inherited from his father who did not have any FFDD3 manifestations, indicating lack of penetrance of the 1p36.22p36.21 microduplication. These findings emphasize phenotypic heterogeneity of the 1p36.22p36.21 copy number variant and the importance of screening the parents of patients with the 1p36.22p36.21 copy number variant to determine whether the duplication/triplication is de novo or inherited, for informed reproductive and genetic counseling.

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Tubulocystic renal cell carcinoma is an entity immunohistochemically and genetically distinct from papillary renal cell carcinoma

Some studies have suggested that tubulocystic carcinoma may be related to papillary renal cell carcinoma. We sought to compare and contrast the molecular and immunohistochemical profiles of tubulocystic carcinoma to those of papillary renal cell carcinoma.

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Integrator mediates the biogenesis of enhancer RNAs

Integrator is a multi-subunit complex stably associated with the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). Integrator is endowed with a core catalytic RNA endonuclease activity, which is required for the 3'-end processing of non-polyadenylated, RNAPII-dependent, uridylate-rich, small nuclear RNA genes. Here we examine the requirement of Integrator in the biogenesis of transcripts derived from distal regulatory elements (enhancers) involved in tissue- and temporal-specific regulation of gene expression in metazoans. Integrator is recruited to enhancers and super-enhancers in a stimulus-dependent manner. Functional depletion of Integrator subunits diminishes the signal-dependent induction of enhancer RNAs (eRNAs) and abrogates stimulus-induced enhancerpromoter chromatin looping. Global nuclear run-on and RNAPII profiling reveals a role for Integrator in 3'-end cleavage of eRNA primary transcripts leading to transcriptional termination. In the absence of Integrator, eRNAs remain bound to RNAPII and their primary transcripts accumulate. Notably, the induction of eRNAs and gene expression responsiveness requires the catalytic activity of Integrator complex. We propose a role for Integrator in biogenesis of eRNAs and enhancer function in metazoans.

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PSF/SFPQ Is a Very Common Gene Fusion Partner in TFE3 Rearrangement– associated Perivascular Epithelioid Cell Tumors (PEComas) and Melanotic Xp11 Translocation Renal Cancers: Clinicopathologic, Immunohistochemical, and Molecular Characteristics Suggesting Classification as a Distinct Entity

An increasing number of TFE3 rearrangement– associated tumors, such as TFE3 rearrangement– associated perivascular epithelioid cell tumors (PEComas), melanotic Xp11 translocation renal cancers, and melanotic Xp11 neoplasms, have recently been reported. We examined 12 such cases, including 5 TFE3 rearrangementassociated PEComas located in the pancreas, cervix, or pelvis and 7 melanotic Xp11 translocation renal cancers, using clinicopathologic, immunohistochemical, and molecular analyses. All the tumors shared a similar morphology, including a purely nested or sheet-like architecture separated by a delicate vascular network, purely epithelioid cells displaying a clear or granular eosinophilic cytoplasm, a lack of papillary structures and spindle cell or fat components, uniform round or oval nuclei containing small visible nucleoli, and, in most cases (11/12), melanin pigmentation. The levels of mitotic activity and necrosis varied. All 12 cases displayed moderately (2+) or strongly (3+) positive immunoreactivity for TFE3 and cathepsin K. One case labeled focally for HMB45 and Melan– A, whereas the others typically labeled moderately (2+) or strongly (3+) for 1 of these markers. None of the cases were immunoreactive for smooth muscle actin, desmin, CKpan, S100, or PAX8. PSF– TFE3 fusion genes were confirmed by reverse transcription polymerase chain reaction in cases (7/7) in which a novel PSF– TFE3 fusion point was identified. All of the cases displayed TFE3 rearrangement associated with Xp11 translocation. Furthermore, we developed a PSF– TFE3 fusion fluorescence in situ hybridization assay for the detection of the PSF– TFE3 fusion gene and detected it in all 12 cases. Clinical follow– up data were available for 7 patients. Three patients died, and 2 patients (cases 1 and 3) remained alive with no evidence of disease after initial resection. Case 2 experienced recurrence and remained alive with disease. Case 5, a recent case, remained alive with extensive abdominal cavity metastases. Our data suggest that these tumors belong to a single clinicopathologic spectrum and expand the known characteristics of TFE3 rearrangement– associated tumors.

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Precision Molecular Pathology in Dermatologic Diseases

Although special techniques have been applied for more than a century to aid the diagnosis of pathology specimens, it is only within the past 10 - 20 years when the field of ancillary techniques has exploded to the current levels. From the beginning of histology and pathology, morphologists have used a wide range of special techniques such as silver stains to detect the presence of axons, colloidal iron stain to detect mucin deposits in the dermis, or Steiner stain to detect spirochetes. During the 1960 and 1970s, electron microscopy allowed examination of the subcellular structures to detect, among others, the capsids of viruses, organelles associated with a particular neoplasm (Birbeck granules in Langerhans cell histiocytosis), or alteration of the basement membrane area in the different subtypes of epidermolysis bullosa. Since the 1980s immunohistochemistry has become widely used to detect antigens, with applications to neoplastic (e.g., differentiation between Paget disease and melanoma), inflammatory (differentiation among the different subtypes of cutaneous immunobullous diseases), and infectious conditions (detection of spirochetes in cutaneous lesions of syphilis). In a sense, we can consider iminunohistochemistry as an early molecular technique since it allows the detection of specific antigens (i.e., molecules).

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Analysis of ALK gene in 133 patients with breast cancer revealed polysomy of chromosome 2 and no ALK amplification

ALK has emerged as a novel tumorigenic factor in several epithelial human cancers. Crizotinib, an ALK tyrosine kinase inhibitor, is currently approved to treat lung cancer patients exhibiting ALK gene rearrangements. Our goal was to determine the incidence of ALK aberrations in relation to different breast cancer types. Tissue micro-arrays were constructed of ER+/PR/HER2– (n = 37), ER–/PR–/HER2+ (n = 15), ER–/PR–/HER2– (n = 61) and ER+/PR+/HER2+ (n = 20) breast cancers; including 13 inflammatory breast carcinomas. FISH was performed using ALK break-apart and chromosome 2 centromere enumeration probes (CEP2). Neither ALK rearrangements nor amplification were identified in the 133 breast cancer cases evaluated. However, copy number gains (CNG) of ALK were identified in 82 of 133 patients (62 %). The CEP2 analysis revealed polysomy of chromosome 2 in all HCNG and LCNG cases, indicating the CNG of ALK are due to polysomy of chromosome 2, rather than true amplification of ALK. To conclude, we observed CNG of ALK secondary to chromosome 2 polysomy in a significant percentage of breast cancer cases, a phenomenon similar to polysomy 17. This study is one of the largest studies to have investigated ALK aberrations in breast cancer and the only study to include all subtypes.

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A clinicopathologic study of diencephalic pediatric low-grade gliomas with BRAF V600 mutation

Among brain tumors, the BRAF V600E mutation is frequently associated with pleomorphic xanthoastrocytomas (PXAs) and gangliogliomas (GGs). This oncogenic mutation is also detected in ~5 % of other pediatric low-grade gliomas (LGGs) including pilocytic astrocytomas (PAs) and diffuse astrocytomas. In the current multi-institutional study of 56 non-PXA/non-GG diencephalic pediatric LGGs, the BRAF V600 mutation rate is 36 %. V600-mutant tumors demonstrate a predilection for infants and young children (<age 3) and have a higher tendency for multicentricity. On neuroimaging, BRAF V600-mutant tumors appear as nodular, yet infiltrative contrast-enhancing masses. Morphologic examination reveals a monophasic, predominantly compact and partially infiltrative architecture. Due to the lack of classic morphologic features associated with PAs, pilomyxoid astrocytomas (PMAs), or diffuse astrocytomas, 75 % of the BRAF V600-mutant tumors could not be definitively classified on initial histopathologic evaluation. At a median follow-up of 55 months, the 5-year progression-free survival (PFS) rate for BRAF V600-mutant diencephalic low-grade astrocytomas (LGAs) was 22 12 %, shorter than BRAF V600-WT PAs (52 13 %) but higher than PMAs (10 6 %). Of note, long-term PFS was observed in several adolescent patients with BRAF V600-mutant tumors. In children aged 0–12 years, 5-year PFS rate and median PFS in BRAF V600-mutant LGAs are 9 9 % and 19 months (95 % CI 337 months), respectively. The PFS is comparable to that in BRAF V600-WT PMAs (5-year PFS rate: 10 9 %; median PFS: 15 months, 95 % CI 332 months; p = 0.96) and significantly shorter than BRAF V600-WT PAs (5-year PFS rate: 46 13 %; median PFS: 51 months, 95 % CI 20? months; p < 0.05). In summary, diencephalic BRAF V600-mutant pediatric LGAs are associated with unique clinicopathologic features and have a more aggressive clinical course, especially in children under age 13. The low rate of CDKN2A deletion also suggests that these tumors are molecularly distinct from secondary pediatric high-grade gliomas.

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Genomic analysis of mycosis fungoides and Sèzary syndrome identifies recurrent alterations in TNFR2

Mycosis fungoides and Sèzary syndrome comprise the majority of cutaneous T cell lymphomas (CTCLs), disorders notable for their clinical heterogeneity that can present in skin or peripheral blood. Effective treatment options for CTCL are limited, and the genetic basis of these T cell lymphomas remains incompletely characterized1. Here we report recurrent point mutations and genomic gains of TNFRSF1B, encoding the tumor necrosis factor receptor TNFR2, in 18% of patients with mycosis fungoides and Sary syndrome. Expression of the recurrent TNFR2 Thr377Ile mutant in T cells leads to enhanced non-canonical NF-kB signaling that is sensitive to the proteasome inhibitor bortezomib. Using an integrative genomic approach, we additionally discovered a recurrent CTLA4-CD28 fusion, as well as mutations in downstream signaling mediators of these receptors.

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Chromosomal aberrations in atypical and anaplastic meningiomas: A fluorescence in situ hybridization study

There is significant variability in the biologic behavior of meningiomas, especially of atypical and anaplastic meningiomas, that cannot be accounted for by just histology and grade of excision. The aim of our study was to analyze deletions in regions 22q, 18p11, 1p32, and 14q32 in grade II and grade III meningiomas and their correlation with tumor grade and recurrence.

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'Committed to Growing'

Empire Genomics could be located anywhere. Why Buffalo?

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Empire Genomics Strengthens Worldwide Distribution Network

Empire Genomics is pleased to announce its growing network of international distributors which spans twenty-nine companies in twenty-three countries, making available the organizations offerings - FISH Probes, cell culture media products, and molecular services including Next-Gen Sequencing - to a wider breadth of clients and potential partners across the globe.

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Comprehensive genomic profiles of small cell lung cancer

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.

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Molecular characterization of the neuronal nucleic acid-binding protein Pur-α

The first goal of this study was to gain insights into the molecular principles of Pur-α's binding to nucleic acids and its cellular functions. For this, structural analysis were combined
with various biochemical in vitro and cellular studies. Here, I present the crystal structure of Pur-α/ssDNA co-complex from Drosophila melanogaster at 2.0 resolution. The structure explains Pur-αs dsDNA-binding and unwinding, and its ssDNA stabilizing activity. The protein disrupts the base stacking of DNA by intercalation of a highly conserved phenylalanine. The importance of this structural feature was confirmed by in vitro unwinding assays. NMR titration experiments and EMSAs suggest that short RNA and DNA oligomers interact with Pur-α in identical ways. Filter-binding assays confirmed that the main nucleic acid binding domain of Pur-α binds two molecules of nucleic acid, as suggested by the crystal structure.

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Fluorescence In Situ Hybridization on Enriched CD138-Positive Cells in Plasma Cell Myeloma

To validate plasma cell enrichment technique for improving the detection of cytogenetic abnormalities in the Plasma cell myeloma (PCM)/multiple myeloma (MM). We compared the abnormality detection rate for overnight unstimulated bone marrow cultures to that for the plasma cell enriched fractions obtained with the use of CD138-coated immunomagnetic beads. Average enrichment factor (EF) was 11. One or more abnormalities were detected in 90% of enriched samples vs. 65% of non-enriched samples, thus resulting in a significantly higher detection rate of total cytogenetic abnormalities in enriched plasma cells (p=0.0038). Additional findings of RB1 deletion, TP53-, 1p-, 1q+ and IGH@ rearrangement seen in the 25% of enriched samples could contribute to the altered risk in the patient. One of the three cases with plasma cells as low as 1% by morphology was positive for a residual disease marker in the enriched sample and negative in the non-enriched sample. The plasma cell enrichment technique increased the detection rate of diagnostic and prognostic markers and is a very sensitive method for detecting minimal residual disease.

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Empire Genomics Raising $15M Venture Capital Round, Seeking New HQ Around Medical Campus

Empire Genomics is raising a $15 million round of venture capital - one that will likely include the local investors that have previously backed the company and expects to close it in the last three months of this year.

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Engineering Targeted Chromosomal Amplifications in Human Breast Epithelial Cells

Chromosomal amplifications are among the most common genetic alterations found in human cancers. However, experimental systems to study the processes that lead to specific, recurrent amplification events in human cancers are lacking. Moreover, some common amplifications, such as that at 8p11-12 in breast cancer, harbor multiple driver oncogenes, which are poorly modeled by conventional overexpression approaches. We sought to develop an experimental system to model recurrent chromosomal amplification events in human cell lines. Our strategy is to use homologous-recombination-mediated gene targeting to deliver a dominantly selectable, amplifiable marker to a specified chromosomal location. We used adeno-associated virus vectors to target human MCF-7 breast cancer cells at the ZNF703 locus, in the recurrent 8p11-12 amplicon, using the E. coli inosine monophosphate dehydrogenase (IMPDH) enzyme as a marker. We applied selective pressure using IMPDH inhibitors. Surviving clones were found to have increased copy number of ZNF703 (average 2.5-fold increase) by droplet digital PCR and FISH. Genome-wide array comparative genomic hybridization confirmed that amplifications had occurred on the short arm of chromosome 8, without changes on 8q or other chromosomes. Patterns of amplification were variable and similar to those seen in primary human breast cancers, including sawtooth patterns, distal copy number loss, and large continuous regions of copy number gain. This system will allow study of the cis- and trans-acting factors that are permissive for chromosomal amplification and provide a model to analyze oncogene cooperativity in amplifications harboring multiple candidate driver genes.

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Multicenter Phase II Study of the AKT Inhibitor MK-2206 in Recurrent or Metastatic Nasopharyngeal Carcinoma from Patients in the Mayo Phase II Consortium and the Cancer Therapeutics Research Group (MC1079)

Background This study investigated the activity of MK-2206, an AKT inhibitor, in metastatic or recurrent nasopharyngeal carcinoma (NPC). Method Oral MK-2206 at a dose of 200 mg was administered on days 1, 8, 15 and 22 of a 28-day cycle until progression. Plasma EBV DNA clearance during the first month of treatment was measured, and archived tumors were analyzed for the expression of AKT and PIK3CA mutation and PIK3CA amplification. The dual primary endpoint was objective response rate and 6-month progression-free survival (PFS) rate. Results 21 patients were enrolled and one patient achieved a partial response (5 %) and 11 had stable disease (52 %), with a median PFS of 3.5 months (95 % confidence interval, CI: 0.9-7.3). The 6-month PFS rate was 43 % (95 % CI: 22-66 %) and the median OS was 10 months (95 % CI: 5.9 months-not reached). Seven patients (33 %) experienced grade 3 toxicities which could be related to MK-2206. Macular-papular rash was the most common (n=6), followed by hyperglycemia (n=2) and fatigue (n=1). In the 12 tumor samples analyzed, PIK3CA amplification was detected in one patient's primary NPC, who had SD lasting over 12 months. Patients with decreasing EBV DNA values over time were more likely to be alive and progression-free for at least 6 months than those without a decrease (p=0.001). Conclusion The study was terminated due to the limited activity observed in this heavily pre-treated group of patients. Further studies are needed to elucidate the optimal way of selecting patients for AKT inhibitors.

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Development and Clinical Validation of a "Home-brew" Dual-Color FISH probe assay for HNRNPK

The heterogeneous nuclear ribonucleoprotein K(hnRNP K) has been linked to basic cellular functions. The HNRNP K gene, located at chromosome 9q21.32, has been observed as a deletion in certain subsets of AML patients. Recent RNA expression analyses have shown a reduction in HNRNP K expression from those AML patients with the gene deletion, but also an increased expression in those without the deletion. Therefore, an effective cytogenetic tool, i.e., home-brew FISH assays, has been used to evaluate the duplication and deletion of the HNRNP K gene, which can be representative of the overexpression and underexpression of hnRNP K that has significant impact on hematological malignancies. We developed dualcolor fluorescence in situ hybridization (FISH) assay using bacterial artificial chromosomes (BACs) RP11- 101L4 containing the entire HNRNP K gene (148kb) and a 198kb RP11-19G1 control probe to the 9p region. Three random bone marrow smears were used as controls. We used the statistical tool, BETAINV, to calculate the cut-off range for each signal pattern. The cut-off ranges were set as 6.8% for
duplication / addition of the red signal and 5.8% for deletion of the red signal. Based on metaphase analysis, the probes showed 100% specificity for the respective regions of HNRNP K and RP11-19G1. Nineteen bone marrow smears from various AML types were tested. Duplication pattern was found to be above the cut-off for 16 samples; while 3 samples with duplication pattern above the cut-off, also had deletion pattern above the cut-off. This suggests that multiple clones are present in the same patient sample, a phenomenon often observed in various haematological malignancies. Additional samples are currently being tested and their results will be compared against their cytogenetics G-banded analysis and other molecular analysis to further investigate these aberrations.

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The Genetic Deletion of 6q21 and PRDM1 and Clinical Implications in Extranodal NK/T Cell Lymphoma, Nasal Type

6q21 genetic deletion has been frequently detected in extranodal NK/T cell lymphoma, nasal type (EN-NK/T-NT) and PRDM1 is considered to be candidate gene. However, direct detection of PRDM1 deletion has not been well documented. We investigated the genetic alteration of 6q21 and PRDM1 in 43 cases of EN-NK/T-NT by FISH, and in vitro cell-lines were also used to detect. PRDM1 expression was evaluated by immunohistochemistry and western blot. The correlation between genetic alteration and PRDM1 expression and the significance in clinic-pathologic were analyzed. Heterozygous deletion of 6q21 and/or PRDM1 was observed in 24 of 43 cases (55.81%) of EN-NK/T-NT, in which 6q21 deletion was 16 cases (37.21%) while PRDM1 deletion was 19 cases (44.19%), respectively. Similarly, heterozygous co-deletion of 6q21 and PRDM1 was identified in NK92 and NKL cells. The heterozygous deletion of 6q21 and/or PRDM1 was correlated with PRDM1 expression. However, genetic deletion of 6q21 and/or PRDM1 was not correlated with clinic-pathological features of EN-NK/T-NT, while PRDM1 expression showed positive effects on the outcome of patients in an expanded cohort, as those as disease site, B symptom, and clinical stage. Thus, heterozygous deletion of 6q21 and/or PRDM1 was frequently detected in EN-NK/T-NT, and correlated with down-regulation of PRDM1 protein. But, compared to PRDM1 expression, the prognostic role of genetic deletion needs to be further evaluated in larger cohort of EN-NK/T-NT patients.

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ADRM1-Amplified Metastasis Gene in Gastric Cancer

The proteasome ubiquitin receptor ADRM1 has been shown to be a driver for 20q13.3 amplification in epithelial cancers including ovarian and colon cancer. We performed array-CGH on 16 gastric cancer cell lines and found 20q13.3 to be amplified in 19% with the minimal amplified region in gastric cancer cell line AGS spanning a 1 Mb region including ADRM1. Expression microarray analysis shows overexpression of only two genes in the minimal region, ADRM1 and OSBPL2. While RNAi knockdown of both ADRM1 and OSBPL2 led to a slight reduction in growth, only ADRM1 RNAi knockdown led to a significant reduction in migration and growth in soft-agar. Treatment of AGS cells with the ADRM1 inhibitor RA190 resulted in proteasome inhibition, but RNAi knockdown of ADRM1 did not. However, RNAi knockdown of ADRM1 led to a significant reduction in specific proteins including MNAT1, HRS, and EGFR. We hypothesize that ADRM1 may act in ADRM1-amplified gastric cancer to alter protein levels of specific oncogenes resulting in an increase in metastatic potential. Selective inhibition of ADRM1 independent of proteasome inhibition may result in a targeted therapy for ADRM1-amplified gastric cancer. In vivo models are now warranted to validate these findings.

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Breakpoint Mapping by Whole Genome Sequencing Identifies PTH2R Gene Disruption in a Patient with Midline Craniosynstosis and a De Novo Balanced Chromosomal Arrangement

Craniosynostosis (CRS) is a premature closure of calvarial sutures caused by gene mutation or environmental factors or interaction between the two. Only a small proportion of non-syndromic CRS (NSC) patients have a known genetic cause, and thus, it would be meaningful to search for a causative gene disruption for the development NSC. We applied a whole genome sequencing approach on a 15-month-old boy with sagittal and metopic synostosis to identify a gene responsible for the development of the disease.

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Clinicopathologic Implications of NF1 Gene Alterations in Diffuse Gliomas

Recent studies have identified somatic alterations in the gene encoding for neurofibromin (NF1) in a subset of glioblastoma (GBM), usually associated with the mesenchymal molecular subtype. To understand the significance of NF1 genetic alterations in diffuse gliomas in general, we evaluated public databases and tested for NF1 copy number alterations in a cohort using fluorescence in situ hybridization (FISH). NF1 genetic loss (homozygous NF1 deletions or mutations with predicted functional consequences) were present in 30 (of 281) (11%) GBM and 21 (of 286) (7%) lower grade gliomas in the Cancer Geneome Atlas (TCGA) data. Furthermore, NF1 loss was associated with worse overall and disease-specific survival in the lower grade glioma, but not GBM, group in this TCGA cohort. IDH1 or 2 mutations co-existed in lower grade gliomas with NF1 loss (36%) but not in GBM. In our cohort studied by FISH, NF1/17q (n=2) or whole Ch17 (n=3) losses were only identified in the GBM group (5/86 (6%)). Tumors with NF1/Ch17 loss were predominantly adult GBM (4/5), lacked EGFR amplification (0/4), strong p53 immunolabeling (1/5) or IDH1 (R132H) protein expression (0/5), but expressed the mesenchymal marker podoplanin in 4/5. NF1 genetic loss occurs in a subset of diffuse gliomas, and its significance deserves further exploration.

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Cryptic insertion of 3'FOXO1 into inverted chromosome arm 2q in the presence of two normal 13's and 13 small interstitial duplications in a patient with alveolar rhabdomyosarcoma

Alveolar rhabdomyosarcoma (ARMS) is a pediatric soft tissue neoplasm with a characteristic translocation, t(2;13)(q35;q14), detected in 70-80% of cases. This well-described translocation produces the gene fusion product PAX3-FOXO1. Cryptic rearrangements of this fusion have never been reported in ARMS. Here we describe a patient with ARMS that showed a cryptic insertion of 3'FOXO1 into inverted chromosome 2q by fluorescence in-situ hybridization ( FISH) and G-banded chromosomes. The inversion breakpoints were depicted as two small interstitial duplications by a-CGH and one involved the PAX3 gene. In addition, the array comparative genome hybridization (a-CGH) revealed 1q gain, 16q loss and 11 more small duplications with one of them involving FOXO1 gene. Although the pathogenesis in classic ARMS cases is thought to be driven by the 5'PAX3-3'FOXO1 fusion on derivative chromosome 13, here we report a novel cryptic insertion of 3'FOXO1 resulting in a pathogenic fusion with 5'PAX3 on inverted chromosome 2q.

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KLF4-dependent phenotypic modulation of smooth muscle cells has a key role in atherosclerotic plaque pathogenesis

Previous studies investigating the role of smooth muscle cells (SMCs) and macrophages in the pathogenesis of atherosclerosis have provided controversial results owing to the use of unreliable methods for clearly identifying each of these cell types. Here, using Myh11-CreERT2 ROSA floxed STOP eYFP Apoe-/- mice to perform SMC lineage tracing, we find that traditional methods for detecting SMCs based on immunostaining for SMC markers fail to detect >80% of SMC-derived cells within advanced atherosclerotic lesions. These unidentified SMC-derived cells exhibit phenotypes of other cell lineages, including macrophages and mesenchymal stem cells (MSCs). SMC-specific conditional knockout of Krpel-like factor 4 (Klf4) resulted in reduced numbers of SMC-derived MSC- and macrophage-like cells, a marked reduction in lesion size, and increases in multiple indices of plaque stability, including an increase in fibrous cap thickness as compared to wild-type controls. On the basis of in vivo KLF4 chromatin immunoprecipitationsequencing (ChIP-seq) analyses and studies of cholesterol-treated cultured SMCs, we identified >800 KLF4 target genes, including many that regulate pro-inflammatory responses of SMCs. Our findings indicate that the contribution of SMCs to atherosclerotic plaques has been greatly underestimated, and that KLF4-dependent transitions in SMC phenotype are critical in lesion pathogenesis.

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Empire Genomics Chosen by First Niagara for the 2015 Sponsor's Award at Amherst Chamber SBA Showcase

First Niagara congratulates Empire Genomics on being named Small Business of the Year, said Trina Burruss, First Niagara Branch Manager. We celebrate their success and are proud to support the innovative work they are doing to personalize medical treatment.

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Retrospective Review of MET Gene Mutations

C-MET proto-oncogene is a tyrosine kinase situated on chromosome 7. C-MET and its ligand hepatocyte growth factor/scatter factor (HGF/SF) play a role in proliferation, differentiation and organ development. C-MET genetic aberrations are found associated with driving tumorigenesis. In this retrospective study, we reviewed molecular analysis data gathered from a cancer institute during a two-year period (2010-2012). Upon detection of tumors harboring c-MET mutations, we determined the status of the other mutations tested and evaluated c-MET expression by fluorescent in-situ hybridization (FISH). Our search resulted in identification of 134 c-MET mutations, 44% of which had mutations of at least one of the other genes tested. No c-MET expression aberrancy was detected in this subset by FISH. Survival amongst the patients with surgically resected metastatic colorectal cancers (CRC) was slightly better in those with only a c-MET mutation compared to those with no mutation detected, although the difference was not statistically significant. When c-MET inhibition becomes an integrated part of chemotherapy practice, our observed frequency of co-mutations will be an argument for utilizing c-MET targeted treatment in combination with other targeted drugs and therapeutic strategies. Larger studies can aid to further parse out c-MET prognostic and therapeutic significance.

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A novel acquired cryptic three-way translocation t(2;11;5)(p21.3;q13.5;q23.2) with a submicroscopic deletion at 11p14.3 in an adult with hypereosinophilic syndrome

Hypereosinophilic syndrome (HES) is a clinically and pathologically heterogeneous disease entity. It is characterized by persistent eosinophilia and organ damage after excluding other causes. Clonal eosinophilia is distinguished from idiopathic eosinophilia by the presence of histologic, cytogenetic, or molecular evidence of an underlying malignancy. There are two distinct subcategories of clonal eosinophilia: chronic eosinophilic leukemia, not otherwise specified and myeloid/lymphoid neoplasms with eosinophilia and mutations involving platelet-derived growth factor receptor α/Β or fibroblast growth factor receptor 1. More than 50% of HES are without knowledge of underlying pathogenic molecular pathways.

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Analyzing Cell Fusion Events Within the Central Nervous System Using Bone Marrow Chimerism

It has emerged that cells which typically reside in the bone marrow have the capacity to cross the blood brain barrier and contribute genetic material to a range of neuronal cell types within the central nervous system. One such mechanism to account for this phenomenon is cellular fusion, occurring between migrating bone marrow-derived stem cells and neuronal cells in-situ. Biologically, the significance as to why cells from distinct lineages fuse with cells of the central nervous system is, as yet, unclear. Growing evidence however suggests that these cell fusion events could provide an efficient means of rescuing the highly complex and differentiated neuronal cell types that cannot be replaced in adulthood. To facilitate further understanding of cell fusion within the central nervous system, we describe here a technique to establish chimeric mice that are stably reconstituted with green fluorescent protein expressing sex-mismatched bone marrow. These chimeric mice are known to represent an excellent model for studying bone marrow cell migration and infiltration throughout the body, while in parallel, as will be described here, also provide a means to neatly analyze both bone marrow-derived cell fusion and trans-differentiation events within the central nervous system.

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The Effects of Chromosome Number on Mitotic Fidelity and Karyotype Stability

The correct number of chromosomes is important for the maintenance of healthy cells and organisms. Maintenance of a correct chromosome number depends on the accurate distribution of chromosomes to the daughter cells during cell division, and errors in chromosome segregation result in abnormal chromosome numbers, or aneuploidy. Aneuploidy is typically associated with deleterious effects on organismal and cellular fitness; however, aneuploidy has also been associated with enhanced cellular growth in certain contexts, such as cancer. Another type of deviation from the normal chromosome number can occur when entire sets of chromosomes are added to the normal (diploid) chromosome number, resulting in polyploidy. Whereas polyploidy is found in certain normal tissues and organisms, tetraploidy (four sets of chromosomes) is associated with a number of precancerous lesions and is believed to promote aneuploidy and tumorigenesis. While it is clear that chromosome missegregation causes aneuploidy, the effect of aneuploidy on chromosome segregation is less clear. Similarly, it is unclear whether and how tetraploidy may affect chromosome segregation. The work described here shows that aneuploidy can cause chromosome missegregation and induces chromosome-specific phenotypic effects. In contrast, tetraploidy does not per seinduce chromosome missegregation, but enables the accumulation of aneuploidy thanks to a genetic buffer effect that allows tetraploid cells to tolerate aneuploidy better than diploid cells.

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G-protein Coupled Receptor Expression Patterns in Medulloblastoma Subgroups: Identifying and Exploiting Molecular Targets

Medulloblastoma is the most common malignant brain tumor in children. Genetic profiling has identified four principle tumor subgroups; each subgroup is characterized by different initiating mutations, genetic and clinical profiles, and prognoses. The two most well-defined subgroups are caused by overactive signaling in the WNT and SHH mitogenic pathways; less is known about Groups 3 and 4 medulloblastomas. Identification of tumor subgroup using molecular classification is poised to become an important component of the medulloblastoma diagnosis and staging and will likely guide therapeutic options.

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Molecular Genetics of Optic Nerve Disease Using Patients with Cavitary Optic Disc Anomaly

Diseases of the optic nerve, which conveys the visual signal from the retina to the brain, are recognized by degeneration (loss of tissue) of the nerves. Glaucoma, the most common form of optic nerve disease, is a leading cause of blindness affecting up to 80 million people worldwide. Another optic nerve disease called cavitary optic disc anomaly (CODA) is very similar to glaucoma in clinical appearance of optic nerves upon eye examination. Although risk factors such as pressure buildup in the eye are known, the events that lead to degeneration are poorly understood, hindering development of treatments. For this reason, we studied the genes of CODA patients in hopes of gaining insight into more common blinding disorders such as glaucoma.

Prior search for changes in DNA sequences inherited with CODA disease revealed a micro-repeated region called a copy number variation (CNV) on chromosome 12 near the matrix metalloproteinase 19 (MMP19) gene. My thesis work shows that this CNV regulates gene expression. I show that it functions as a strong enhancer of gene expression and that MMP19 is located in human optic nerves where the abnormalities of CODA and glaucoma occur. I further identified similar CNVs near MMP19 in other unrelated CODA patients.

Overall, this research shows that CNVs near MMP19 found in CODA subjects regulate gene expression e.g. MMP19, may cause a significant fraction of CODA cases,and provides a new target for future therapies. Further studies are needed to understand the impact of MMP19 activity in the optic nerve.

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The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets

The development of molecularly targeted anticancer agents relies on large panels of tumour-specific preclinical models closely recapitulating the molecular heterogeneity observed in patients. Here we describe the mutational and gene expression analyses of 151 colorectal cancer (CRC) cell lines. We find that the whole spectrum of CRC molecular and transcriptional subtypes, previously defined in patients, is represented in this cell line compendium. Transcriptional outlier analysis identifies RAS/BRAF wild-type cells, resistant to EGFR blockade, functionally and pharmacologically addicted to kinase genes including ALK, FGFR2, NTRK1/2 and RET. The same genes are present as expression outliers in CRC patient samples. Genomic rearrangements (translocations) involving the ALK and NTRK1 genes are associated with the overexpression of the corresponding proteins in CRC specimens. The approach described here can be used to pinpoint CRCs with exquisite dependencies to individual kinases for which clinically approved drugs are already available.

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Ataxin-2 Regulates RGS8 Translation in a New BAC-SCA2 Transgenic Mouse Model

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells (PCs) and other neurons caused by expansion of a glutamine (Q) tract in the ATXN2 protein. We generated BAC transgenic lines in which the full-length human ATXN2 gene was transcribed using its endogenous regulatory machinery. Mice with the ATXN2 BAC transgene with an expanded CAG repeat (BAC-Q72) developed a progressive cellular and motor phenotype, whereas BAC mice expressing wild-type human ATXN2 (BAC-Q22) were indistinguishable from control mice. Expression analysis of laser-capture microdissected (LCM) fractions and regional expression confirmed that the BAC transgene was expressed in PCs and in other neuronal groups such as granule cells (GCs) and neurons in deep cerebellar nuclei as well as in spinal cord. Transcriptome analysis by deep RNA-sequencing revealed that BAC-Q72 mice had progressive changes in steady-state levels of specific mRNAs including Rgs8, one of the earliest down-regulated transcripts in the Pcp2-ATXN2[Q127] mouse line. Consistent with LCM analysis, transcriptome changes analyzed by deep RNA-sequencing were not restricted to PCs, but were also seen in transcripts enriched in GCs such as Neurod1. BAC-Q72, but not BAC-Q22 mice had reduced Rgs8 mRNA levels and even more severely reduced steady-state protein levels. Using RNA immunoprecipitation we showed that ATXN2 interacted selectively with RGS8 mRNA. This interaction was impaired when ATXN2 harbored an expanded polyglutamine. Mutant ATXN2 also reduced RGS8 expression in an in vitro coupled translation assay when compared with equal expression of wild-type ATXN2-Q22. Reduced abundance of Rgs8 in Pcp2-ATXN2[Q127] and BAC-Q72 mice supports our observations of a hyper-excitable mGluR1-ITPR1 signaling axis in SCA2, as RGS proteins are linked to attenuating mGluR1 signaling.

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TP53 loss creates therapeutic vulnerability in colorectal cancer

TP53, a well-known tumour suppressor gene that encodes p53, is frequently inactivated by mutation or deletion in most human tumours. A tremendous effort has been made to restore p53 activity in cancer therapies. However, no effective p53-based therapy has been successfully translated into clinical cancer treatment owing to the complexity of p53 signalling. Here we demonstrate that genomic deletion of TP53 frequently encompasses essential neighbouring genes, rendering cancer cells with hemizygous TP53 deletion vulnerable to further suppression of such genes. POLR2A is identified as such a gene that is almost always co-deleted with TP53 in human cancers. It encodes the largest and catalytic subunit of the RNA polymerase II complex, which is specifically inhibited by α-amanitin. Our analysis of The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) databases reveals that POLR2A expression levels are tightly correlated with its gene copy numbers in human colorectal cancer. Suppression of POLR2A with α-amanitin or small interfering RNAs selectively inhibits the proliferation, survival and tumorigenic potential of colorectal cancer cells with hemizygous TP53 loss in a p53-independent manner. Previous clinical applications of α-amanitin have been limited owing to its liver toxicity. However, we found that α-amanitin-based antibodydrug conjugates are highly effective therapeutic agents with reduced toxicity. Here we show that low doses of α-amanitin-conjugated anti-epithelial cell adhesion molecule (EpCAM) antibody lead to complete tumour regression in mouse models of human colorectal cancer with hemizygous deletion of POLR2A. We anticipate that inhibiting POLR2A will be a new therapeutic approach for human cancers containing such common genomic alterations.

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Empire Genomics Unveils Signature Fellowship Training Program

The promise of personalized medicine will only be realized with smart, passionate, and experienced people to help shape the industrys development. Empire Genomics, through its Fellowship Program, seeks to bridge the gap between academic theory and industry application.

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Familial transmission of 5p13.2 duplication due to maternal der(X)ins(X;5)

Submicroscopic duplications of 5p13 have been recently reported in several cases, warranting the description of a new clinical entity (Chromosome 5p13 Duplication Syndrome; MIM 613174). These microduplications, while variable in size, all contain at least part of the NIPBL gene. Patients with duplications in this region present with intellectual disability/developmental delay (ID/DD) and dysmorphic facies. In addition, skeletal and brain abnormalities have been variably reported, as well as propensity for obesity in adulthood and hypotonia. We report a family with two affected sons and two affected daughters, each carrying a duplication at 5p13.2 encompassing the 3' portion of SLC1A3 and the 5' portion of NIPBL. Upon confirming the SNP microarray finding by FISH in the proband, it was discovered that the 5p13.2 duplication was located on the short arm of the X chromosome. Further FISH studies on the family demonstrated that all affected children and their mother carried a derivative X chromosome with insertion of material from 5p13.2 into the intermediate region of Xp [der(X)ins(X;5)(p2?2.1;p13.2p13.2)]. To our knowledge, this is the first report of an inherited duplication of 5p13.2 with multiple affected family members. This family underscores the need to confirm array findings by FISH, both in the proband and family members, to discern implications for pathogenicity and more accurately define the recurrence risk.

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Diagnostic Value of Wilms Tumor 1 and CD44 in Langerhans Cell Sarcoma: Case Series of 4 Patients

Langerhans cell sarcoma (LCS) is a rare tumor with markedly malignant cytological features originating from Langerhans cells. LCS diagnosis is difficult and requires differentiation from other malignant tumors and Langerhans cell histiocytosis (LCH). Immunochemical antibodies, such as langerin, S-100 protein, and CD1a, have been used to diagnose LCS, but the results are crossed with LCH. To determine more significant biomarkers of LCS, we studied the expression and distribution pattern of Wilms tumor 1 (WT1) and cluster of differentiation 44 (CD44) in LCS.

A broad panel of antibodies was used for immunohistochemical technology. Simultaneously, dual immunofluorescence staining examination and fluorescence in situ hybridization staining methods were used to study the location of WT1 and CD44 in LCS tumor cells.

The results showed that tumor cells expressed WT1, CD44, and other special Langerhans cell markers (langerin, CD1a, and S-100 protein). LCS cells in all the cases showed normal cytogenetic findings without overexpression of WT1 and CD44. The expression of WT1 and CD44 was observed on langerin+ tumor cells by dual immunofluorescence staining examination in LCS.

Our results suggest that WT1 and CD44 are potential biomarkers for LCS diagnosis. Clear understanding of their functional roles may further explain the pathogenesis of this highly malignant tumor and develop some novel immunotherapy strategies.

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CDK4 amplification reduces sensitivity to CDK4/6 inhibition in fusion-positive rhabdomyosarcoma

Fusion-positive rhabdomyosarcoma (RMS) represents the more aggressive, refractory subtype of this pediatric cancer. A subset of fusion-positive RMS tumors harbors amplification of the CDK4-containing chromosomal region 12q13-q14. Other tumor types with CDK4 amplification or overexpression, including liposarcoma and neuroblastoma, are sensitive to CDK4/6 inhibition, suggesting that CDK4/6-targeted therapies may provide a new treatment strategy in fusion-positive RMS. To evaluate the potential clinical utility of CDK4/6 inhibition in this disease setting, we examined the activity of LEE011, a highly selective, orally available small molecule inhibitor targeting CDK4/6, in fusion-positive RMS in vitro and in vivo. We demonstrate overall sensitivity to CDK4/6 inhibition in all fusion-positive RMS models tested, with evidence of differential antitumor activity resulting from an inverse relationship between CDK4 expression and inhibitor vulnerability. Collectively, our data provide preclinical evidence supporting further investigation of CDK4/6-targeted therapies in treatment regimens for fusion-positive RMS.

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Partial monosomy of 11q22.2q22.3 including the SDHD gene in individuals with developmental delay

Deletions in the middle portion of 11q are not as well described in the literature as terminal 11q deletions that result in Jacobsen syndrome. One confounding factor in the older literature is that the G-banding pattern of 11q13q21 is very similar to 11q21q23. The advent of fluorescence in situ hybridization and later microarray technologies have allowed for a better resolution of many of these deletions, but genotype-phenotype correlations are still difficult since these deletions are rare events. We present five individuals who presented with developmental delays with de novo 11q22.2q23.3 deletions. Deletions were observed by standard G-banded chromosome analysis with clarification of breakpoints and gene content by SNP microarray analysis. Of note, all individuals had identical distal breakpoints. All deletions include SDHD, which is implicated in hereditary paraganglioma/pheochromocytoma, for which the patients will need to be monitored in adulthood. In spite of the large deletions of 8.6 Mb (Patients 1 and 3), 13.98 Mb (Patient 2), and 12.6 Mb (Patients 4 and 5) all patients show somewhat mild intellectual disability and dysmorphism.

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Basal Cell Carcinoma of the Prostate is an Aggressive Tumor with Frequent Loss of PTEN Expression and Overexpression of EGFR

Basal cell carcinoma (also referred to as adenoid cystic carcinoma) is a rare tumor of the prostate. Although largely characterized as indolent, poor outcomes have been reported in a considerable fraction of cases. As yet, optimum treatment strategies for this cancer have not been developed. This study investigates protein expression of common or potential molecular therapeutic targets and reports on the clinicopathologic features of nine new cases. We evaluated the expression of ERBB2, KIT, androgen receptor, PTEN, EGFR, ERG, and TP53 via immunohistochemistry. We also examined EGFR amplification and TMPRSS2-ERG gene rearrangement by fluorescence in situ hybridization. The mean clinical followup was 44 months. We found that basal cell carcinoma behaved aggressively with almost half of cases displaying high risk pathologic features or local recurrence (44%). One patient died as a result of metastatic disease. The most consistent abnormalities included a loss of PTEN expression (56% of cases) and EGFR overexpression (67% of cases). EGFR overexpression occurred in the absence of gene amplification. The TMPRSS2-ERG rearrangement was not detected in any of the tumors studied, nor was ERG protein positivity identified by immunostaining. Additionally, ERBB2, KIT, TP53, and androgen receptor expression were either absent or showed only weak, limited reactivity. Our results suggest that there is a high morbidity associated with this tumor and more intense follow up and additional treatment may be indicated. Also, targeted therapies directed against the EGFR and PTEN proteins or their constitutive pathways may be promising for future clinical management.

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Double minute amplification of mutant PDGF receptor α in a mouse glioma model

In primary brain tumors, oncogenes are frequently amplified and maintained on extrachromosomal DNA as double minutes (DM), but the underlying mechanisms remain poorly understood. We have generated a mouse model of malignant glioma based on knock-in of a mutant PDGF receptor α (PDGFRα) that is expressed in oligodendrocyte precursor cells (OPCs) after activation by a Cre recombinase. In the tumor suppressor INK4/Arf-/- background, mutant animals frequently developed brain tumors resembling anaplastic human gliomas (WHO grade III). Besides brain tumors, most animals also developed aggressive fibrosarcomas, likely triggered by Cre activation of mutant PDGFRα in fibroblastic cell lineages. Importantly, in the brain tumors and cell lines derived from brain tumor tissues, we identified a high prevalence of DM Pdgfra gene amplification, suggesting its occurrence as an early mutational event contributing to the malignant transformation of OPCs. Amplicons extended beyond the Pdgfra locus and included in some cases neighboring genes Kit and Kdr. Our genetically defined mouse brain tumor model therefore supports OPC as a cell of origin for malignant glioma and offers an example of a defined temporal sequence of mutational events, thus providing an entry point for a mechanistic understanding of DM gene amplification and its functionality in gliomagenesis.

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Current Issue Editorial Board Archives Advance Publications Submission Instructions for Authors/Editorial Policies Search Featured Papers Contact TR4 nuclear receptor enhances prostate cancer initiation via altering the stem cell population and EMT signals in the PPARG-deleted prostate cells

A recent report indicated that the TR4 nuclear receptor might suppress the prostate cancer (PCa) initiation via modulating the DNA damage/repair system. Knocking-out peroxisome proliferator-activated receptor gamma (PPARG), a nuclear receptor that shares similar ligands/activators with TR4, promoted PCa initiation. Here we found 9% of PCa patients have one allele of PPARG deletion. Results from in vitro cell lines and in vivo mouse model indicated that during PCa initiation TR4 roles might switch from suppressor to enhancer in prostate cells when PPARG was deleted or suppressed (by antagonist GW9662). Mechanism dissection found targeting TR4 in the absence of PPARG might alter the stem cell population and epithelial-mesenchymal transition (EMT) signals. Together, these results suggest that whether TR4 can enhance or suppress PCa initiation may depend on the availability of PPARG and future potential therapy via targeting PPARG to battle PPARG-related diseases may need to consider the potential side effects of TR4 switched roles during the PCa initiation.

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The current state of molecular cytogenetics in cancer diagnosis

Cytogenetics and molecular cytogenetics are and will continue to be indispensable tools in cancer diagnostics. Leukemia and lymphoma diagnostics are still emphases of routine (molecular) cytogenetics and corresponding studies of solid tumors gain more and more prominence. Here, first a historical perspective of molecular tumor cytogenetics is provided, which is followed by the basic principles of the fluorescence in situ hybridization (FISH) approach. Finally the current state of molecular cytogenetics in cancer diagnostics is discussed. Nowadays routine diagnostics includes basic FISH approaches rather than multicolor-FISH. The latter together with modern high-throughput methods have their impact on research to identify new tumor-associated genomic regions.

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TR4 nuclear receptor enhances prostate cancer initiation via altering the stem cell population and EMT signals in the PPARG- deleted prostate cells

A recent report indicated that the TR4 nuclear receptor might suppress the prostate cancer (PCa) initiation via modulating the DNA damage/repair system. Knocking-out peroxisome proliferator-activated receptor gamma (PPARG), a nuclear receptor that shares similar ligands/activators with TR4, promoted PCa initiation. Here we found 9% of PCa patients have one allele of PPARG deletion. Results from in vitro cell lines and in vivo mouse model indicated that during PCa initiation TR4 roles might switch from suppressor to enhancer in prostate cells when PPARG was deleted or suppressed (by antagonist GW9662). Mechanism dissection found targeting TR4 in the absence of PPARG might alter the stem cell population and epithelial-mesenchymal transition (EMT) signals. Together, these results suggest that whether TR4 can enhance or suppress PCa initiation may depend on the availability of PPARG and future potential therapy via targeting PPARG to battle PPARG-related diseases may need to consider the potential side effects of TR4 switched roles during the PCa initiation.

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A novel acquired inv(2)(p23.3q24.3) with concurrent submicroscopic deletions at 2p23.3, 2p22.1, 2q24.3 and 1p13.2 in a patient with chronic thrombocytopenia and anemia

Thrombocytopenia can result from a wide range of conditions and may be determined by multiple mechanisms. It can be due to a reduced platelet production or an increased destruction of platelets. Increased destruction is seen in conditions such as disseminated intravascular coagulation (DIC) and thrombotic microangiopathies, whereas decreased production is seen in bone marrow (BM) failure syndromes such as aplastic anemia, myelodysplastic syndromes, and chemotherapy-induced thrombocytopenia. In BM failure syndromes thrombocytopenia is often accompanied by anemia and/or leucopenia. Recognition of the cause of thrombocytopenia is often crucial for correct management of patients.

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Global Reorganization of the Nuclear Landscape in Senescent Cells

Cellular senescence has been implicated in tumor suppression, development, and aging and is accompanied by large-scale chromatin rearrangements, forming senescence-associated heterochromatic foci (SAHF). However, how the chromatin is reorganized during SAHF formation is poorly understood. Furthermore, heterochromatin formation in senescence appears to contrast with loss of heterochromatin in Hutchinson-Gilford progeria. We mapped architectural changes in genome organization in cellular senescence using Hi-C. Unexpectedly, we find a dramatic sequence- and lamin-dependent loss of local interactions in heterochromatin. This change in local connectivity resolves the paradox of opposing chromatin changes in senescence and progeria. In addition, we observe a senescence-specific spatial clustering of heterochromatic regions, suggesting a unique second step required for SAHF formation. Comparison of embryonic stem cells (ESCs), somatic cells, and senescent cells shows a unidirectional loss in local chromatin connectivity, suggesting that senescence is an endpoint of the continuous nuclear remodelling process during differentiation.

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Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome-sequencing analyses, we report a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Here we demonstrate that the chromosomal translocation t(10;12)(q26;q12) leading to FGFR2-PPHLN1 fusion possesses transforming and oncogenic activity, which is successfully inhibited by a selective FGFR2 inhibitor in vitro. Among the ARAF mutations, N217I and G322S lead to activation of the pathway and N217I shows oncogenic potential in vitro. Screening of a cohort of 107 iCCA patients reveals that FGFR2 fusions represent the most recurrent targetable alteration (45%, 17/107), while they are rarely present in other primary liver tumours (0/100 of hepatocellular carcinoma (HCC); 1/21 of mixed iCCA-HCC). Taken together, around 70% of iCCA patients harbour at least one actionable molecular alteration (FGFR2 fusions, IDH1/2, ARAF, KRAS, BRAF and FGF19) that is amenable for therapeutic targeting.

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CEO & President, Anthony Johnson, Shares His Experiences on Entrepreneurship at Startup Grind

Startup Grind has a great lineup of speakers for 2015 that will really help entrepreneurs make 2015 the best year yet for Buffalo.

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Norma Nowak named Executive Director of UB's New York State Center of Excellence in Bioinformatics and Life Sciences

Norma Jean Nowak, PhD, a renowned research scientist, educator, collaborator and entrepreneur, has been named executive director of the University at Buffalos New York State Center of Excellence in Bioinformatics and Life Sciences (CBLS).

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Dr. Nowak, A Keynote Speaker, at Buffalo Institute for Genomics and Data Analytics (BIG) Annual Update

Founded in 2014, the Buffalo Institute for Genomics and Data Analytics (BIG) brings together industry experts in genomics, high performance computing and health care data analysis to advance genomic medicine, and to become a community resource that provides the operational support needed to create innovation and new jobs within the industry and among BIG's collaborative partners.

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Heterozygous Triplication of Upstream Regulatory Sequences Leads to Dysregulation of Matrix Metalloproteinase 19 (MMP19) in Patients with Cavitary Optic Disc Anomaly (CODA)

Patients with a congenital optic nerve disease, cavitary optic disc anomaly (CODA), are born with profound excavation of the optic nerve resembling glaucoma. We previously mapped the gene that causes autosomal dominant CODA in a large pedigree to a chromosome 12q locus. Using comparative genomic hybridization and quantitative PCR analysis of this pedigree, we report identifying a 6Kbp heterozygous triplication upstream of the matrix metalloproteinase 19 (MMP19) gene, present in all 17 affected family members and no normal members. Moreover, the triplication was not detected in 78 control subjects or in the Database of Genomic Variants. We further detected the same 6Kbp triplication in 1 of 24 unrelated CODA patients and in none of 172 glaucoma patients. Analysis with a luciferase assay showed that the 6Kbp sequence has transcription enhancer activity. A 773bp fragment of the 6Kbp DNA segment increased downstream gene expression 8-fold, suggesting that triplication of this sequence may lead to dysregulation of the downstream gene, MMP19, in CODA patients. Lastly, immunohistochemical analysis of human donor eyes revealed strong expression of MMP19 in optic nerve head. These data strongly suggest that triplication of an enhancer may lead to overexpression of MMP19 in the optic nerve which causes CODA.

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Genistein Protects Hematopoietic Stem Cells against G-CSF-Induced DNA Damage

Granulocyte colony-stimulating factor (G-CSF) has been utilized to treat neutropenia in various clinical settings. Although clearly beneficial, there are concerns that the chronic use of G-CSF in certain conditions increases the risk of myelodysplastic syndrome (MDS) and/or acute myeloid leukemia (AML). The most striking example is in severe congenital neutropenia (SCN). SCN patients develop MDS/AML at a high rate that is directly correlated to the cumulative lifetime dosage of G-CSF. MDS and AML that arise in these settings are commonly associated with chromosomal deletions. We have demonstrated in this study that chronic G-CSF treatment in mice results in expansion of the hematopoietic stem cell population. In addition, primitive hematopoietic progenitors from G-CSFtreated mice show evidence of DNA damage as demonstrated by an increase in double strand breaks and recurrent chromosomal deletions. Concurrent treatment with genistein, a natural soy isoflavone, limits DNA damage in this population. The protective effect of genistein appears to be related to its preferential inhibition of G-CSFinduced proliferation of hematopoietic stem cells. Importantly, genistein does not impair G-CSFinduced proliferation of committed hematopoietic progenitors, nor diminish neutrophil production. The protective effect of genistein was accomplished with plasma levels that are attainable through dietary supplementation.

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Empire Genomics Acquires ID Labs, Inc. A Leading Molecular Diagnostic Reagent Company

Empire Genomics today announced the acquisition of ID Labs, Inc., a leading molecular diagnostic reagent company operating out of London Ontario. ID Labs has been providing high quality products for well over 20 years and has strong distribution and customer relationships globally.

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Microfluidic single sperm entrapment and analysis

Selection of healthy spermatozoa is of crucial importance for the success rates of assisted reproduction technologies (ART) such as in vitro fertilization and intra-cytoplasmic sperm injection. Although sperm selection for ART procedures is predominantly based on sperm motility, successful fertilization is not predicted by good motility alone. For example, sperm characteristics such as the acrosome state and DNA integrity have shown significant impact on ART outcome. Although fertilization can be achieved with a single spermatozoon of high quality, current quality assessments are population-based and do not allow investigation of multiple sperm characteristics on a single spermatozoon simultaneously. In order to study sperm cells on the single cell level, we designed and characterized a PDMS microfluidic platform that allows single sperm entrapment. After spatially confining individual sperm cells within microfluidic cell traps, the cell viability, chromosomal content and acrosome state were studied. This platform is suitable for the analysis of individual sperm cells, which could be exploited for (non-invasive) sperm analysis and selection by impedance or Raman spectroscopy.

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Cervical cancer screening by enhanced cytology: application of novel markers

Cervical cytological examination is the most widely applied screening method for cervical cancer and its precursors. Liquid-based cytology produces good-quality smears and enables the use of ancillary laboratory techniques to distinguish neoplastic from benign cells.

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FISH labeling reveals a horizontally transferred algal (Vaucheria litorea) nuclear gene on a sea slug (Elysia chlorotica) chromosome

The horizontal transfer of functional nuclear genes, coding for both chloroplast proteins and chlorophyll synthesis, from the food alga Vaucheria litorea to the sea slug Elysia chlorotica has been demonstrated by pharmacological, polymerase chain reaction (PCR), real time PCR (qRT-PCR), and transcriptome sequencing experiments. However, partial genomic sequencing of E. chlorotica larvae failed to find evidence for gene transfer. Here, we have used fluorescent in situ hybridization to localize an algal nuclear gene, prk, found in both larval and adult slug DNA by PCR and in adult RNA by transcriptome sequencing and RT-PCR. The prk probe hybridized with a metaphase chromosome in slug larvae, confirming gene transfer between alga and slug.

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Hepatic stellate cells contribute to progenitor cells and liver regeneration

Retinoid-storing hepatic stellate cells (HSCs) have recently been described as a liver-resident mesenchymal stem cell (MSC) population; however, it is not clear whether these cells contribute to liver regeneration or serve as a progenitor cell population with hepatobiliary characteristics. Here, we purified HSCs with retinoid-dependent fluorescence-activated cell sorting from eGFP-expressing rats and transplanted these GFP+ HSCs into wild-type (WT) rats that had undergone partial hepatectomy in the presence of 2-acetylaminofluorene (2AAF) or retrorsine, both of which are injury models that favor stem cellbased liver repair. Transplanted HSCs contributed to liver regeneration in host animals by forming mesenchymal tissue, progenitor cells, hepatocytes, and cholangiocytes and elevated direct bilirubin levels in blood sera of GUNN rats, indicating recovery from the hepatic bilirubinhandling defect in these animals. Transplanted HSCs engrafted within the bone marrow (BM) of host animals, and HSC-derived cells were isolated from BM and successfully retransplanted into new hosts with injured liver. Cultured HSCs transiently adopted an expression profile similar to that of progenitor cells during differentiation into bile acidsynthesizing and transporting hepatocytes, suggesting that stellate cells represent a source of liver progenitor cells. This concept connects seemingly contradictory studies that favor either progenitor cells or MSCs as important players in stem cellbased liver regeneration.

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Aortopathy in the 7q11.23 microduplication syndrome

The 7q11.23 microduplication syndrome, caused by the reciprocal duplication of the Williams-Beuren syndrome deletion region, is a genomic disorder with an emerging clinical phenotype. Dysmorphic features, congenital anomalies, hypotonia, developmental delay highlighted by variable speech delay, and autistic features are characteristic findings. Congenital heart defects, most commonly patent ductus arteriosus, have been reported in a minority of cases. Included in the duplicated region is elastin (ELN), implicated as the cause of supravalvar aortic stenosis in patients with WilliamsBeuren syndrome. Here we present a series of eight pediatric patients and one adult with 7q11.23 microduplication syndrome, all of whom had aortic dilation, the opposite vascular phenotype of the typical supravalvar aortic stenosis found in WilliamsBeuren syndrome. The ascending aorta was most commonly involved, while dilation was less frequently identified at the aortic root and sinotubular junction. The findings in these patients support a recommendation for cardiovascular surveillance in patients with 7q11.23 microduplication syndrome.

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Primary alveolar soft part sarcoma of the uterine cervix: a case report and literature review

Alveolar soft part sarcoma (ASPS) is a tumor of unknown histogenesis, composed of large, epithelioid cells with eosinophilic cytoplasm, having an alveolar pattern. Primary ASPS of uterine cervix is very rare. In this report, we present a 21-aged-old female with primary ASPS in the uterine cervix and discuss the clinicopathological characteristics, immunophenotype, molecular genetic feature and differential diagnosis of ASPS of cervix.

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Chromosome instability in diffuse large B cell lymphomas is suppressed by activation of the noncanonical NF-κB pathway

ABC-DLBCL tolerates genomic instability by activating signals like NF-κB. Although much is known about the survival role of the canonical NF-κB pathway in DLBCL, the role the noncanonical pathway is unclear. Here, we discovered that the noncanonical NF-κB pathway suppress DLBCLs chromosome instability by regulating DNA damage and centrosome duplication through direct modulation GADD45α, REDD1 and CCNG2 expression. Thus, targeting DLBCL dependency on noncanonical NF-κB activation may be a promising strategy to overcome chemotherapy resistance.

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Characterization of HPV and host genome interactions in primary head and neck cancers

A significant proportion of head and neck cancer is driven by human papillomavirus (HPV) infection, and the expression of viral oncogenes is involved in the development of these tumors. However, the role of HPV integration in primary tumors beyond increasing the expression of viral oncoproteins is not understood. Here, we describe how HPV integration impacts the host genome by amplification of oncogenes and disruption of tumor suppressors as well as driving inter- and intrachromosomal rearrangements. Tumors that do and do not have HPV integrants display distinct gene expression profiles and DNA methylation patterns, which further support the view that the mechanisms by which tumors with integrated and nonintegrated HPV arise are distinct.

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Identification of a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic Mesenchymal Tumour

Phosphaturic mesenchymal tumours (PMT) are uncommon soft tissue and bone tumours that typically cause hypophosphataemia and tumour-induced osteomalacia (TIO) through secretion of phosphatonins including fibroblast growth factor 23 (FGF23). PMT has recently been accepted by the World Health Organization as a formal tumour entity. The genetic basis and oncogenic pathways underlying its tumourigenesis remain obscure. In this study, we identified a novel FN1-FGFR1 fusion gene in 3 out of 4 PMTs by next-generation RNA sequencing. The fusion transcripts and proteins were subsequently confirmed with RT-PCR and western blotting. Fluorescence in situ hybridisation analysis showed 6 cases with FN1-FGFR1 fusion, out of an additional 11 PMTs. Overall, 9 out of 15 PMTs (60%) harboured this fusion. The FN1 gene possibly provides its constitutively active promoter and the encoded protein's oligomerisation domains to over-express and facilitate the activation of the FGFR1 kinase domain. Interestingly, unlike the prototypical leukaemia-inducing FGFR1 fusion genes which are ligand-independent, the FN1-FGFR1 chimeric protein was predicted to preserve its ligand-binding domains, suggesting an advantage of the presence of its ligands (such as FGF23 secreted at high levels by the tumour) in the activation of the chimeric receptor tyrosine kinase, thus effecting an autocrine or paracrine mechanism of tumourigenesis.

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A novel insertion ins(18;5)(q21.1;q31.2q35.1) in acute myeloid leukemia associated with microdeletions at 5q31.2, 5q35.1q35.2 and 18q12.3q21.1 detected by oligobased array comparative genomic hybridization

Background: Nonrandom clonal chromosomal aberrations can be detected in approximately 55% of adult patients with acute myeloid leukemia (AML). Recurrent cytogenetic abnormalities play an important role in diagnosis, classification and prognosis of AML. However, several chromosomal abnormalities have not been completely determined or characterized, primarily because of their low incidence and limited amount of data.

Results: We characterized an AML patient with a novel apparently balanced insertion ins(18;5)(q21;q31.2q35.1) that was cryptic by G-banding. The rearrangement was further examined by molecular cytogenetic methods and oligobased high-resolution array CGH (oaCGH) analysis. We show that an approximately 31.8 Mb large segment from chromosome 5 bands q31.2 to q35.1 has been inserted, by a direct mechanism, into chromosome 18 between bands q12.3 and q21.1. The insertion was unbalanced with concurrent submicroscopic deletions at 5q31.2 (approximately 0.37 Mb in size), 5q35.1q35.2 (approximately 1.98 Mb in size), and 18q12.3q21.1 (approximately 2.07 Mb in size). The microdeletions affect genes on 5q and 18q that have been associated with hematological malignancy and other cancers. A novel juxtaposition of the genes NPM1 and HAUS1 at 5q35.1 and 18q21.1, respectively, was detected by FISH analysis. Searching the literature and the Mitelman database revealed no previously reported ins(18;5) cases. Interestingly, however, two AML patients with translocation t(5;18)(q35;q21) encompassing the 5q35 and 18q21 breakpoint regions as detected in our present ins(18;5) patient have been reported.

Conclusions: It is well-known that cytogenetic abnormalities on the long arm of chromosome 5 affect hematopoiesis. However, the precise mechanism of their involvement in myeloid transformation is elusive. Our present data shed new light onto the frequent abnormalities on 5q as well as to the less frequent abnormalities observed on 18q in myeloid malignancies. In addition, we show that oaCGH analysis is a useful adjunct to revealing submicroscopic aberrations in regions of clinical importance. Reporting rare and nonrandom chromosomal abnormalities contribute to the identification of the whole spectrum of cytogenetic abnormalities in AML and their prognostic significance.

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Chronic lymphocytic leukemia with a FGFR3 translocation: Case report and literature review of an uncommon cytogenetic event

The t(4;14)(p16; q32) with fusion of the IGH and FGFR3 genes (immunoglobulin heavy chain/fibroblast growth factor receptor 3) are rarely present in patients with chronic lymphocytic leukemia, with only two previously reported cases. Here we describe a unique case of chronic lymphocytic leukemia with the occurrence of t(4;14)(p16;q32), trisomy 12 and deletion of 11q13-q23 in the same clonal cells. In contrast to myeloma in which FGFR3 translocations are a common early cytogenetic hit, FGFR3 rearrangement in chronic lymphocytic leukemia appears to occur later in the disease course.

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Perivascular epithelioid cell tumor (PEComa) with TFE3 gene rearrangement: Clinicopathological, immunohistochemical, and molecular features

Perivascular epithelioid cell tumors (PEComas) have been increasingly associated with gene rearrangement of the transcription factor E3 (TFE3). We present three cases of PEComa with a TFE3 gene abnormality detected by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Their clinical features, pathological morphology, and prognosis were investigated. Histologically, the tumors in these three cases showed predominantly epithelioid cells arranged in nests or sheets separated by a delicate vascular network, within two of the three cases nuclear atypia, mitotic figures, and necrosis. All three cases showed strong TFE3 and cathepsin K immunoreactivity and weak to strong reactivity for HMB45. One case of PEComa with TFE3 gene fusion exhibited a benign course. The other two cases of PEComa with both TFE3 translocation and X-chromosome polysomy were histologically malignant and showed aggressive growth. In summary, unusual cases of PEComa with TFE3 gene rearrangement might present malignant histological features and aggressive clinical behavior. Our results add cases to the literature and describe an association of polysomy with aggressive behavior.

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Expression Of FGFR2b In Gastric Cancer As Measured By Immunohistochemistry With A Highly Specific Monoclonal Antibody

Gastric cancer is the second leading cause of death from cancer worldwide. Amplification of the FGFR2 oncogene has been reported in 3 to 9% of gastric cancers, and several studies have also reported overexpression of the FGFR2 protein in about 15-35% of the cases using immunohistochemistry (IHC). Both amplification of the FGFR2 gene and overexpression of the FGFR2b protein have been shown to correlate with an aggressive disease phenotype, making FGFR2 an attractive therapeutic target.

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Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome

Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multiple target sequencing (3C-MTS) technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B, and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in LCL. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.

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Development and Characterization of a Novel Mouse Line Humanized for the Intestinal Peptide Transporter PEPT1

The proton-coupled oligopeptide transporter PEPT1 (SLC15A1) is abundantly expressed in the small intestine, but not colon, of mammals and found to mediate the uptake of di-/tri-peptides and peptide-like drugs from the intestinal lumen. However, species differences have been observed in both the expression (and localization) of PEPT1 and its substrate affinity. With this in mind, the objectives of this study were to develop a humanized PEPT1 mouse model (huPEPT1) and to characterize hPEPT1 expression and functional activity in the intestines. Thus, after generating huPEPT1 mice in animals previously nulled for mouse Pept1, phenotypic, PCR and immunoblot analyses were performed, along with in situ single-pass intestinal perfusion and in vivo oral pharmacokinetic studies with a model dipeptide, glycylsarcosine (GlySar). Overall, the huPEPT1 mice had normal survival rates, fertility, litter size, gender distribution and body weight. There was no obvious behavioral or pathological phenotype. The mRNA and protein profiles indicated that huPEPT1 mice had substantial PEPT1 expression in all regions of the small intestine (i.e., duodenum, jejunum and ileum) along with low but measurable expression in both proximal and distal segments of the colon. In agreement with PEPT1 expression, the in situ permeability of GlySar in huPEPT1 mice was similar to but lower than wildtype animals in small intestine, and greater than wildtype mice in colon. However, a species difference existed in the in situ transport kinetics of jejunal PEPT1, in which the maximal flux and Michaelis constant of GlySar were reduced 7-fold and 2- to 4-fold, respectively, in huPEPT1 compared to wildtype mice. Still, the in vivo function of intestinal PEPT1 appeared fully restored (compared to Pept1 knockout mice) as indicated by the nearly identical pharmacokinetics and plasma concentration-time profiles following a 5.0 nmol/g oral dose of GlySar to huPEPT1 and wildtype mice. This study reports, for the first time, the development and characterization of mice humanized for PEPT1. This novel transgenic huPEPT1 mouse model should prove useful in examining the role, relevance and regulation of PEPT1 in diet and disease, and in the drug discovery process.

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Empire Genomics Partners with Quadpharma to Manufacture ASRs

Empire Genomics, LLC, (www.empiregenomics.com), a leading molecular diagnostics company in the field of personalized cancer medicine, and QuaDPharma, (www.qdpharma.com), a rapidly growing commercial contract manufacturer, announced the completion of the first batch of GMP manufactured products.

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Neural tube defects and atypical deletion on 22q11.2

The 22q11.2 deletion syndrome (22q11.2DS) is a common microdeletion disorder. Most of the patients show the common 3Mb deletion but proximal 1.5Mb deletion and unusual deletions located outside the common deleted region, have been detected particularly with the advance of comparative cytogenomic microarray technologies. The individuals reported in the literature with unusual deletions involving the 22q11 region, showed milder facial phenotypes, decreased incidence of cardiac anomalies, and intellectual disability. We describe two sibs with an atypical 0.8Mb microdeletion of chromosome 22q11 who both showed myelomeningocele and mild facial dysmorphisms. The association between neural tube defect and the clinical diagnosis of Di George anomaly/velocardiofacial syndrome is well documented in the literature, but not all cases had molecular studies to determine breakpoint regions. This report helps to narrow a potential critical region for neural tube defects associated with 22q11 deletions.

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Malignant round cell tumor of bone with EWSR1-NFATC2 gene fusion

Gene rearrangements involving the Ewing sarcoma breakpoint region 1 (EWSR1) gene are seen in a broad range of sarcomas and some nonmesenchymal neoplasms. Ewing sarcoma is molecularly defined by a fusion of the EWSR1 gene (or rarely the related FUS gene) to a member of the E26 transformation-specific (ETS) family of transcription factors, frequently the EWSR1-FLI1 fusion. More recently, EWSR1 gene fusion to non-ETS family members, including the nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 2 (NFATC2) gene, has been reported in a histological variant of Ewing sarcoma. Here, we report a malignant round cell tumor of bone with an EWSR1-NFATC2 fusion gene. This report builds upon the unusual morphological and clinical presentation of bone neoplasms containing an EWSR1-NFATC2 fusion gene.

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Empire Genomics Partner in New York Genome Center-University at Buffalo Project

"Building out our ability to take large-scale sequencing data will allow us to sift through that data and create assays that companies like Empire and Lineage will use to build the suite theyre putting out there," said Norma Nowak, founder and chief scientific officer of Empire Genomics and a professor in UBs School of Medicine and BioMedical Sciences.

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Empire Genomics Advances to Semi-Finals in Global Business Competition

"By attracting talented entrepreneur and promising businesses to Buffalo, the 43North business competition is helping to bring new life into the economy in Western New York. This competition is all about bringing the most innovative start-up ventures from around the globe to Buffalo, where they can tap into a world-class workforce and unparalleled environment to thrive for years to come," said Governor Cuomo.

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Immunohistochemical Application of a Highly Sensitive and Specific Murine Monoclonal Antibody Recognising the Extracellular Domain of the Human Hepatocyte Growth Factor Receptor (MET)

Development of novel targeted therapies directed against hepatocyte growth factor (HGF) or its receptor (MET) necessitates the availability of quality diagnostics to facilitate their safe and effective use. Limitations of some commercially available anti-MET antibodies have prompted development of the highly sensitive and specific clone A2H2-3. Here we report its analytical properties when applied by an automated immunohistochemistry method.

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Rand Partners With Innovate NY Fund to Invest in Personalized Cancer Medicine Business, Empire Genomics, LLC

Empire Genomics has proprietary assays for prostate and multiple myeloma, with expertise in employing genomic technologies to improve clinical outcomes. Its customers include many well-known hospitals, pharmaceutical clients and academic centers. These funds will be used to accelerate the pace of growth through acquiring new technologies, growing staff and increase its test offerings.

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First Case Report of an Extraskeletal Myxoid Chondrosarcoma with a t(9;16)(q22;p11.2) Resulting in Fusion of FUS and NR4A3

Extraskeletal myxoid chondrosarcoma (EMC) is a rare neoplasm characterized by rearrangement of NR4A3. A t(9;22)(q22;q12), creating a fusion protein of EWSR1 and NR4A3, has been reported as a unique, recurring translocation in the majority of cases. Reported variant translocations have resulted in fusion of NR4A3 with three other genes: TAF15, TCF12, and TFG. We report a case of EMC in a 59-year-old man who presented with a six month history of an enlarging mass in the proximal right thigh. Karyotype of fresh tissue from tumor taken at incisional biopsy revealed a t(9;16)(q22;p11.2). There was no evidence of EWSR1 rearrangement by dual color break apart FISH. Dual color FISH probes revealed fusion of NR4A3 and FUS, a member of the TET family of genes which includes EWSR1 and TAF15. Break apart FISH probe confirmed rearrangement of FUS. These findings show a fusion product of FUS and NR4A3 may be an additional pathway to development of EMC.

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Chief Scientific Officer, Dr. Norma Nowak, Speaks Today at UB on Your Genome & Personalized Medicine

Sequencing of the first human genome and its ensuing revolution has profound consequences for all of us. Dr. Nowak will talk about genomic medicine - understanding and treating disease based on our genome by taking the right drug at the right dose to minimize adverse effects. It also can provide a strategy for healthy living.

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Brain MRI abnormalities and spectrum of neurological and clinical findings in three patients with proximal 16p11.2 microduplication

The phenotype of recurrent -600 kb microdeletion and microduplication on proximal 16p11.2 is characterized by a spectrum of neurodevelopmental impairments including developmental delay and intellectual disability, epilepsy, autism and psychiatric disorders which are all subject to incomplete penetrance and variable expressivity. A variety of brain MRI abnormalities were reported in patients with 16p11.2 rearrangements, but no systematic correlation has been studied among patients with similar brain anomalies, their neurodevelopmental and clinical phenotypes. We present three patients with the proximal 16p11.2 microduplication exhibiting significant developmental delay, anxiety disorder and other variable clinical features. Our patients have abnormal brain MRI findings of cerebral T2 hyperintense foci (3/3) and ventriculomegaly (2/3). The neuroradiological or neurological findings in two cases prompted an extensive diagnostic work-up. One patient has exhibited neurological regression and progressive vision impairment and was diagnosed with juvenile neuronal ceroid-lipofuscinosis. We compare the clinical course and phenotype of these patients in regard to the clinical significance of the cerebral lesions and the need for MRI surveillance. We conclude that in all three patients the lesions were not progressive, did not show any sign of malignant transformation and could not be correlated to specific clinical features. We discuss potential etiologic mechanisms that may include overexpression of genes within the duplicated region involved in control of cell proliferation and complex molecular mechanisms such as the MAPK/ERK pathway. Systematic studies in larger cohorts are needed to confirm our observation and to establish the prevalence and clinical significance of these neuroanatomical abnormalities in patients with 16p11.2 duplications.

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Papillomavirus Genomes Associate with BRD4 to Replicate at Fragile Sites in the Host Genome

It has long been recognized that oncogenic viruses often integrate close to common fragile sites. The papillomavirus E2 protein, in complex with BRD4, tethers the viral genome to host chromatin to ensure persistent replication. Here, we map these targets to a number of large regions of the human genome and name them Persistent E2 and BRD4-Broad Localized Enrichments of Chromatin or PEB-BLOCs. PEB-BLOCs frequently contain deletions, have increased rates of asynchronous DNA replication, and are associated with many known common fragile sites. Cell specific fragile sites were mapped in human C-33 cervical cells by FANCD2 ChIP-chip, confirming the association with PEB-BLOCs. HPV-infected cells amplify viral DNA in nuclear replication foci and we show that these form adjacent to PEB-BLOCs. We propose that HPV replication, which hijacks host DNA damage responses, occurs adjacent to highly susceptible fragile sites, greatly increasing the chances of integration here, as is found in HPV-associated cancers.

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Atypical breakpoint in a t(6;17) translocation case of acampomelic campomelic dysplasia

Campomelic dysplasia (CD) is a skeletal dysplasia characterized by Pierre Robin sequence (PRS), shortened and bowed long bones, airway instability, and the potential for sex reversal. A subtype of CD, acampomelic CD (ACD), is seen in approximately 10% of cases and preserves long bone straightness. Both syndromes are caused by alterations in SOX9, with translocations and missense mutations being overrepresented in ACD cases. We report a term infant with PRS, severe cervical spine abnormalities, eleven rib pairs, hypoplastic scapulae, and female genitalia. Chromosome analysis identified a 46,XY,t(6;17)(q25;q24) karyotype. FISH analysis with a series of BAC probes localized the translocation breakpoints to 6q27 and a region at 17q24.3 in the range of 459-379 kb upstream of SOX9. Therefore, this case extends the region classified as the proximal breakpoint cluster. In addition, the comorbidity of acampomelia, complete sex reversal, and severe spinal anomalies in our patient underscores the variability in the level of malformation in the CD/ACD family of disorders.

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Mesenchymal Stem Cells Induce Epithelial Proliferation Within the Inflamed Stomach

Bone marrow-derived mesenchymal stem cells (MSCs) sustain cancer cells by creating a microenvironment favorable for tumor growth. In particular, MSCs have been implicated in gastric cancer development. There is extensive evidence suggesting that Hedgehog signaling regulates tumor growth. However, very little is known regarding the precise roles of Hedgehog signaling and MSCs in tumor development within the stomach. The current study tests that hypothesis that Shh, secreted from MSCs, provides a proliferative stimulus for the gastric epithelium in the presence of inflammation. RFP-expressing MSCs transformed in vitro (stMSCs) were transduced with lentiviral constructs containing a vector control (stMSCvect) or shRNA targeting the Shh gene (stMSCShhKO). Gastric submucosal transplantation of wild type MSCs (wtMSCs), wild type MSCs over-expressing Shh (wtMSCShh), stMSCvect or stMSCShhKO cells in C57BL/6 control (BL/6) or gastrin-deficient (GKO) mice was performed and mice analyzed 30 and 60 days post-transplantation. Compared to BL/6 mice transplanted with wtMSCShh and stMSCvect cells, inflamed GKO mice developed aggressive gastric tumors. Tumor development was not observed in mouse stomachs transplanted with wtMSC or stMSCShhKO cells. Compared to stMSCShhKO transplanted mice, within the inflamed GKO mouse stomach Shh-expressing stMSCsvect and wtMSCsShh induced proliferation of CD44-positive cells. CD44-positive cells clustered in gland-like structures within the tumor stroma and were positive for Ptch expression. We conclude that Shh, secreted from MSCs, provides a proliferative stimulus for the gastric epithelium that is associated with tumor development, a response that is sustained by chronic inflammation.

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Intragenic CAMTA1 deletions are associated with a spectrum of neurobehavioral phenotypes

Intragenic copy number variations involving the calmodulin-binding transcription activator 1 (CAMTA1) gene have recently been reported in four unrelated families with intellectual disability (ID), ataxia, behavioral- and cerebellar abnormalities.

We report a detailed phenotypic and molecular characterization of three individuals with novel intragenic CAMTA1 deletions from two unrelated families and compare the findings to those of previously reported patients.

Our patients had deletions of exons 6-11 and presented with ID, developmental delay (DD), attention deficit hyperactivity disorder (ADHD) and constipation. Two individuals from one family had also unsteady gait. Consistent phenotypes associated with CAMTA1 intragenic rearrangements include ID, speech problems and some dysmorphic features whereas neurobehavioral abnormalities are variable. We did not observe obvious phenotypic differences between patients with in-frame and those with frameshift rearrangements.

There is increased evidence that CAMTA1 has a role in brain and cerebellar function. CAMTA1 should be added to the growing list of genes associated with ID/DD, especially when behavioral problems, cerebellar signs, and/or dysmorphism are also present.

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Xq28 duplication overlapping the int22h-1/int22h-2 region and including RAB39B and CLIC2 in a family with intellectual and developmental disability

Duplications involving terminal Xq28 are a known cause of intellectual disability (ID) in males and in females with unfavorable X-inactivation patterns. Within Xq28, functional disomy of MECP2 causes a severe ID syndrome, however the dosage sensitivity of other Xq28 duplicated genes is less certain. Duplications involving the int22h-1/int22h-2 LCR-flanked region in distal Xq28 have recently been linked to a novel ID-associated phenotype. While evidence for the dosage sensitivity of this region is emerging, the phenotypic contribution of individual genes within the int22h-1/int22h-2-flanked region has yet to be determined. We report a familial case of a novel 774 kb Xq28-qter duplication, detected by cytogenomic microarray analysis, that partially overlaps the int22h-1/int22h-2-flanked region. This duplication and a 570 kb Xpter-p22.33 loss within the pseudoautosomal region were identified in three siblings, one female and two males, who presented with developmental delays/intellectual disability, mild dysmorphic features and short stature. Although unconfirmed, these results are suggestive of maternal inheritance of a recombinant X. We compare our clinical findings to patients with int22h-1/int22h-2-mediated duplications and discuss the potential pathogenicity of genes within the duplicated region, including those within the shared region of overlap, RAB39B and CLIC2.

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Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

The human 8q24 gene desert contains multiple enhancers that form tissue-specific long-range chromatin loops with the MYC oncogene, but how chromatin looping at the MYC locus is regulated remains poorly understood. Here we demonstrate that a long noncoding RNA (lncRNA), CCAT1-L, is transcribed specifically in human colorectal cancers from a locus 515 kb upstream of MYC. This lncRNA plays a role in MYC transcriptional regulation and promotes long-range chromatin looping. Importantly, the CCAT1-L locus is located within a strong super-enhancer and is spatially close to MYC. Knockdown of CCAT1-L reduced long-range interactions between the MYC promoter and its enhancers. In addition, CCAT1-L interacts with CTCF and modulates chromatin conformation at these loop regions. These results reveal an important role of a previously unannotated lncRNA in gene regulation at the MYC locus.

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MYB Gene Abnormalities t(6;9) in Adenoid Cystic Carcinoma Fine-Needle Aspiration Biopsy Using Fluorescence In Situ Hybridization

Adenoid cystic carcinomas (AdCCs) are infrequently encountered malignant neoplasms of the salivary glands that can present difficulties in specific preoperative diagnosis by fine-needle aspiration (FNA) biopsy. On aspirate smears, they frequently show small, round, bland nuclei without the typical features of malignancy noted in other carcinomas (nuclear enlargement, marked atypia, and pleomorphism). They can aggregate in small, 3-dimensional, tight groups with a background showing varying amounts of dense, matrixlike material. This general pattern overlaps with other benign and malignant basaloid-type salivary gland neoplasms, with the primary differential considerations being pleomorphic adenoma (PA) and, less-commonly, basal cell adenoma and basal cell carcinoma. These entities can often have indistinguishable, overlapping morphologic features, and although subtle differences can be noted, they are insufficient for a clear, definitive distinction on FNA biopsy. This typically results in a descriptive FNA biopsy diagnosis and is reported as a basaloid neoplasm with a comment detailing the differential diagnostic possibilities and limitations of definitive classification because of the morphologic appearance.

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Molecular subtyping of metastatic renal cell carcinoma: implications for targeted therapy

Renal cell carcinoma (RCC) is known for its ability to metastasize synchronously or metachronously to various anatomic sites. Distinguishing histologic subtypes of metastatic RCC has become increasingly important, as prognosis and therapy can differ dramatically between subtypes. We propose a combination of immunohistochemistry (IHC) and molecular cytogenetics for subtyping metastatic RCC in light of these potential therapeutic implications.

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Tumor derived vasculogenesis in von Hippel-Lindau disease-associated tumors

von Hippel-Lindau disease (VHL) patients develop highly vascular tumors, including central nervous system hemangioblastomas. It has been hypothesized that the vascular nature of these tumors is the product of reactive angiogenesis. However, recent data indicate that VHL-associated hemangioblastoma neoplastic cells originate from embryologically-arrested hemangioblasts capable of blood and endothelial cell differentiation. To determine the origin of tumor vasculature in VHL-associated hemangioblastomas, we analyzed the vascular elements in tumors from VHL patients. We demonstrate that isolated vascular structures and blood vessels within VHL-associated hemangioblastomas are a result of tumor-derived vasculogenesis. Further, similar to hemangioblastomas, we demonstrate that other VHL-associated lesions possess vascular tissue of tumor origin and that tumor-derived endothelial cells emerge within implanted VHL deficient UMRC6 RCC murine xenografts. These findings further establish the embryologic, developmentally arrested, hemangioblast as the tumor cell of origin for VHL-associated hemangioblastomas and indicate that it is also the progenitor cell for other VHL-associated tumors.

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USCAP 2014 | March 1-7 | San Diego, CA | Booth# 1024

Empire Genomics is proud to be exhibiting at the upcoming USCAP 2014 Annual Meeting in San Diego, California, March 1-7.

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Identification of the 12q15 Amplicon within the Homogeneously Staining Regions in the Embryonal Rhabdomyosarcoma Cell Line RMS-YM

Gene amplification represents one of the molecular mechanisms of oncogene overexpression in many types of tumors. Homogeneously staining regions (HSRs) are cytogenetic hallmarks of gene amplification. Rhabdomyosarcoma is the most common malignant soft-tissue tumor in children. RMS-YM is an embryonal rhabdomyosarcoma cell line that possesses 3 HSRs. This cytogenetic finding suggests the presence of gene amplifications associated with tumor development or progression in RMS-YM. Here, using fluorescence in situ hybridization, we detected high amplification of the MDM2 gene in the HSRs of RMS-YM. We also refined the region of the amplicon and identified that the FRS2 gene and others are amplified in RMS-YM. MDM2 and FRS2 play important roles as a regulator of p53 and a mediator of FGF signaling, respectively, and thus are potential molecular targets for therapy in many different tumors. RMS-YM may be useful for studies of the molecular pathways of tumorigenesis and tumor progression in rhabdomyosarcoma and for in vitro evaluation of newly developed therapeutic agents that target MDM2 or FRS2.

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Detailed Phenotypic and Genotypic Characterization of Bietti Crystalline Dystrophy

To provide a detailed phenotype/genotype characterization of Bietti crystalline dystrophy (BCD).

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Scoliosis and vertebral anomalies: Additional abnormal phenotypes associated with chromosome 16p11.2 rearrangement

The typical chromosome 16p11.2 rearrangements are estimated to occur at a frequency of approximately 0.6% of all samples tested clinically and have been identified as a major cause of autism spectrum disorders, developmental delay, behavioral abnormalities, and seizures. Careful examination of patients with these rearrangements revealed association with abnormal head size, obesity, dysmorphism, and congenital abnormalities. In this report, we extend this list of phenotypic abnormalities to include scoliosis and vertebral anomalies. We present detailed characterization of phenotypic and radiological data of 10 new patients, nine with the 16p11.2 deletion and one with the duplication within the coordinates chr16:29,366,195 and 30,306,956 (hg19) with a minimal size of 555 kb. We discuss the phenotypical and radiological findings in our patients and review 5 previously reported patients with 16p11.2 rearrangement and similar skeletal abnormalities. Our data suggest that patients with the recurrent 16p11.2 rearrangement have increased incidence of scoliosis and vertebral anomalies. However, additional studies are required to confirm this observation and to establish the incidence of these anomalies. We discuss the potential implications of our findings on the diagnosis, surveillance and genetic counseling of patients with 16p11.2 rearrangement.

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Dr. Norma Nowak Speaks At West Seneca Life Sciences Academy Induction Ceremony

The iSciWNY workforce development program, created by the University at Buffalo's New York Center for Excellence in Bioinformatics and Life Sciences and Educational Opportunity Center (EOC), has collaborated with the West Seneca Central School District to create a first-of-its-kind academy that links high school students with potential employers in Western New York's growing life sciences industry.

The new academy will help fill a regional gap in pre-college preparation in STEM (science, technology, engineering, mathematics). Through classroom-based activities and internships, it aims to provide high school students with the practical skills they need to pursue careers in the life sciences industry, and create an educated workforce for area employers.

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Identification of a Distinct Small Cell Population from Human Bone Marrow Reveals Its Multipotency In Vivo and In Vitro

Small stem cells, such as spore-like cells, blastomere-like stem cells (BLSCs), and very-small embryonic-like stem cells (VSELs) have been described in recent studies, although their multipotency in human tissues has not yet been confirmed. Here, we report the discovery of adult multipotent stem cells derived from human bone marrow, which we call StemBios (SB) cells. These isolated SB cells are smaller than 6 and are DAPI+ and Lgr5+ (Leucine-Rich Repeat Containing G Protein-Coupled Receptor 5). Because Lgr5 has been characterized as a stem cell marker in the intestine, we hypothesized that SB cells may have a similar function. In vivo cell tracking assays confirmed that SB cells give rise to three types of cells, and in vitro studies demonstrated that SB cells cultured in proprietary media are able to grow to 625 in size. Once the SB cells have attached to the wells, they differentiate into different cell lineages upon exposure to specific differentiation media. We are the first to demonstrate that stem cells smaller than 6 can differentiate both in vivo and in vitro. In the future, we hope that SB cells will be used therapeutically to cure degenerative diseases.

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CSO & Founder Dr. Norma Nowak delivers her inspirational lecture 'Why Not You?' at Tedx Buffalo Women

Norma Nowak, the Founder and CSO of Empire Genomics, speaks at TEDxBuffaloWomen.

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Chromosome fragility and the abnormal replication of the FMR1 locus in Fragile X syndrome

Fragile X Syndrome (FXS) is a learning disability seen in individuals who have >200 CGG-CCG-repeats in the 5' untranslated region of the X-linked FMR1 gene. Such alleles are associated with a fragile site, FRAXA, a gap or constriction in the chromosome that is coincident with the repeat and is induced by folate-stress or thymidylate synthase inhibitors like fluorodeoxyuridine (FdU). The molecular basis of the chromosome fragility is unknown. Previous work has suggested that the stable intrastrand structures formed by the repeat may be responsible, perhaps via their ability to block DNA synthesis. We have examined the replication dynamics of normal and FXS cells with and without FdU. We show here that an intrinsic problem with DNA replication exists in the FMR1 gene of individuals with FXS even in the absence of FdU. Our data suggests a model for chromosome fragility in FXS in which the repeat impairs replication from an origin of replication (ORI) immediately adjacent to the repeat. The fact that the replication problem occurs even in the absence of FdU suggests that this phenomenon may have in vivo consequences, including perhaps accounting for the loss of the X chromosome containing the fragile site that causes Turner syndrome (45, X0) in female carriers of such alleles. Our data on FRAXA may also be germane for the other FdU-inducible fragile sites in humans, that we show here share many common features with FRAXA.

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More Economic Activity In Store For Buffalo from Genomics Project

The research accelerated by the two projects "could really revolutionize health care here in Western New York and across our entire state," said Anthony Johnson, Empire Genomics' President and CEO.

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Empire Genomics to benefit from Governor Cuomo's public-private partnership program to make NYS a Genomics Research Leader

Four companies will be the initial beneficiaries of the collaboration, according to UB and state officials. They are Computer Task Group, a Buffalo-based information technology solutions firm; Empire Genomics, which arose out of research at Roswell Park; AESKU Diagnostics, a German-based life sciences firm seeking to establish a new operation in the Buffalo area and Lineagen, a Salt Lake City, Utah-based firm seeking to expand its medical diagnostics business.

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Cribriform adenocarcinoma of the lung: clinicopathologic, immunohistochemical, and molecular analysis of 15 cases of a distinctive morphologic subtype of lung adenocarcinoma

Lung adenocarcinoma is characterized by marked heterogeneity and may be composed of an admixture of histologic growth patterns, including acinar, papillary, solid, and lepidic (bronchioloalveolar). Tumors displaying a prominent or predominant cribriform architecture are rare and most often confused for metastases from other organs. We report the clinical, histologic, immunohistochemical, and molecular features in 15 primary lung adenocarcinomas with a predominant cribriform histology. All patients were adults between 30 and 80 years of age (median: 64), and all but one reported a history of heavy cigarette smoking. All cases showed a predominant (>70%) cribriform architecture that resembled a variety of tumors arising in other organs, including breast, prostate, ovary, pancreas, uterus, colon, and thyroid. Immunohistochemical stains showed a phenotype consistent with a primary lung tumor (ie, TTF1+/CK7+), with negative results for other markers. Molecular analysis in six cases showed that none harbored an EGFR-activating mutation. KRAS mutation was detected in one case, and an ALK1 and ROS1 gene rearrangement were each detected in an additional two cases. Cribriform adenocarcinomas of the lung represent a distinctive histologic subtype of lung cancer that may be morphologically difficult to differentiate from metastases with a predominant cribriform architecture.

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Current and Proposed Molecular Diagnostics in a Genitourinary Service Line Laboratory at a Tertiary Clinical Institution

The idea that detailed knowledge of molecular oncogenesis will drive diagnostic, prognostic, and therapeutic clinical decision making in an increasingly multidisciplinary practice of oncologic care has been anticipated for many years. With the recent rapid advancement in our understanding of the molecular underpinnings of genitourinary malignancies, this concept is now starting to take shape in the fields of prostate, kidney, bladder, testicular, and penile cancer. Such breakthroughs necessitate the development of robust clinical-grade assays that can be quickly made available for patients to facilitate diagnosis in challenging cases, risk-stratify patients for subsequent clinical management, select the appropriate targeted therapy from among increasingly diverse and numerous options, and enroll patients in advanced clinical trials. This rapid translation of basic and clinical cancer research requires a streamlined, multidisciplinary approach to clinical assay development, termed here the molecular diagnostics service line laboratory. In this review, we summarize the current state and explore the future of molecular diagnostics in genitourinary oncology to conceptualize a genitourinary service line laboratory at a tertiary clinical institution.

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Correlation of WWOX, RUNX2 and VEGFA protein expression in human osteosarcoma

To investigate associations between WW domain-containing oxidoreductase (WWOX), runt-related transcription factor 2 (RUNX2) and vascular endothelial growth factor alpha (VEGFA) in human osteosarcoma (OS).

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Activated 5′ flanking region of NANOGP8 in a self-renewal environment is associated with increased sphere formation and tumor growth of prostate cancer cells

NANOGP8 is a retrogene which encodes a full-length protein similar to the NANOG1 gene. The expression of NANOGP8 has been documented in several cancers and is related to cell proliferation and tumor development. However, the regulation of NANOGP8 expression has not been investigated. Therefore, the role of NANOGP8 in cell proliferation has not been completely understood.

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MLL Rearrangment and EVI1 Deletion in BCR/ABL1 Positive Chronic Myeloid Leukemia

We present unusual cytogenetic findings in a 65-year-old female with blast phase (BC) of Philadelphia chromosome positive chronic myeloid leukemia (CML). Chromosome analysis revealed two related abnormal clones, one characterized by a t(9;22)(q34;q11.2), and the other showing a t(11;19)(q23;p13.1) in addition to the t(9;22)(q34;q11). Fluorescence in situ hybridization (FISH) testing confirmed that the t(11;19) involved the MLL gene on 11q23. High-density whole-genome SNP array analysis of leukemia cells showed a number of submicroscopic copy number abnormalities, including a deletion of the MECOM (MDS1 and EVI1 complex locus protein EVI1) gene at 3q26. Clinical course was aggressive, and the patient failed to respond to both imatinib and dasatinib despite the absence of resistance associated mutations in the BCR/ABL1 gene. To our knowledge, the combination of a t(9;22) with t(11;19)(q23;p13.1) has only been reported in one case, while a deletion of the EVI1 gene has never been reported in CML.

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A case of pediatric B-Lymphoblastic leukemia presenting with a t(9;12)(p24;q11.2) involving JAK2 and concomitant MLL rearrangement with apparent insertion at 6q27

B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy in pediatric patients and the leading cause of cancer-related death in children and young adults. Translocations of 9p24 involving JAK2 (9p24) and gain-of-function mutations of JAK2 with subsequent activation of the JAK2 kinase have been described in several hematological malignancies including B-ALL. However, rearrangements involving JAK2 are rare in B-ALL as only few cases have been described in the literature.

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Study on lung cancer cells express VEGFR2 and impact on the effect of RHES combined with radiotherapy in the treatment of brain metastases

Brain metastases (BM) is often accompanied by edema, Endostatin (ES) can prevent tumor tissue edema. Therefore, we investigated the therapeutic effects of ES combined with radiotherapy in the treatment of BM of NSCLC and discuss the relations between the effect and VEGFR2 expression.

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Brd4 Is Displaced from HPV Replication Factories as They Expand and Amplify Viral DNA

Replication foci are generated by many viruses to concentrate and localize viral DNA synthesis to specific regions of the cell. Expression of the HPV16 E1 and E2 replication proteins in keratinocytes results in nuclear foci that recruit proteins associated with the host DNA damage response. We show that the Brd4 protein localizes to these foci and is essential for their formation. However, when E1 and E2 begin amplifying viral DNA, Brd4 is displaced from the foci and cellular factors associated with DNA synthesis and homologous recombination are recruited. Differentiated HPV-infected keratinocytes form similar nuclear foci that contain amplifying viral DNA. We compare the different foci and show that, while they have many characteristics in common, there is a switch between early Brd4-dependent foci and mature Brd4-independent replication foci. However, HPV genomes encoding mutated E2 proteins that are unable to bind Brd4 can replicate and amplify the viral genome. We propose that, while E1, E2 and Brd4 might bind host chromatin at early stages of infection, there is a temporal and functional switch at later stages and increased E1 and E2 levels promote viral DNA amplification, displacement of Brd4 and growth of a replication factory. The concomitant DNA damage response recruits proteins required for DNA synthesis and repair, which could then be utilized for viral DNA replication. Hence, while Brd4 can enhance replication by concentrating viral processes in specific regions of the host nucleus, this interaction is not absolutely essential for HPV replication.

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New York State Department of Health Issues Clinical Laboratory Permit to Empire Genomics

Buffalo, New York - Empire Genomics, LLC (www.empiregenomics.com), an emerging molecular diagnostics company in the field of personalized medicine, announced today that its clinical laboratory facility has met the rigorous standards and obtained approval by the New York State Department of Health, and is now fully licensed (#PFI 8680) in Cytogenetics-Cancer. Simultaneously, Empire Genomics lab received Clinical Laboratory Improvements Amendments (CLIA) certification of registration (#33D2043745) from the Centers for Medicare and Medicaid Services (CMS).

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Join Us at our 'Tips For The Cure' Fundraiser!

President and CEOs Anthony Johnson of Empire Genomics and Stephen Panaro of QuaDPharma will bartend at our Halloween happy hour fundraising event in which all tips will benefit CanLiv (www.canliv.org) and The Jacquie Hirsch For A.L.L. Foundation (http://www.jacquieforall.com), on Wednesday, October 30, 2013 from 5-8pm, at The Chocolate Bar in Buffalo.

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Empire Genomics and QuaDPharma Join Forces for Cancer Research Fundraiser

The President and CEOs of Empire Genomics, LLC, a global molecular diagnostics company in the field of oncology, and QuaDPharma, a rapidly growing small-to-medium scale commercial contract manufacturer, will consort to host a Halloween happy hour (5-8pm) to raise funds on October 30, 2013 for bile duct cancer research and The Jacquie Hirsch for A.L.L. (acute lymphocytic leukemia ) Foundation.

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Chromosomal Contact Permits Transcription between Coregulated Genes

Transcription of coregulated genes occurs in the context of long-range chromosomal contacts that form multigene complexes. Such contacts and transcription are lost in knockout studies of transcription factors and structural chromatin proteins. To ask whether chromosomal contacts are required for cotranscription in multigene complexes, we devised a strategy using TALENs to cleave and disrupt gene loops in a well-characterized multigene complex. Monitoring this disruption using RNA FISH and immunofluorescence microscopy revealed that perturbing the site of contact had a direct effect on transcription of other interacting genes. Unexpectedly, this effect on cotranscription was hierarchical, with dominant and subordinate members of the multigene complex engaged in both intra- and interchromosomal contact. This observation reveals the profound influence of these chromosomal contacts on the transcription of coregulated genes in a multigene complex.

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A novel ALK rearrangement in an inflammatory myofibroblastic tumor (IMT) in a neonate

Inflammatory myofibroblastic tumors (IMTs) are uncommon lesions primarily affecting children and young adults. They have rarely been described in infants, with a very small number described in neonates. Structural rearrangement in the anaplastic large cell lymphoma kinase gene (ALK) has contributed to our categorizing this lesion as a neoplasm. In addition, rearrangements of the ALK gene have been implicated in the pathogenicity of many other hematolymphoid and non-hematolymphoid tumors, typically involving 2p23 with different partners, or with pericentric inversion. We report a previously undescribed cryptic deletion and intrachromosomal-insertional translocation of 3-region of the ALK gene from 2p23 to 2q33-35 region in an IMT of a newborn patient with apparently normal G-band karyotype of the tumor.

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Founder Norma Nowak Presents At 5th International Leaders in Biobanking Congress 2013

Today, biospecimen collections are used by multiple research groups for varying research aims, from basic research through clinical trials. A well-managed biobank is a critical prerequisite for high-quality biological research. The proper collection, processing, storage and tracking of biospecimens are critical components allowing researchers to better link molecular and clinical information. Thus, by necessity, biobanking is both a science and a business. Cambridge Healthtech Institutes Fifth Annual Leaders in Biobanking: Maximizing Your Investment in Biospecimens addresses both the business and science of biobanking, bringing together biomedical and biopharmaceutical researchers, regulators, biorepository managers and practitioners to investigate the best strategies for effective use of biospecimens within todays cutting-edge research.

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Deletion of the Olfactomedin 4 Gene Is Associated with Progression of Human Prostate Cancer

The olfactomedin 4 (OLFM4) gene is located on chromosome 13q14.3, which frequently is deleted in human prostate cancer. However, direct genetic evidence of OLFM4 gene alteration in human prostate cancer has not yet been obtained. In this study, we investigated the genetics, protein expression, and functions of the OLFM4 gene in human prostate cancer. We found overall 25% deletions within the OLFM4 gene in cancerous epithelial cells compared with adjacent normal epithelial cells that were microdissected from 31 prostate cancer specimens using laser-capture microdissection and genomic DNA sequencing. We found 28% to 45% hemizygous and 15% to 57% homozygous deletions of the OLFM4 gene via fluorescence in situ hybridization analysis from 44 different prostate cancer patient samples. Moreover, homozygous deletion of the OLFM4 gene significantly correlated with advanced prostate cancer. By using immunohistochemical analysis of 162 prostate cancer tissue array samples representing a range of Gleason scores, we found that OLFM4 protein expression correlated inversely with advanced prostate cancer, consistent with the genetic results. We also showed that a truncated mutant of OLFM4 that lacks the olfactomedin domain eliminated suppression of PC-3 prostate cancer cell growth. Together, our findings indicate that OLFM4 is a novel candidate tumor-suppressor gene for chromosome 13q and may shed new light on strategies that could be used for the diagnosis, prognosis, and treatment of prostate cancer patients.

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46,XY disorder of sexual development and developmental delay associated with a novel 9q33.3 microdeletion encompassing NR5A1

Steroidogenic factor 1 (SF1) is a nuclear receptor encoded by the NR5A1 gene. SF1 affects both sexual and adrenal development through the regulation of target gene expression. Genotypic male and female SF1 knockout mice have adrenal and gonadal agenesis with persistent Mlerian structures and early lethality. There have been several reports of NR5A1 mutations in individuals with 46,XY complete gonadal dysgenesis (CGD) or other disorders of sexual development (DSD) with or without an adrenal phenotype. To date microdeletions involving NR5A1 have been reported in only two patients with DSDs.

We report a novel microdeletion encompassing NR5A1 in a patient with 46,XY DSD and developmental delay. The phenotypically female patient initially presented with mild developmental delay and dysmorphisms. Chromosome analysis revealed a 46,XY karyotype. A 1.54 Mb microdeletion of chromosome 9q33.3 including NR5A1 was detected by array CGH and confirmed by FISH. Normal maternal FISH results indicated that this was most likely a de novo event. Since most NR5A1 mutations have been ascertained through gonadal or adrenal abnormalities, the additional findings of developmental delay and minor facial dysmorphisms are possibly related to haploinsufficiency of other genes within the 1.54 Mb deleted region. This report further confirms the role of NR5A1 deletions in 46,XY DSD and reinforces the utility of aCGH in the work up of DSDs of unclear etiology.

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USP6 Gene Rearrangement in Spindle Cell Neoplasms: A Diagnostic Tool for Nodular Fasciitis

Nodular fasciitis (NF), once thought to be a reactive proliferation, has recently been characterized by a recurrent translocation involving USP6, which is seen in approximately 90% of cases. NF is a benign lesion but may be misdiagnosed as a more locally aggressive or even a malignant neoplasm. We sought to assess the utility of the USP6 gene rearrangement to differentiate nodular fasciitis from other spindle cell lesions within the differential diagnosis, focusing on those that occur in childhood.

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Targeting EGFR and PI3K pathways in ovarian cancer

The epidermal growth factor receptor (EGFR) is expressed in ovarian cancer, but agents targeting this pathway have shown little effect as single agents. This may be due to the presence of alternative pathways, particularly activation of the PI3K/Akt/MTOR pathway.

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An Enhancer Element Harboring Variants Associated with Systemic Lupus Erythematosus Engages the TNFAIP3 Promoter to Influence A20 Expression

Functional characterization of causal variants present on risk haplotypes identified through genome-wide association studies (GWAS) is a primary objective of human genetics. In this report, we evaluate the function of a pair of tandem polymorphic dinucleotides, 42kb downstream of the promoter of TNFAIP3, (rs148314165, rs200820567, collectively referred to as TT>A) recently nominated as causal variants responsible for genetic association of systemic lupus erythematosus (SLE) with tumor necrosis factor alpha inducible protein 3 (TNFAIP3). TNFAIP3 encodes the ubiquitin-editing enzyme, A20, a key negative regulator of NF-κB signaling. A20 expression is reduced in subjects carrying the TT>A risk alleles; however, the underlying functional mechanism by which this occurs is unclear. We used a combination of electrophoretic mobility shift assays (EMSA), mass spectrometry (MS), reporter assays, chromatin immunoprecipitation-PCR (ChIP-PCR) and chromosome conformation capture (3C) EBV transformed lymphoblastoid cell lines (LCL) from individuals carrying risk and non-risk TNFAIP3 haplotypes to characterize the effect of TT>A on A20 expression. Our results demonstrate that the TT>A variants reside in an enhancer element that binds NF-κB and SATB1 enabling physical interaction of the enhancer with the TNFAIP3 promoter through long-range DNA looping. Impaired binding of NF-κB to the TT>A risk alleles or knockdown of SATB1 expression by shRNA, inhibits the looping interaction resulting in reduced A20 expression. Together, these data reveal a novel mechanism of TNFAIP3 transcriptional regulation and establish the functional basis by which the TT>A risk variants attenuate A20 expression through inefficient delivery of NF-κB to the TNFAIP3 promoter. These results provide critical functional evidence supporting a direct causal role for TT>A in the genetic predisposition to SLE.

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Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization

Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1 kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci.

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Undifferentiated Small Round Cell Sarcoma With t(4;19)(q35;q13.1) CIC-DUX4 Fusion: A Novel Highly Aggressive Soft Tissue Tumor With Distinctive Histopathology

A subset of small round cell sarcomas remains difficult to classify. Among these, a rare tumor harboring a t(4;19)(q35;q13.1) with CIC-DUX4 fusion has been described. The aim of this study is to better understand its clinicopathologic features. Four cases of CIC-DUX4 sarcoma, all arising in adults (3 women, 1 man, aged 20 to 43 y), were identified using conventional cytogenetic, reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) methods. All 4 tumors demonstrated CIC-DUX4 fusion transcript by both RT-PCR and FISH and CIC rearrangement by FISH. Cytogenetic results from 2 tumors showed t(4;19)(q35;q13.1) occurring as part of a simple karyotype in 1 tumor and as part of a complex karyotype in the other, the latter from a postchemotherapy specimen. Both tumors harbored trisomy 8 and lacked any other known sarcoma-associated translocation.

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Reactivation of Χ chromosome upon reprogramming leads to changes in the replication pattern and 5hmC accumulation

Once set, the inactive status of the X chromosome in female somatic cells is preserved throughout subsequent cell divisions. The inactive status of the X chromosome is characterized by many features, including late replication. In contrast to induced pluripotent stem cells (iPSCs) in mice, the X chromosome in human female iPSCs usually remains inactive after reprogramming of somatic cells to the pluripotent state, although recent studies point to the possibility of reactivation of the X chromosome. Here, we demonstrated that, during reprogramming, the inactive X chromosome switches from late to synchronous replication, with restoration of the transcription of previously silenced genes. This process is accompanied by accumulation of a new epigenetic mark or intermediate of the DNA demethylation pathway, 5-hydroxymethylcytosine (5hmC), on the activated X chromosome. Our results indicate that the active status of the X chromosome is better confirmed by early replication and the reappearance of 5hmC, rather than by appearance of histone marks of active chromatin, removal of histone marks of inactive chromatin, or an absence of XIST coating.

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Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity

The ability of the immune system to distinguish self from foreign (self-tolerance) is largely established in the thymus, a primary lymphoid organ where T cells develop. Intriguingly, T cells encounter most tissue-specific constituents already in the thymus, thus imposing a broad scope of tolerance before T cells circulate through the body. This preemption of the immunological self is afforded by the promiscuous expression of numerous tissue-specific antigens in medullary thymic epithelial cells. Here, we identified principles by which promiscuous gene expression at the single-cell level adds up to the full diversity of self-antigens displayed at the population level.

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lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

Although recent studies have indicated roles of long non-coding RNAs (lncRNAs) in physiological aspects of cell-type determination and tissue homeostasis, their potential involvement in regulated gene transcription programs remains rather poorly understood. The androgen receptor regulates a large repertoire of genes central to the identity and behaviour of prostate cancer cells, and functions in a ligand-independent fashion in many prostate cancers when they become hormone refractory after initial androgen deprivation therapy. Here we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 (also known as PCAT8) and PCGEM1, bind successively to the androgen receptor and strongly enhance both ligand-dependent and ligand-independent androgen-receptor-mediated gene activation programs and proliferation in prostate cancer cells.

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Role of hypoxia inducible factor-1α in the regulation of the cancer-specific variant of organic anion transporting polypeptide 1B3 (OATP1B3), in colon and pancreatic cancer

Organic anion transporting polypeptide 1B3 (OATP1B3) was initially considered to be a liver-specific transporter, mediating the uptake of a variety of endogenous and xenobiotic substances. Over the past decade, several investigations reported that OATP1B3 is also expressed across multiple types of cancers. Only recently, our laboratory and others demonstrated the identity of cancer-specific OATP1B3 variants (csOATP1B3) arising from the use of an alternative transcription initiation site, different from the wildtype (WT) OATP1B3 expressed in the normal liver. However, the mechanisms regulating the expression of csOATP1B3 remained unknown. In our current study, we investigated the role of hypoxia and the involvement of hypoxia inducible factor-1α (HIF-1α) in regulating the transcription of csOATP1B3. Our RT-PCR and immunoblotting results indicated that csOATP1B3, but not WT OATP1B3, can be induced in response to ambient or chemical hypoxia (upon exposure to 1% O2 or cobalt chloride). Reporter assays with deletion and mutated constructs of the csOATP1B3 promoter revealed a functional hypoxia response element (HRE) located in the proximal upstream region. Constructs harboring the HRE displayed the upregulated reporter gene expression in response to hypoxia, but not when mutated. Electrophoretic mobility shift assays using a biotin-labeled csOATP1B3 promoter HRE probe indicated the binding of HIF-1α, which was blocked by an excess of unlabeled csOATP1B3 probe. Furthermore, siRNA-based knockdown of HIF-1α caused a substantial decrease in the expression level of csOATP1B3. Taken together, these findings demonstrate that the transcription of csOATP1B3 is actively engaged during hypoxia, through a commonly utilized pathway involving HIF-1α.

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Subtype of Highly Aggressive Prostate Cancer Increasing; Tied to Drug Resistance to Hormone Therapy

Currently there is a Catch-22 occurring in advanced prostate cancer treatment. Newly FDA-approved, highly potent, anti-androgen medications used to treat advanced prostate cancer have improved survival time in men with treatment-resistant prostate cancer; however, those very drugs may be inducing some mens cancer to further evolve into a subtype of cancer called neuroendocrine prostate cancer that is highly lethal.

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Another Voice: Buffalo has its visionaries, but we don't follow them

We have many visionaries in Buffalo, such as Jordan Levy, Norma Nowak, Dr. Nick Hopkins and Dr. Donald Trump. The problem is that, unlike Albany, our region hasnt embraced their visionary ideas. If Buffalo doesnt tear down the wall of resistance to change, then the New York billion will go nowhere but down the drain. Next time we have a major project to undertake, we should ask ourselves: Would Alain Kaloyeros do it this way? We have visionaries with ideas. Now lets use them.

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Frequent TMPRSS2-ERG rearrangement in prostatic small cell carcinoma detected by fluorescence in situ hybridization: the superiority of fluorescence in situ hybridization over ERG immunohistochemistry

Small cell carcinoma of the prostate is both morphologically and immunohistochemically similar to small cell carcinoma of other organs such as the urinary bladder or lung. TMPRSS2-ERG gene fusion appears to be a highly specific alteration in prostatic carcinoma that is frequently shared by small cell carcinoma. In adenocarcinoma, immunohistochemistry for the ERG protein product has been reported to correlate well with the presence of the gene fusion, although in prostatic small cell carcinoma, this relationship is not completely understood.

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De novo MECP2 disomy in a Mexican male carrying a supernumerary marker chromosome and no typical Lubs syndrome features

Here we report a Mexican male patient carrying a supernumerary marker chromosome with de novo Xq28 gain. By MLPA, duplication of MECP2, GDI1, and SLC6A8 was found and a subsequent a-CGH analysis demonstrated that the gain spanned ~ 2.1 Mb. Despite gain of the MECP2 gene, the features of this patient do not evoke Lubs syndrome. Probably the mosaicism of the supernumerary marker chromosome is modifying the phenotype in this patient.

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Patent ruling won't alter Empire Genomics approach

A Buffalo biotech firm says the U.S. Supreme Court decision this week on patents and genetics won't likely have a major impact on its business, but the ruling does provide some clarity. Thursdays Supreme Court decision involved patents by Salt Lake City-based Myriad Genetics Inc., which holds patents related to the discovery and sequence of two genes, which it used to develop tests for breast and ovarian cancer. Simply put: The court said naturally-occurring human genes cannot be patented.

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An unusual presentation of glomeruloid hemangioma in a patient with VHL syndrome: A case report and review of literature

Von Hippel-Lindau (VHL) is an inherited neoplasia syndrome caused by inactivation of the VHL tumor suppressor gene, characterized by the development of sporadic clear cell renal carcinoma, pheochromocytomas, retinal angioma, pancreatic cysts, and CNS hemangioblastomas. Glomeruloid hemangioma is a vascular lesion, previously considered to be specifically associated with POEMS (polyneuropathy, or- ganomegaly, endocrinopathy/edema, M-protein and skin abnormalities) syndrome. However, there are reports of solitary glomeruloid hemangioma in patients without POEMS syndrome. We report the case of a 39-year-old male with VHL disease, with known bilateral clear cell renal carcinomas, CNS heman- gioblastoma and pancreatic cysts. The patient presented with a 0.35 cm red papule on the left lateral neck, which was easily irritated, and bleed frequently. Histopathologically, there were irregular areas of ectatic vascular channels of small capillaries, resembling renal glomeruli, surrounded by actin-positive pericytes, within the dermis. These findings were consistent with a glomeruloid hemangioma. Fluorescent in-situ hybridization studies confirmed a deletion in the 3p25.3 region. As per clinical tests, no evidence of POEMS syndrome was found in this patient. Only six reports of glomeruloid hemangioma have been previously reported in patients without POEMS syndrome and this constitutes the first report of glomeruloid hemangioma in a patient with VHL.

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Human papillomavirus-related carcinoma with adenoid cystic-like features: a peculiar variant of head and neck cancer restricted to the sinonasal tract

Human papillomavirus (HPV)-related carcinomas of the head and neck are characterized by a predilection for the oropharynx, a nonkeratinizing squamous morphology, and infection with the HPV 16 type; but comprehensive HPV testing across all head and neck sites has shown that the pathologic features of HPV-related carcinoma may be more wide ranging than initially anticipated. In particular, a subset of sinonasal carcinomas are HPV positive, and these include a variant that is histologically similar to adenoid cystic carcinoma (ACC). Cases were identified by retrospective and prospective analyses of head and neck carcinomas with ACC features. HPV analysis was performed using p16 immunohistochemistry and high-risk HPV in situ hybridization. HPV-positive cases were confirmed and typed using HPV type-specific quantitative polymerase chain reaction and further characterized on the basis of their immunohistochemical profile and MYB gene status. HPV was detected in 8 carcinomas of the sinonasal tract, but it was not detected in any ACCs arising outside of the sinonasal tract. The HPV types were 33 (n=6), 35 (n=1), and indeterminate (n=1). Six patients were women, and 2 were men, ranging in age from 40 to 73 years (mean 55 y). The carcinomas were characterized by a nested growth, a prominent basaloid component showing myoepithelial differentiation and forming microcystic spaces, and a minor epithelial component with ductal structures. Squamous differentiation, when present, was restricted to the surface epithelium. The carcinomas were not associated with the MYB gene rearrangement that characterizes a subset of ACCs. These cases draw attention to an unusual variant of HPV-related carcinoma that has a predilection for the sinonasal tract. Despite significant morphologic overlap with ACC, it is distinct in several respects including an association with surface squamous dysplasia, absence of the MYB gene rearrangement, and an association with HPV, particularly type 33. As HPV positivity confers distinct clinicopathologic characteristics when encountered in the oropharynx, a more comprehensive analysis of risk factors, response to therapy, and clinical outcomes is warranted for HPV-related carcinomas of the sinonasal tract.

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ERG Expression in Epithelioid Sarcoma: A Diagnostic Pitfall

ERG transcription factor is constitutively expressed in endothelial cells. Because benign and malignant vascular endothelia retain the ERG expression, ERG is considered a useful marker for angiosarcomas and related tumors. ERG is also expressed in a subset of prostate carcinomas and Ewing sarcomas due to ERG-involved translocations; therefore, this marker is also of high interest in the study of these malignancies. In this study, we evaluated 109 epithelioid sarcomas for ERG expression, on the basis of an initial observation of an ERG-positive case. We also studied expression of other endothelial antigens in epithelioid sarcoma.

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UB, Empire Genomics partner with Life Technologies to accelerate innovative, genetics-based clinical research in Western New York

Empire Genomics, Life Technologies Corporation and the University at Buffalo will embark on a new partnership to develop world-class gene sequencing facilities for genetics-based clinical research on the Buffalo Niagara Medical Campus. The collaboration capitalizes on each organizations strengths to help establish a new standard for genomic research in Western New York and continue to grow the life sciences sector of the regions economy.

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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNAs (lncRNAs) in mammalian cells, bidirectional ncRNAs are transcribed on enhancers, and are thus referred to as enhancer RNAs (eRNAs). However, it has remained unclear whether these eRNAs are functional or merely a reflection of enhancer activation. Here we report that in human breast cancer cells 17?-oestradiol (E2)-bound oestrogen receptor ? (ER-?) causes a global increase in eRNA transcription on enhancers adjacent to E2-upregulated coding genes.

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Chromosome 20p inverted duplication deletion identified in a Thai female adult with mental retardation, obesity, chronic kidney disease and characteristic facial features

We report on a 21-year-old Thai woman presenting with mental retardation, developmental delays, selective mutism, distinctive facial features, sensorineural hearing loss, single right kidney, uterine didelphys and obesity. A longitudinal clinical course beginning in childhood revealed excessive weight gain, poor language skills and poor school performance.

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Differential nuclear organization of translocation-prone genes in nonmalignant B cells from patients with t(14;16) as compared with t(4;14) or t(11;14) myeloma

Gene organization in nonmalignant B cells from t(4;14) and t(11;14) multiple myeloma (MM) patients differs from that of healthy donors. Among recurrent IGH translocations in MM, the frequency of t(4;14) (IGH and FGFR3) or t(11;14) (IGH and CCND1) is greater than the frequency of t(14;16) (IGH and MAF). Gene organization in t(14;16) patients may influence translocation potential of MAF with IGH.

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TFE3 Break-Apart FISH Has a Higher Sensitivity for Xp11.2 Translocation-Associated Renal Cell Carcinoma Than TFE3 or Cathepsin K Immunohistochemical Staining Alone: Expanding the Morphologic Spectrum

Renal cell carcinoma (RCC) associated with Xp11.2 translocation is uncommon, characterized by various translocations involving the TFE3 gene. Renal cell carcinoma (RCC) associated with Xp11.2 translocation is uncommon, characterized by various translocations involving the TFE3 gene. Recognition commonly depends on nuclear overexpression of TFE3 protein by immunohistochemistry (IHC), although staining can be variable. Break-apart fluorescence in situ hybridization (FISH) for TFE3 has shown promise for detecting these gene alterations.

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Empire Genomics Awarded SBIR Phase I Grant from NCI for Companion Diagnostics for Multiple Myeloma

Empire Genomics, LLC (www.empiregenomics.com) has been awarded a Phase I SBIR Grant by the National Institute of Health/National Cancer Institute to develop a genomic companion diagnostic test for multiple myeloma (MM). This is the first SBIR grant Empire Genomics has been awarded and it will be funded through October 2013. The Company plans to use these funds to further develop its licensed technology to investigate methods in genomics to predict MM patient response to therapeutic treatments.

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Empire Genomics Licenses Novel DNA Biomarker for Use in Diagnosing and Creating a Companion Diagnostic Test for Neuroendocrine Prostate Cancer

Empire Genomics announced today it has acquired an exclusive license for a patent pending novel genomic biomarker from Cornell University for use in developing a molecular diagnostic test that could help in diagnosing and determining treatment for patients with neuroendocrine (NEPC) prostate cancer.

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Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis

X-linked congenital generalized hypertrichosis (Online Mendelian Inheritance in Man 307150) is an extremely rare condition of hair overgrowth on different body sites. We previously reported linkage in a large Mexican family with X-linked congenital generalized hypertrichosis cosegregating with deafness and with dental and palate anomalies to Xq24-27. Using SNP oligonucleotide microarray analysis and whole-genome sequencing, we identified a 389-kb interchromosomal insertion at an extragenic palindrome site at Xq27.1 that completely cosegregates with the disease. Among the genes surrounding the insertion, we found that Fibroblast Growth Factor 13 (FGF13) mRNA levels were significantly reduced in affected individuals, and immunofluorescence staining revealed a striking decrease in FGF13 localization throughout the outer root sheath of affected hair follicles. Taken together, our findings suggest a role for FGF13 in hair follicle growth and in the hair cycle.

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Familial KANK1 deletion that does not follow expected imprinting pattern

Deletion of the KANK1 gene (also called ANKRD15), located at chromosome position 9p24.3, has been associated with neurodevelopmental disease including congenital cerebral palsy, hypotonia, quadriplegia, and intellectual disability in a four-generation family. The inheritance pattern in this family was suggested to be maternal imprinting, as all affected individuals inherited the deletion from their fathers and monoallelic protein expression was observed.

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Clinical Comparison of Overlapping Deletions of 19p13.3

We present three patients with overlapping interstitial deletions of 19p13.3 identified by high resolution SNP microarray analysis. All three had a similar phenotype characterized by intellectual disability or developmental delay, structural heart abnormalities, large head relative to height and weight or macrocephaly, and minor facial anomalies.

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Higher Expression of Peroxisome Proliferator-activated Receptor γ or Its Activation by Agonist Thiazolidinedione-rosiglitazone Promotes Bladder Cancer Cell Migration and Invasion

To investigate the role of peroxisome proliferator-activated receptor γ (PPARγ) in bladder cancer (BCa) progression. The gene copy number of PPARγ in human BCa tissue samples was analyzed by fluorescence in situ hybridization. The migration and invasive ability of human BCa cell lines with different PPARγ expression levels or treated with thiazolidinedione-rosiglitazone, a PPARγ agonist and an antidiabetic drug, were investigated.

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Buffalo has a presence at major Chicago event

A contingent including representatives from 12 area life-sciences companies and the major institutions on the Buffalo Niagara Medical Campus is in Chicago this week for the BIO International Convention. Local convention attendees include representatives Empire Genomics.

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Haploinsufficiency of ZNF238 is associated with corpus callosum abnormalities in 1q44 deletions

A variety of candidate genes have been proposed to cause corpus callosum abnormalities (CCAs) in patients with terminal chromosome 1q deletions. Recent data excluded AKT3 and implicated ZNF238 and/or CEP170 as genes causative of corpus callosum anomalies in patients with 1q431q44 deletions. We report on a girl with dysmorphic features, seizures beginning in infancy, hypotonia, marked developmental delay, and dysgenesis of the corpus callosum.

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Late replication of the inactive x chromosome is independent of the compactness of chromosome territory in human pluripotent stem cells

Dosage compensation of the X chromosomes in mammals is performed via the formation of facultative heterochromatin on extra X chromosomes in female somatic cells. Facultative heterochromatin of the inactivated X (Xi), as well as constitutive heterochromatin, replicates late during the S-phase. It is generally accepted that Xi is always more compact in the interphase nucleus. The dense chromosomal folding has been proposed to define the late replication of Xi. In contrast to mouse pluripotent stem cells (PSCs), the status of X chromosome inactivation in human PSCs may vary significantly. Fluorescence in situ hybridization with a whole X-chromosome- specific DNA probe revealed that late-replicating Xi may occupy either compact or dispersed territory in human PSCs. Thus, the late replication of the Xi does not depend on the compactness of chromosome territory in human PSCs. However, the Xi reactivation and the synchronization in the replication timing of X chromosomes upon reprogramming are necessarily accompanied by the expansion of X chromosome territory.

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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

We report intron chromosomal expression FISH (iceFISH), a multiplex imaging method for measuring gene expression and chromosome structure simultaneously on single chromosomes. We find substantial differences in transcriptional frequency between genes on a translocated chromosome and the same genes in their normal chromosomal context in the same cell. Correlations between genes on a single chromosome pointed toward a cis chromosome-level transcriptional interaction spanning 14.3 megabases.

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Monoallelic expression of TMPRSS2/ERG in prostate cancer stem cells

While chromosomal translocations have a fundamental role in the development of several human leukaemias, their role in solid tumour development has been somewhat more controversial. Recently, it was shown that up to 80% of prostate tumours harbour at least one such gene fusion, and that the most common fusion event, between the prostate-specific TMPRSS2 gene and the ERG oncogene, is a critical, and probably early factor in prostate cancer development.

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EGFR and TTF-1 Gene Amplification in Surgically Resected Lung Adenocarcinomas: Clinicopathologic Significance and Effect on Response to EGFR-Tyrosine Kinase Inhibitors in Recurred Cases

Gene amplifications are implicated in cancer development and progression. In this study we investigated the clinicopathologic characteristics associated with EGFR or TTF-1 amplification in lung adenocarcinomas and its prognostic significance.

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A20 (TNFAIP3) Inactivation Is a Rare Event in Follicular Lymphoma

A20, also known as TNF alpha-induced protein 3 (TNFAIP3), is located on chromosome band 6q23 and is a negative regulator of NFkB activation pathway. Loss of A20 resulting in increased NFkB signaling has been shown to play a role in some B-cell lymphomas. A few previous studies, that included only a small number of follicular lymphoma (FL) cases, demonstrated A20 deletion/mutation in a small subset of FL. The aim of this study was to investigate A20 expression and genetic alterations in a large cohort of FL to elucidate its role in FL pathogenesis and progression.

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Use state's billion for start-ups

Norma Jean Nowak knows firsthand how hard it can be to turn a scientific breakthrough into a profitable business and she hopes the programs that are part of Gov. Andrew Cuomos promised Buffalo Billion will make the path a little easier for those who follow. The goal, she said, is to create a village within the Buffalo Niagara region where startups can easily get the management and business development support they need, along with access to the capital thats so essential to survival in the days before the sales start rolling in.

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Empire Genomics Licenses First Known DNA Biomarker for Use in Determining Drug Response in Multiple Myeloma and Potentially Lymphoma Patients

Empire Genomics announced today it has acquired an exclusive license for patent pending novel genomic biomarkers from Emory University for use in developing a molecular diagnostic test that could help satisfy a large unmet medical need in determining ideal therapeutic treatment for multiple myeloma patients.

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The Jobs of Buffalo's Future Growing

Gone are the days of 12 hour shifts milling flour in what was once the world's largest flour mill or sweating in the queen city's massive iron and steel factories. buffalo's coveted labor jobs of the forties and fifties have now been at least partly replaced by hi-tech and high paying jobs in the medical sciences and research fields.

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Diagnostics company develops cancer test

Empire Genomics LLC announced Nov. 1 that it will begin development of a new cancer test it said will help physicians select the right drug therapies based on the individual patients genetic markers.


The diagnostics company, based on the Buffalo Niagara Medical Campus, said the test will be the first proprietary therapeutic guiding test on the market to deliver precise treatment options for oncology patients with multiple myeloma and lymphoma, while bringing the company closer to delivering personalized medicines.

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Empire Genomics plans to expand

A company that develops tests to pinpoint whether a specific medical drug or treatment will help an individual patient announced Thursday plans to hire 50 new employees over the next five years at its offices on the edge of the Buffalo Niagara Medical Campus.

Empire Genomics will hire the workers to conduct, manufacture and market a new test meant to determine the best form of treatment for multiple myeloma, a blood-based cancer.

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Buffalo company develops cancer test

The evolution of Buffalo's medical corridor is paving the way for healthier lives as a new procedure developed in western New York adds more firepower to the war on cancer. Empire Genomics on Michigan Avenue has developed the very first test for multiple myeloma. This procedure can help determine the treatment of malignant blood cell cancer. The new test will also create about 50-new jobs over the next few years.

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Empire Genomics Unveils New Multiple Myeloma Molecular Cancer Test and New Clinical Laboratory

Empire Genomics, a growing cancer molecular diagnostics company, today unveiled the first ever multiple myeloma cancer test and its plans to hire 50 new employees over the next five years. Empire Genomics, a growing cancer molecular diagnostics company founded in Buffalo in 2006, today unveiled the first ever multiple myeloma cancer test.

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12 Western New York and 3 Ontario, Canada Companies Selected to Present in Statewide Venture Forum

Empire Genomics has been chosen to present for the 2012 Venture Forum, a collaboration between the Bright Buffalo Niagara Forum and the Center for Economic Growth's (CEG) SmartStart UNYTECH Forum

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UB Partnerships Allow Empire Genomics to Flourish

Local life sciences start-up Empire Genomics has gone global thanks to a partnership with the University at Buffalo. The firm has grown the business from a concept to product to a company with rapidly growing revenues and a significant global customer base.

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Empire Genomics Names Funakoshi its Japan Distributor

Empire Genomics today announced Funakoshi will distribute its products in Japan.

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Science Afterhours

Join your cambridge colleagues to confer on the latest scientific topics in early-phase development with an exciting, interactive format and your choice of round table discussions on Thursday, May 10th from 5:00pm to 7:00pm at the Le Meridien MIT Hotel.

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Congresswoman Kathy Hochul Visits Empire Genomics

Before hosting an Economic Action Summit for Western New York, Congresswoman Kathy Hochul visited Empire Genomics along with a number of other major economic stakeholders in the region.

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As life sciences sector grows, so does the need for capital

Empire Genomics has nine employees, including Johnson, who since the beginning in 2006 has been CEO of the company, which is located on Michigan Avenue in the Western New York Medical Arts Building on the medical campus. The company hopes to open a clinical lab so that it can begin processing patient samples and giving disease diagnoses itself. Empire Genomics hopes to hire five to 10 employees for this clinical lab and the companys clinical trial partnerships.

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Empire Genomics, Icon Team on Personalized Medicine Services

NEW YORK (GenomeWeb News) - Irish drug development services firm Icon said this week that it has signed an agreement with Empire Genomics to provide personalized medicine development services.

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Lower Cost and Faster Product Approval Through Proper Software Design Controls

The market success of a medical device depends in large part on how well its software is programmed. Focusing heavily on the device while treating the software as an afterthought can lead to costly recalls and liability concerns.

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Funds flow to WNY expansion projects

Empire State Development announced that seven Western New York companies have been awarded $5.75 million in loans and grants to assist with various expansion projects. The states top economic development agency said collectively, these companies, operating in Cattaraugus, Erie and Niagara counties, will make capital investments totaling $112.6 million, retaining 1,785 jobs and creating 329 full-time jobs.

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Testing your own personal genome - opening a Pandora's Box?

Anthony Johnson, President & CEO of Empire Genomics discusses personal genomic testing and the necessary precautions that must be put in place before this technology can effectively be used as an informative tool for patients interested in having these tests performed.

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One Cell Systems and Empire Genomics Initiate DNA Probe Product Development and Distribution Agreement

One Cell and Empire Genomics come together to offer 24 Chromosome/24 Hour PGD FISH Panel to launch in January 2009 along with other high quality products and services to follow.

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Good Morning America Co-Anchor receives Gilda Radner Courage Award from Roswell Park Cancer Institute

Robin Roberts, co-anchor of ABC's Good Morning America and a breast cancer survivor received the Gilda Radner Courage Award tonight at Roswell Park Cancer Institute's All Star Night gala. Roberts has served as a highly visible advocate for breast cancer screening and early detection since being diagnosed with the disease in 2007.

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Empire Genomics Names Leading Genetic Researchers and Industry Experts to Scientific Advisory Board

Empire Genomics, developing high throughput technologies that enable genome-wide analyses to determine the underlying mechanisms for diseases, today announced the formation of its Scientific Advisory Board.

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Dr. Norma Nowak- AACR 2008 Team Science Award Winner

Empire Genomics Founder Dr. Norma Nowak, along with 11 other experts in the field, have been honored for their active roles in the conception, technical implementation, dissemination and pioneering applications of comparative genomic hybridization (CGH) and array CGH.

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Autophagy and cellular senescence mediated by Sox2 suppress malignancy of cancer cells

Autophagy is a critical cellular process required for maintaining cellular homeostasis in health and disease states, but the molecular mechanisms and impact of autophagy on cancer is not fully understood. Here, we found that Sox2, a key transcription factor in the regulation of the stemness of embryonic stem cells and induced-pluripotent stem cells, strongly induced autophagic phenomena, including intracellular vacuole formation and lysosomal activation in colon cancer cells. The activation occurred through Sox2-mediated ATG10 gene expression and resulted in the inhibition of cell proliferation and anchorage-independent colony growth ex vivo and tumor growth in vivo. Further, we found that Sox2-induced-autophagy enhanced cellular senescence by up-regulating tumor suppressors or senescence factors, including p16INK4a, p21 and phosphorylated p53 (Ser15). Notably, knockdown of ATG10 in Sox2-expressing colon cancer cells restored cancer cell properties. Taken together, our results demonstrated that regulation of autophagy mediated by Sox2 is a mechanism-driven novel strategy to treat human colon cancers.

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GPR158, an orphan member of G protein-coupled receptor Family C: glucocorticoid-stimulated expression and novel nuclear role

Members of the large G protein-coupled receptor (GPCR) clan are implicated in many physiological and disease processes, making them important therapeutic drug targets. In the present study, we follow up on results of a pilot study suggesting a functional relationship between glucocorticoid (GC)-induced ocular hypertension and GPR158, one of three orphan members of the GPCR Family C. GC treatment increases levels of GPR158 mRNA and protein through transcriptional mechanisms, in cultured trabecular meshwork (TBM) cells derived from the eye's aqueous outflow pathway. Like treatment with GCs, transient overexpression of GPR158 stimulates cell proliferation, while siRNA knockdown of endogenous GPR158 has the opposite effect. Both endogenous and overexpressed GPR158 show an unusual subcellular localization pattern, being found almost entirely in the nucleus. However, when cells are treated with inhibitors of clathrin-mediated endocytosis, GPR158 is shifted to the plasma membrane. Mutation of a bipartite nuclear localization signal (NLS) in the 8(th) helix also shifts GPR158 out of the nucleus, but in this case the protein is found in vesicles localized in the cytoplasm. These results suggest that newly synthesized GPR158 first traffics to the plasma membrane, where it rapidly undergoes endocytosis and translocation to the nucleus. Significantly, mutation of the NLS abrogates GPR158-mediated enhancement of cell proliferation, indicating a functional requirement for nuclear localization. GPR158 overexpression upregulates levels of the cell cycle regulator cyclin D1, but mutation of the NLS reverses this. Overexpression of GPR158 enhances the barrier function of a TBM cell monolayer, which is associated with an increase in the levels of tight junction proteins ZO-1 and occludin, similar to reported studies on GC treatment. Regulated paracellular permeability controls aqueous outflow facility in vivo. Since GCs stimulate GPR158 expression, the result is consistent with a role for elevation of GPR158 expression in GC-induced ocular hypertension.

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TBK1 and Flanking Genes in Human Retina

The gene that causes normal tension glaucoma (NTG) in a large pedigree was recently mapped to a region of chromosome 12q14 (GLC1P) that contains the genes TBK1, XPOT, RASSF3, and GNS. We sought to investigate the structure of the chromosome 12q14 duplication and explore the ocular expression of GLC1P locus genes.

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Sensitivity and Specificity of USP6 Gene Break-Apart Assay and Protein Expression in Nodular Fasciitis

Nodular fasciitis (NF) is a common benign mesenchymal lesion that may progress through myxoid, cellular, and fibrous phases. The differential diagnosis of NF includes many other spindle cell neoplasms and it may be misdiagnosed as a sarcoma due to its rapid growth and active mitotic activity. Recently, it was discovered that the entire coding region of ubiquitin-specific peptidase 6 (USP6), an oncogene translocated in aneurysmal bone cyst (ABC), is fused to the MYH9 promoter region in up to 92% of NFs. This finding indicates a potential application of USP6 gene expression or gene break-apart as a biomarker of NF. However, the sensitivity and specificity of USP6 as a biomarker for nodular fasciitis is not known.

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Two cases of localized neuroblastoma with multiple segmental chromosomal alterations and metastatic progression

Surgery alone is curative for most children with localized MYCN-non-amplified neuroblastoma. However, 1015% will develop recurrent loco-regional disease, and very rarely, patients will relapse metastatically. Currently, it is not possible to predict which child with localized, MYCN-non-amplified neuroblastoma will develop disseminated disease. We report two children who presented with favorable biology, localized neuroblastoma and subsequently relapsed with metastatic disease after treatment with surgery.

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A boy with partial trisomy of chromosome 3q24-q28 from paternal balanced insertion and multiple congenital anomalies

Although many patients with duplication 3q syndrome have been described reports on duplication derivatives from an insertion are rare in the previous literature. Here we describe the genotype and phenotype of a 32-month-old boy with a partial trisomy of 3q24q28. We carefully mapped the aberration with SNP-array analysis, and found a duplication region of 44Mb.

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A systematic analysis of small supernumerary marker chromosomes using array CGH exposes unexpected complexity

A small supernumerary marker chromosome is often seen in patients with developmental disorders. Prior to array-based comparative genomic hybridization markers were rarely genotyped end to end. In this study, a valid genotype-to-phenotype correlation was possible because the supernumerary marker chromosomes were fully characterized by array-based comparative genomic hybridization in a genome-wide analysis.

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HACE1 is a tumor suppressor gene candidate in natural killer cell neoplasms

HACE1 is an E3 ubiquitin ligase located in 6q21, the genomic region frequently deleted in natural killer (NK) cell malignancies. Here, we report HACE1 as a candidate tumor suppressor gene silenced through a combination of deletion and cytosine phosphate guanine island hypermethylation. We detected deletion of HACE1 in malignant NK cell lines (6 of 9, 67%) and primary biopsies (5 of 15, 33%) by quantitative PCR, with most of the specimen showing cytosine phosphate guanine island hypermethylation in the remaining allele, leading to low mRNA transcription. The ectopic expression of HACE1 in an HACE1-null NK cell line led to apoptosis and G2/M cell cycle arrest. Moreover, HACE1 expression was up-regulated in IL-2-activated normal NK cells and NK cells cocultured with an engineered NK cell target, K562 Clone 9.mbIL21, suggesting its role in the regulation of NK cell homeostasis. In conclusion, HACE1 is another potent tumor suppressor gene located within the 6q21 region, and loss of function of multiple tumor suppressor genes within 6q21 may be a critical determinant of NK cell lymphomagenesis.

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Co-existence of 9p deletion and Silver-Russell syndromes in a patient with maternally inherited cryptic complex chromosome rearrangement involving chromosomes 4, 9, and 11

We report a patient with a maternally inherited unbalanced complex chromosomal rearrangement (CCR) involving chromosomes 4, 9, and 11 detected by microarray comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). This patient presents with clinical features of 9p deletion syndrome and Silver-Russell syndrome (SRS).

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Phenotypic heterogeneity in a family with a small atypical microduplication of chromosome 22q11.2 involving TBX1

The chromosome 22q11.2 region is commonly involved in non-allelic homologous recombination (NAHR) events. Microduplications of 22q11.2, usually involving a 3 Mb or 1.5 Mb region constitute the 22q11 microduplication syndrome. Both microdeletions and microduplications of 22q11.21 are reported to share several phenotypic characteristics, including dysmorphic facial features, velopharyngeal insufficiency, congenital heart disease, urogenital abnormalities, and immunologic defects. We report a child who presented at 8 months of age for evaluation of microcephaly and mild motor delay. Head circumference at birth, at 8 months, and at 19 months of age was below the 3rd centile. Other findings included left-sided cryptorchidism and developmental dysplasia of the left hip. In addition, echocardiography revealed a restrictive patent ductus arteriosus. Chromosomal microarray analysis using Affymetrix Genome-Wide Human SNP Array 6.0 revealed a novel 437 kb interstitial duplication at 22q11.21, involving TBX1, whose breakpoints did not coincide with known low copy repeat (LCR) regions. The same duplication was confirmed by fluorescent in situ hybridization (FISH) in the patient's mother and an older sister. The mother has a history of anxiety disorder and depression. The sister had a history of delayed motor milestones. None of the three duplication carriers has any documented renal anomalies or other significant medical problems. This report demonstrates the clinical heterogeneity associated with microduplications of 22q11.2 and illustrates the difficulties related to providing prognostic information and accurate genetic counseling to families when this finding is detected. The described microduplication is the smallest in this genomic region reported to date and further implicates abnormal gene dosage of TBX1 in disorders resulting from 22q11.2 rearrangements.

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A 0.7Mb de novo duplication at 7q21.3 including the genes DLX5 and DLX6 in a patient with split-hand/split-foot malformation

Split-hand/split-foot malformation (SHFM1) has been reported to be caused by deletions, duplications or rearrangements involving the 7q21.3 region harboring DSS1, DLX5, and DLX6. We report on a female patient with unilateral syndactyly of the third and fourth fingers of the right hand and overgrowth and lateral deviation of the right great toe. There was a split foot malformation on the right, with absent fifth toe. The left hand was apparently normal and left foot was intact. The patient has no hearing loss. We performed conventional G-banding karyotype analysis, array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). G-banding karyotype result was normal 46,XX. However, a duplication of 719kb (96,303,736-97,022,335; NCBI build36/hg18, March 2006) was identified at the 7q21.3 region by aCGH. The array result was also confirmed by FISH analysis. The duplicated region harbors only DLX5 and DLX6, which are known for their role in SHFM1. Additionally, FISH analysis of parental samples showed de novo origin of this abnormality in the patient. This is the first report that highlights the duplication of 719kb at 7q21.3, harboring only DLX5 and DLX6 associated with the SHFM1 phenotype.

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CNTF receptor subunit α as a marker for glioma tumor-initiating cells and tumor grade: laboratory investigation

Tumor-initiating cells are uniquely resilient to current treatment modalities and play an important role in tumor resistance and recurrence. The lack of specific tumor-initiating cell markers to identify and target these cells presents a major obstacle to effective directed therapy.

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TRPS1 and Its Target Gene SOX9 Regulate Epithelial Proliferation in the Developing Hair Follicle and are Associated with Hypertrichosis

Hereditary hypertrichoses are a group of hair overgrowth syndromes that are extremely rare in humans. We have previously demonstrated that a position effect on TRPS1 is associated with hypertrichosis in humans and mice. To gain insight into the functional role of Trps1, we analyzed the late morphogenesis vibrissae phenotype of Trps1Δgt mutant mice, which is characterized by follicle degeneration after peg downgrowth has been initiated. We found that Trps1 directly represses expression of the hair follicle stem cell regulator Sox9 to control proliferation of the follicle epithelium. Furthermore, we identified a copy number variation upstream of SOX9 in a family with hypertrichosis that significantly decreases expression of the gene in the hair follicle, providing new insights into the long-range regulation of SOX9. Our findings uncover a novel transcriptional hierarchy that regulates epithelial proliferation in the developing hair follicle and contributes to the pathology of hypertrichosis.

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Thyroid transcription factor 1 and Napsin A double stain: utilizing different vendor antibodies for diagnosing lung adenocarcinoma

A combined thyroid transcription factor 1 (TTF-1) and Napsin A double stain has been shown to be useful in the diagnosis of adenocarcinoma (ADC). This study compares differences in double staining patterns among vendor antibodies (Leica, Dako, and Biocare).

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2q24 deletions: further characterization of clinical findings and their relation to the SCN cluster

As the resolution of molecular cytogenetic methods continues to improve, it has become increasingly possible to refine genotype-phenotype correlations based upon gene involvement. We report three new patients with nonrecurrent deletions involving subbands of 2q24. These patients were referred for evaluation of developmental delay, but were found to have unique, nonoverlapping clinical features. Patient 1 presented with infantile seizures, microcephaly, and brain anomalies, along with facial dysmorphism, growth retardation, neuromuscular scoliosis, and later with developmental regression. Array comparative genomic hybridization (aCGH) detected an 8 Mb interstitial deletion encompassing the neuronal sodium channel (SCN) gene cluster. Patient 2 presented with growth retardation, congenital heart defect, and hypotonia. Patient 3 presented with developmental delay and behavioral problems. Patients 2 and 3 had no history of seizures, microcephaly, or brain anomalies and were found to have deletions of 2q24, ?8 Mb and <500 kb respectively, centromeric to and outside the SCN cluster. It has been demonstrated that mutations and copy number variants (CNVs) affecting the SCN gene cluster result in severe, early-onset seizures. It is however, less clear whether haploinsufficiency of regions outside the SCN cluster may result in phenotypically recognizable and clinically significant features. We discuss additional dosage sensitive genes that may exist outside the SCN cluster. Our and published data indicate that 2q24 deletions not involving the SCN cluster are associated with fewer neurobehavioral problems, but may predispose to congenital malformations.

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Long noncoding RNAs with snoRNA ends

We describe the discovery of sno-lncRNAs, a class of nuclear-enriched intron-derived long noncoding RNAs (lncRNAs) that are processed on both ends by the snoRNA machinery. During exonucleolytic trimming, the sequences between the snoRNAs are not degraded, leading to the accumulation of lncRNAs flanked by snoRNA sequences but lacking 5' caps and 3' poly(A) tails. Such RNAs are widely expressed in cells and tissues and can be produced by either box C/D or box H/ACA snoRNAs. Importantly, the genomic region encoding one abundant class of sno-lncRNAs (15q11-q13) is specifically deleted in Prader-Willi Syndrome (PWS). The PWS region sno-lncRNAs do not colocalize with nucleoli or Cajal bodies, but rather accumulate near their sites of synthesis. These sno-lncRNAs associate strongly with Fox family splicing regulators and alter patterns of splicing. These results thus implicate a previously unannotated class of lncRNAs in the molecular pathogenesis of PWS.

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Michael J. Becich, M.D., Ph.D. Joins Empire Genomics Scientific Advisory Board

Empire Genomics, a leader in the field of genomic molecular diagnostics and personalized medicine, is pleased to announce the appointment of Michael J. Becich, M.D., Ph.D., to its Scientific Advisory Board. Dr. Becich is a leading expert on cancer biology and biomedical informatics.

"We are excited to welcome Dr. Becich to our SAB," commented Anthony Johnson, President/CEO of Empire Genomics. "He has tremendous knowledge in cancer biology and informatics, both of which are critical aspects of our corporate objectives in personalized medicine. We look forward to working with Dr. Becich to continually innovate and translate cutting edge research into clinical molecular testing solutions."

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Empire Genomics Sponsors The Belle Center Golf Classic

Empire Genomics will be sponsoring the second annual Belle Center Golf Classic on July 23rd, 2012 from 11AM to 7:30PM at The Orchard Park Country Club located in Orchard Park New York. Proceeds from The Belle Center Golf Classic benefit youth and families who utilize programs and services at The Belle Center.

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12 Western New York and 3 Ontario, Canada Companies Selected to Present in Statewide Venture Forum

The final slate of presenting companies has been chosen for the 2012 Venture Forum, a collaboration between the Bright Buffalo Niagara Forum and the Center for Economic Growth's (CEG) SmartStart UNYTECH Forum.

A total of 32 high-growth early stage companies will be featured, including 12 from Buffalo and three from Ontario, Canada. The 2012 Venture Forum will be held May 16-17 in Buffalo. Since its inception three years ago, the Bright Forum has featured nearly 100 high-tech companies.

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UB Partnerships Allow Empire Genomics to Flourish

Local life sciences start-up Empire Genomics has gone global thanks to a partnership with the University at Buffalo. The firm has grown the business from a concept to product to a company with rapidly growing revenues and a significant global customer base.

At a time when state and local officials are hoping to lure new companies to the Buffalo Niagara region, stories like Empire Genomics' are key to understanding the value of collaborations between industry and academia. University entities such as UB's New York State Center of Excellence in Bioinformatics and Life Sciences and the UB Center for Advanced Biomedical and Bioengineering Technology (UB CAT) help to facilitate these connections in the life sciences.

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Molecular genetic evidence supporting the neoplastic nature of fibrous stroma in testicular teratoma

Testicular teratoma typically consists of heterogeneous mixtures of diverse epithelial and stromal components. The biological nature and genetic characteristics of the fibrous stroma of testicular teratomas have not been thoroughly investigated. Chromosome 12p abnormalities are the hallmark genetic alterations of germ cell tumors. We studied chromosome 12p abnormalities in the fibrous stroma and other components of pure testicular teratomas from 32 patients using interphase fluorescence in situ hybridization. Overall, 72% (23/32) of pure testicular teratomas had chromosome 12p abnormalities.

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Preparation of Chorionic Villus Samples for Metaphase Chromosome Analysis and Chromosomal Microarray Analysis

Chorionic villi are composed of an outer layer of trophoblastic cells and an inner mesenchymal cell core. They can be prepared for chromosome analysis using a culture method wherein villi are disaggregated by mechanical and enzymatic methods and the resulting cell suspension is used to establish primary cultures. Mesenchymal cells of the villus core are released by this procedure and the fibroblasts are actively proliferative in tissue culture. Cultures can be used for cytogenetic analysis after ~1 week. Slides prepared by this technique can be stained using trypsin-Giemsa banding and analyzed for chromosomal abnormalities in fetal tissue. Chorionic villi may also be assessed by chromosomal microarray analysis (CMA). For this purpose, a method for extraction of high-quality DNA from CVS tissue is also described here.

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BRAF duplications and MAPK pathway activation are frequent in gliomas of the optic nerve proper

Optic pathway gliomas represent a specific subtype of astrocytoma with unique clinicopathologic and biologic properties, but studies of tumors in the optic nerve proper have been hampered by limited tissue availability. We analyzed optic nerve gliomas of 59 patients (median age, 9 years; range, 3 months-66 years; 33 female, 26 male) using formalin-fixed paraffin-embedded material in tissue microarrays. Seven patients had the clinical diagnosis of neurofibromatosis type 1 (NF1). Fluorescence in situ hybridization studies were performed for BRAF, PTEN, CDKN2A (p16), and NF1. Immunohistochemistry was performed for glial fibrillary acidic protein, phospho-ERK, and mutant IDH1 protein. The BRAF duplication was present in 11 (73%) of 15 evaluable tumors, including 1 NF1 patient (1 of 4 tested; 25%). The single tumor lacking BRAF duplication or NF1 association had histologic features of a ganglioglioma. Conversely, heterozygous PTEN deletions were present in 2 (8%) of 25 evaluable cases, one of which was BRAF duplicated and the other was NF1 associated. CDKN2A and NF1 deletions were absent in all tumors tested. Phospho-ERK immunoreactivity was present in 55 (96%) of 57 tumors and was mostly strong and diffuse (80%). Only 1 case of 53 expressed IDH1. Thus, optic nerve gliomas demonstrated molecular alterations typical of pilocytic astrocytomas, including the universal presence of either BRAF duplication or NF1 association and common mitogen-activated protein kinase pathway activation but very rare mutant IDH1 expression.

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Tetrasomy 15q25.2→qter identified with SNP microarray in a patient with multiple anomalies including complex cardiovascular malformation

We report on a male neonate with prenatally diagnosed mosaicism for a supernumerary marker chromosome and multiple congenital anomalies. Prenatal ultrasound imaging revealed a heart defect, pleural effusion, clubbed feet, and absent right kidney. Clinical cytogenetic analysis of amniocytes identified a marker chromosome present in 10 out of 15 cells analyzed. Clinical evaluation of the neonate revealed distinct facial features, complex heart defects, solitary left kidney, and arachnodactyly. Chromosome analysis of lymphocytes demonstrated an abnormal male karyotype with a marker chromosome present in all 24 cells examined. To identify the marker chromosome, SNP microarray analysis was performed which detected the presence of a two copy gain of 17.7Mb of DNA from the distal long arm of chromosome 15 (15q25.2-qter). FISH analysis using a probe specific to the 15q26.3 region showed one signal on each normal 15q and two signals, one on each arm of the marker chromosome resulting in four copies. Distal tetrasomy 15q is rare. Only 11 cases have been described in the literature, all due to a supernumerary analphoid marker chromosome consisting of an inverted duplication of the distal long arm of chromosome 15. We report on a unique patient with tetrasomy 15q with complex cardiovascular malformation (CVM) involving progressive diffuse pulmonary vein stenosis (PVS). We propose overexpression of three genes, ADAMTSL3, MESP1, and MESP2 as a potential mechanism for cardiac and vessel malformations associated with tetrasomy 15q. Finally, we believe cardiac defects with this genetic syndrome are a poor prognostic finding associated with high mortality.

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Adult hematopoietic progenitors are multipotent in chimeric mice

Embryonic stem cells (ESCs) and adult somatic cells, induced to pluripotency (iPSCs), can differentiate into multiple cell lineages. We previously reported that adult mammalian bone marrow contains a sub-population of CD34+ cells that express genes of ESCs and genes required to generate iPSCs. They also express lineage genes of the three embryonic germ layers. Are these CD34+ cells multipotent? Here, CD34+ bone marrow stem cells from adult male ROSA mice, which carry two markers: the β-galactosidase gene and the male Y chromosome, were transplanted into blastocysts of wildtype mice. Each female ROSA chimera generated had a distinct pattern of male-derived organs expressing β-galactosidase; e.g., ectodermal brain, dorsal root ganglia and skin; mesodermal heart, bone and bone marrow; and endodermal pancreas, intestine, and liver. Thus, adult mammals carry cells that appear to exhibit a developmental potential reminiscent of ESCs and iPSCs suggesting they could be used for cell replacement therapy.

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Intra-hematopoietic cell fusion as a source of somatic variation in the hematopoietic system

Cell fusion plays a well-recognized, physiological role during development. Bone-marrow-derived hematopoietic cells have been shown to fuse with non-hematopoietic cells in a wide variety of tissues. Some organs appear to resolve the changes in ploidy status, generating functional and mitotically-competent events. However, cell fusion exclusively involving hematopoietic cells has not been reported. Indeed, genomic copy number variation in highly replicative hematopoietic cells is widely considered a hallmark of malignant transformation. Here we show that cell fusion occurs between cells of the hematopoietic system under injury as well as non-injury conditions. Experiments reveal the acquisition of genetic markers in fusion products, their tractable maintenance during hematopoietic differentiation and long-term persistence after serial transplantation. Fusion events were identified in clonogenic progenitors as well as differentiated myeloid and lymphoid cells. These observations provide a new experimental model for the study of non-pathogenic somatic diversity in the hematopoietic system.

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Delineation of the interstitial 6q25 microdeletion syndrome: refinement of the critical causative region

Interstitial deletions of the long arm of chromosome 6 are rare. Clinically, this is a recognizable microdeletion syndrome associated with intellectual disability (ID), acquired microcephaly, typical dysmorphic features, structural anomalies of the brain, and nonspecific multiple organ anomalies. Most of the reported cases have cytogenetically visible interstitial deletions or subtelomeric microdeletions. We report on a boy with global developmental delay, distinct dysmorphic features, dysgenesis of the corpus callosum, limb anomalies, and genital hypoplasia who has a small interstitial deletion of the long arm of chromosome 6 detected by comparative genomic hybridization (CGH). The deleted region spans around 1 Mb of DNA and contains only two coding genes, ARID1B and ZDHHC14. To the best of our knowledge, this case represents the typical phenotype with the smallest deletion reported so far. We discuss the possible role of these genes in the phenotypic manifestations.

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Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

Adjuvant hormonal therapy is administered to all early stage ER+ breast cancers, and has led to significantly improved survival. Unfortunately, a subset of ER+ breast cancers suffer early relapse despite hormonal therapy. To identify molecular markers associated with early relapse in ER+ breast cancer, an outlier analysis method was applied to a published gene expression dataset of 268 ER+ early-stage breast cancers treated with tamoxifen alone. Increased expression of sets of genes that clustered in chromosomal locations consistent with the presence of amplicons at 8q24.3, 8p11.2, 17q12 (HER2 locus) and 17q21.33-q25.1 were each found to be independent markers for early disease recurrence. Distant metastasis free survival (DMFS) after 10 years for cases with any amplicon (DMFS = 56.1%, 95% CI = 48.363.9%) was significantly lower (P = 0.0016) than cases without any of the amplicons (DMFS = 87%, 95% CI = 76.3% 97.7%). The association between presence of chromosomal amplifications in these regions and poor outcome in ER+ breast cancers was independent of histologic grade and was confirmed in independent clinical datasets. A separate validation using a FISH-based assay to detect the amplicons at 8q24.3, 8p11.2, and 17q21.33-q25.1 in a set of 36 early stage ER+/HER2- breast cancers treated with tamoxifen suggests that the presence of these amplicons are indeed predictive of early recurrence. We conclude that these amplicons may serve as prognostic markers of early relapse in ER+ breast cancer, and may identify novel therapeutic targets for poor prognosis ER+ breast cancers.

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Down-regulation of replication factor C-40 (RFC40) causes chromosomal missegregation in neonatal and hypertrophic adult rat cardiac myocytes

Adult mammalian cardiac myocytes are generally assumed to be terminally differentiated; nonetheless, a small fraction of cardiac myocytes have been shown to replicate during ventricular remodeling. However, the expression of Replication Factor C (RFC; RFC140/40/38/37/36) and DNA polymerase δ (Pol δ) proteins, which are required for DNA synthesis and cell proliferation, in the adult normal and hypertrophied hearts has been rarely studied.

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MicroRNA profiling of hepatocarcinogenesis identifies C19MC cluster as a novel prognostic biomarker in hepatocellular carcinoma

Progressive hepatocarcinogenesis is a stepwise process that drives liver transformation. However, the molecular mechanisms of early liver transformation are far from clear. A role for microRNAs (miRNA) as diagnostic and prognostic factors in human tumours, including hepatocellular carcinoma (HCC), is promising. We aimed to identify novel miRNA as biomarkers for differential diagnosis and predictors of disease progression.

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Simultaneous translocation of both TCR Loci (14q11) with rare partner loci (Xq22 and 12p13) in a case of T-lymphoblastic leukemia

The most common recurrent cytogenetic abnormalities in T-lymphoblastic leukemia (T-acute lymphoblastic leukemia [T-ALL]) involve T-cell receptor (TCR) loci and a variety of partner genes, including HOX11, HOX11L2, MYC, and TAL1. In this report, we present a rare case involving simultaneous translocation of the TCR α/δ loci with different partner loci (Xq22 and 12p13); this resulted in a poor prognosis. Chromosomal analysis showed 46,Y,t(X;14)(q22;q11.2),t(12;14)(p13;q11.2) and FISH analysis by using a T-cell receptor alpha delta DNA probe, Split Signal (DakoCytomation, Denmark), showed translocations at the same TCR α/δ locus on both chromosomes. FISH with 2 bacterial artificial chromosome clones showed break apart signal, which suggests involvement of the IRS4 gene. To our knowledge, this is the first report of T-ALL in which both TCR α/δ loci were translocated with different partner loci, and 1 of the partner loci, Xq22, was a rare translocation partner locus that included IRS4 gene.

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Role of Cyclin E as an Early Event in Ovarian Carcinogenesis

At the genetic level, ovarian cancer is characterized by a large degree of genetic instability. High copy-number amplification at the CCNE1 (cyclin E) gene locus is the single most notable recurrent change, occurring in about 20% of tumors. We have hypothesized that CCNE1 gene amplification is an initiating event in the carcinogenic process of a subset of epithelial ovarian cancers.

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Cellular Phenotype-Dependent and -Independent Effects of Vitamin C on the Renewal and Gene Expression of Mouse Embryonic Fibroblasts

Vitamin C has been shown to delay the cellular senescence and was considered a candidate for chemoprevention and cancer therapy. To understand the reported contrasting roles of vitamin C: growth-promoting in the primary cells and growth-inhibiting in cancer cells, primary mouse embryonic fibroblasts (MEF) and their isogenic spontaneously immortalized fibroblasts with unlimited cell division potential were used as the model pair. We used microarray gene expression profiling to show that the immortalized MEF possess human cancer gene expression fingerprints including a pattern of up-regulation of inflammatory response-related genes. Using the MEF model, we found that a physiological treatment level of vitamin C (10-5 M), but not other unrelated antioxidants, enhanced cell growth. The growth-promoting effect was associated with a pattern of enhanced expression of cell cycle- and cell division-related genes in both primary and immortalized cells. In the immortalized MEF, physiological treatment levels of vitamin C also enhanced the expression of immortalization-associated genes including a down-regulation of genes in the extracellular matrix functional category. In contrast, confocal immunofluorescence imaging of the primary MEF suggested an increase in collagen IV protein upon vitamin C treatment. Similar to the cancer cells, the growth-inhibitory effect of the redox-active form of vitamin C was preferentially observed in immortalized MEF. All effects of vitamin C required its intracellular presence since the transporter-deficient SVCT2-/- MEF did not respond to vitamin C. SVCT2-/- MEF divided and became immortalized readily indicating little dependence on vitamin C for the cell division. Immortalized SVCT2-/- MEF required higher concentration of vitamin C for the growth inhibition compared to the immortalized wildtype MEF suggesting an intracellular vitamin C toxicity. The relevance of our observation in aging and human cancer prevention was discussed.

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Xq;autosome translocation in POF: Xq27.2 deletion resulting in haploinsufficiency for SPANX

A case of POF with an Xq;autosome translocation near the POF2 region and a cryptic deletion in the POF1 resulting in halpoinsufficiency for SPANX.

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Recombinant chromosome 7 in a mosaic 45,X/47,XXX patient

Individuals with pericentric inversions are at risk for producing offspring with chromosomal gains and losses, while those carrying paracentric inversions usually produce unviable gametes [Madan, 1995]. In this current study, we present a newborn with dysmorphic features and malformations, whose karyotype showed an abnormal copy of chromomosome 7 described at first as add(7)(q32) as well as mos 45,X/47,XXX. Array comparative genomic hybridization (CGH) revealed an interstitial deletion in the long arm of chromosome 7 involving bands q35 to q36.3 but retaining the 7q subtelomere. The patient's deletion is believed to be due to meiotic recombination in the inversion loop in the phenotypically normal father who seems to carry two paracentric inversions in the long arm of chromosome 7, which was described as rec(7)(7pter- > q35::q36.3- > 7qter)pat. The abnormal copy of chromosome 7 in the father has been described as: der(7)(7pter- > q22.1::q36.3- > q35::q22.1- > q35::q36.3- > 7qter). This is a unique karyotype that to our knowledge has not been previously reported in the literature and predisposes to meiotic recombination that can result in deletions or duplications of 7q35-36.

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Chromosomal loss of 3q26.3-3q26.32, involving a partial neuroligin 1 deletion, identified by genomic microarray in a child with microcephaly, seizure disorder, and severe intellectual disability

Neuroligin 1 (NLGN1) is one of five members of the neuroligin gene family and may represent a candidate gene for neurological disorders, as members of this family are involved in formation and remodeling of central nervous system synapses. NLGN1 is expressed predominantly in the central nervous system, where it dimerizes and then binds with β-neurexin to form a functional synapse. Mutations in neurexin 1 (NRXN1) as well as two other members of the neuroligin family, NLGN3 and NLGN4, have been associated with autism and mutations in NLGN4 have also been associated with intellectual disability, seizures, and EEG abnormalities.

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Affect of Amp5q31 and Del12p13 on Survival of Patients with Multiple Myeloma Treated with Novel Agent-Based Regimens: A Single Center Experience on 172 Patients

The presence of chromosomal aberrations is a characteristic feature of multiple myeloma (MM). Recently, Avet-Loiseau et al reported that amp5q31.3 and del12p13.31, detected by high-density, single-nucleotide polymorphism arrays analysis correlate with prognosis in MM patients who were treated upfront with conventional chemotherapy (JCO 2009; 27:458590). The aim of our study was to evaluate the effect of these chromosomal abberations on survival of patients with newly diagnosed MM or with relapsed/refractory myeloma who were treated with novel agent-based regimens.

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Expression of caveolin in trabecular meshwork cells and its possible implication in pathogenesis of primary open angle glaucoma

Primary open-angle glaucoma (POAG), which is the most common form of glaucoma, has been associated with a heterogeneous genetic component. A genome-wide association study has identified a common sequence variant at 7q31 (rs4236601 [A]) near the caveolin genes in patients with POAG. Caveolins are a family of integral membrane proteins which participate in many cellular processes, including vesicular transport, cholesterol homeostasis, signal transduction, cell adhesion and migration. The goal of this study was to investigate the expression and regulation of caveolin 1 (CAV-1) and caveolin 2 (CAV-2) in normal and glaucoma trabecular meshwork (TM) cells.

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A small homozygous microdeletion of 15q13.3 including the CHRNA7 gene in a girl with a spectrum of severe neurodevelopmental features

A broad spectrum of neurodevelopmental and psychiatric disorders with variable expressivity has been reported to be associated with 15q13.3 heterozygous microdeletions. Using oligonucleotide-based array-CGH analysis, we identified a small homozygous 15q13.3 deletion in a 6-year-old girl with significant global developmental delay, severe hypotonia, cortical visual impairment, staring spell seizure, and abnormal electroencephalogram. She inherited this deletion from both parents, each of them being a heterozygous carrier.

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Genetic amplification of the vascular endothelial growth factor (VEGF) pathway genes, including VEGFA, in human osteosarcom

Osteosarcoma is the most common primary tumor of bone. It is a highly vascular and extremely destructive malignancy that mainly affects children and young adults. The authors conducted microarray-based comparative genomic hybridization (aCGH) and pathway analyses to gain a systemic view of pathway alterations in the genetically altered genes.

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Clinically relevant single gene or intragenic deletions encompassing critical neurodevelopmental genes in patients with developmental delay, mental retardation, and/or autism spectrum disorders

Recent studies suggest that copy number variations (CNVs) encompassing several genes involved in neurodevelopmental pathways are associated with a variety of neuropsychiatric phenotypes, including developmental delay (DD), mental retardation (MR), and autism spectrum disorders (ASDs). Here we present eight patients in a cohort of -1,200 patients referred for clinical array CGH testing for various neurodevelopmental phenotypes, who were identified to carry either total gene or intragenic deletions encompassing critical synaptic and other neurodevelopmental genes.

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Development and characterization of xenograft model systems for adenoid cystic carcinoma

Adenoid cystic carcinoma (ACC) is one of the most common malignancies to arise in human salivary glands, and it also arises in the glandular tissue of other organ systems. To address the paucity of experimental model systems for this tumor type, we have undertaken a program of transplanting tissue samples of human ACC into immunodeficient nu/nu mice to create xenograft model systems. In 17 of 23 attempts (74%), xenograft tumors were successfully grown. In all cases, the histologic appearance of the donating tumor was recapitulated in the subsequent xenograft. Characterization of a subset of xenograft models by immunohistochemical biomarkers and by RNA transcript microarray analysis showed good fidelity in the recapitulation of gene expression patterns in the xenograft tumors compared with the human donor tumors. As ACC is known to frequently contain a t(6;9) translocation that fuses the MYB and NFIB genes, fluorescence in situ hybridization (FISH) of 12 ACC xenograft models was performed that assayed MYB locus break-apart and MYB-NFIB locus fusion. Of 12 xenograft models, 11 (92%) revealed MYB locus rearrangement and 10 (83%) showed evidence of fusion of the MYB and NFIB loci. The two related xenograft models (derived from primary and metastatic tumors, respectively, of the same human subject) were karyotyped, showing a t(1;6) translocation, suggesting MYB translocation to a novel fusion partner gene. Overall, our results indicate that ACC is amenable to xenografting and that ACC xenograft models recapitulate the molecular and morphologic characteristics of human tumors, suggesting utility as valid experimental and preclinical model systems for this disease.

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TMPRSS2 - ERG Loci Abnormality in Salvage Radiation Therapy (sRT) Refractory Prostate Cancer Patients

TMPRSS2-ETS translocation has been identified in greater than 50% of prostate cancer patients and has been associated with a more aggressive molecular subtype of prostate cancer. In a highly resistant cohort of prostate cancer patients that have failed both radical prostatectomy (RP) and sRT, we screened for abnormalities in the ERG and TMPRSS2 loci in prostatectomy tissue sections using a dual-color break-apart fluorescence in situ hybridization (FISH) assay.

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Transgenic Expression of Human LAMA5 Suppresses Murine Lama5 mRNA and Laminin α5 Protein Deposition

Laminin α5 is required for kidney glomerular basement membrane (GBM) assembly, and mice with targeted deletions of the Lama5 gene fail to form glomeruli. As a tool to begin to understand factors regulating the expression of the LAMA5 gene, we generated transgenic mice carrying the human LAMA5 locus in a bacterial artificial chromosome. These mice deposited human laminin α5 protein into basement membranes in heart, liver, spleen and kidney. Here, we characterized two lines of transgenics; Line 13 expressed ~6 times more LAMA5 than Line 25. Mice from both lines were healthy, and kidney function and morphology were normal. Examination of developing glomeruli from fetal LAMA5 transgenics showed that the human transgene was expressed at the correct stage of glomerular development, and deposited into the nascent GBM simultaneously with mouse laminin α5. Expression of human LAMA5 did not affect the timing of the mouse laminin α1α5 isoform switch, or that for mouse laminin β1β2. Immunoelectron microscopy showed that human laminin α5 originated in both glomerular endothelial cells and podocytes, known to be origins for mouse laminin α5 normally. Notably, in neonatal transgenics expressing the highest levels of human LAMA5, there was a striking reduction of mouse laminin α5 protein in kidney basement membranes compared to wildtype, and significantly lower levels of mouse Lama5 mRNA. This suggests the presence in kidney of a laminin expression monitor, which may be important for regulating the overall production of basement membrane protein.

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t(8;22)/BCR-FGFR1 myeloproliferative disorder presenting as B-acute lymphoblastic leukemia: Report of a case treated with sorafenib and review of the literature

The 8p11 myeloproliferative syndrome (EMS) is a rare and aggressive hematological neoplasm caused by rearrangements involving fibroblast growth factor receptor 1 (FGFR1) gene on chromosome 8p11, and one of 11 identified partner genes. The result is a variety of fusion genes encoding aberrant tyrosine kinases and activating multiple signal transduction pathways. Involvement of t(8;22)/BCR-FGFR1 is exceedingly rare, with only 8 cases reported to date. It usually presents as chronic myelogenous leukemia (CML)-like disease rapidly evolving into acute myeloid leukemia (AML), but one reported case presented as Bacute lymphoblastic leukemia (B-ALL). Herein, we report the second case of t(8;22) presenting as B-ALL, and the first to be treated with targeted therapy against tyrosine kinase following chemotherapy.

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ERG-TMPRSS2 rearrangement is shared by concurrent prostatic adenocarcinoma and prostatic small cell carcinoma and absent in small cell carcinoma of the urinary bladder: evidence supporting monoclonal origin

Prostatic carcinoma is a heterogeneous disease with frequent multifocality and variability in morphology. Particularly, prostatic small cell carcinoma is a rare variant with aggressive behavior. Distinction between small cell carcinoma of the prostate and urinary bladder may be challenging, especially in small biopsy specimens without associated prostatic adenocarcinoma or urothelial carcinoma. Recently, gene fusions between ETS genes, particularly ETS-related gene (ERG), and transmembrane protease, serine 2 (TMPRSS2) have been identified as a frequent event in prostate cancer. Thus, molecular methods may be helpful in determining the primary site of small cell carcinoma. Thirty cases of prostatic small cell carcinoma from the authors' archives were studied, among which 13 had concurrent prostatic adenocarcinoma. Tricolor fluorescence in situ hybridization (FISH) was performed on formalin-fixed paraffin-embedded tissue sections with a probe cocktail for 3'/5' ERG and TMPRSS2. Cases of small cell carcinoma of the bladder and conventional prostatic adenocarcinoma (25 each) were also tested as controls. ERG gene alterations were found only in prostate malignancies and not in benign prostatic tissue or bladder small cell carcinoma. TMPRSS2-ERG gene fusion was found in 47% (14/30) of prostatic small cell carcinoma. Of cases with concurrent prostatic adenocarcinoma, 85% (11/13) had identical findings in both components. In 20% of rearranged cases, the ERG abnormality was associated with 5' ERG deletion. In 17% (5/30) of cases, gain of the 21q22 locus was present. Two cases showed discordant aberrations in the small cell carcinoma and adenocarcinoma, one with deletion of 5' ERG and one with gain of chromosome 21q, both in only the adenocarcinoma component. Small cell carcinoma of the prostate demonstrates TMPRSS2-ERG rearrangement with comparable frequency to prostatic adenocarcinoma. In cases with concurrent adenocarcinoma and small cell carcinoma, the majority showed identical abnormalities in both components, indicating a likely common clonal origin. Discordant alterations were present in rare cases, suggesting that acquisition of additional genetic changes in multifocal tumors may be responsible for disease progression to a more aggressive phenotype. TMPRSS2-ERG fusion is absent in bladder small cell carcinoma, supporting the utility of FISH in distinguishing prostate from bladder primary tumors and identifying metastatic small cell carcinoma of unknown origin.

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Spontaneous metastasis in mouse models of testicular germ-cell tumours

Testicular germ-cell tumours (TGCTs) are the most common cancer in young men; the incidence is increasing worldwide and they have an unusually high rate of metastasis. Despite significant work on TGCTs and their metastases in humans, absence of a mouse model of spontaneous metastasis has greatly limited our understanding of the mechanisms by which metastatic potential is acquired and on their modes of dissemination. We report a new model of spontaneous TGCT metastasis in the 129 family of mice and provide evidence that these are true metastases derived directly from primary testicular cancers rather than independently from ectopic stem cells.

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Ventricular noncompaction and absent thumbs in a newborn with tetrasomy 5q35.2-5q35.3

An association with HunterMcAlpine syndrome? Report on an infant with tetrasomy of 5q35.2-5q35.3, an interstitial triplication on one chromosome and normal complement on the other.

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PARK2 copy number aberrations in two children presenting with autism spectrum disorder

Microdeletions of PARK2 have been reported previously in seven patients with autism spectrum disorder. There are no reports of PARK2 microduplications in this population. Presented are two patients, one with deletion and the other with duplication, both with autism spectrum disorder, though their syndromic phenotypes vary. The deletion patient is cognitively normal and ectomorphic: the duplication patient is cognitively impaired, underweight and short. Further, the microduplication patient has demonstrated adverse medication reactions to psychotropic medications active in the dopamine metabolic pathway: cyclopentolate, lisdexamfetamine, methylphenidate. These patients support an association between PARK2 mutations and autism spectrum disorder and suggest that duplications may be equally causative. It is hypothesized that the disparate patient phenotypes may represent a deletion/duplication syndrome and that the adverse medication reactions may be a pharmacogenetic phenomenon.

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Identification of BRCA1-deficient ovarian cancers

It is believed that 2440% of ovarian cancers have dysfunction in the BRCA1 or BRCA2 (BRCAness) genes, due to either inherited or somatic mutations or due to epigenetic inactivation. Demonstration of ovarian cancers with BRCAness is becoming important both due to the possibility of offering genetic counseling and due to beneficial effects of polyadenosine diphosphate ribose polymerase inhibitor treatment in this group.

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KIT gene mutation and amplification in dysgerminoma of the ovary

Dysgerminoma, the ovarian counterpart of seminoma, is the most common type of malignant ovarian germ cell tumor. The role of KIT mutation and amplification in the development of dysgerminoma is not currently established. The purpose of this study was to analyze alterations of the KIT gene in a large series of dysgerminomas and correlate the findings with clinicopathological parameters.

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Unknown partner for USP6 and unusual SS18 rearrangement detected by fluorescence in situ hybridization in a solid aneurysmal bone cyst

USP6 rearrangement is the most common genetic abnormality in primary aneurysmal bone cyst, and SS18 rearrangement has not been previously described in any type of tumor where synovial sarcoma was excluded from the differential diagnosis. We report a case of solid aneurysmal bone cyst in which fluorescence in situ hybridization (FISH) analysis indicated rearrangements of both USP6 and SS18, but histologic features were consistent with aneurysmal bone cyst throughout the lesion. Reverse-transcription polymerase chain reaction (RT-PCR) for the SS18-SSX1 and SS18-SSX2 translocations, identity testing, and SS18 FISH were performed on cytogenetic monolayer cultures and formalin-fixed paraffin-embedded (FFPE) tissue. Genomic microarray, FISH, and immunohistochemistry were performed on follow-up studies of the FFPE specimen. The karyotype was 45,X,add(X)(p11.2),add(4)(q13),add(8)(p21),-13,add(17)(p11.2),add(18)(q11.2) in all 20 cells analyzed from monolayer cultures. The karyotype showed no cytogenetically visible alterations of chromosomal regions harboring known partners for USP6. Metaphase FISH with a commercial SS18 break-apart probe showed translocation of the 5' portion of the SS18 probe to the short arm of the derivative X, as is observed in synovial sarcoma. RT-PCR showed no evidence of a SS18-SSX fusion, and immunohistochemistry was negative for TLE1, EMA, and cytokeratin AE1/3 expression. FISH on FFPE sections with a custom break-apart probe flanking USP6 showed evidence for a USP6 rearrangement throughout the tumor (25-50%). FISH on FFPE sections with a commercial SS18 break-apart FISH probe showed more variable results (0-50% split signals). There was no evidence of a SS18-USP6 fusion by FISH or RT-PCR. A molecular inversion probe array revealed a deletion encompassing the entire SS18 gene and its promoter, as well as portions of the region targeted by the commercial SS18 FISH probe. In conclusion, results obtained from commercially available FISH probes may occasionally yield misleading results. In this case, the SS18 rearrangement by FISH resulted from a complex rearrangement of 18q11.2 with a deletion of the SS18 gene. The translocation partner for USP6 remains unknown in this case.

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9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the 9p21 gene desert associated with coronary artery disease (CAD) and type 2 diabetes. Despite evidence for a role of the associated interval in neighbouring gene regulation, the biological underpinnings of these genetic associations with CAD or type 2 diabetes have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene desert for predicted enhancers and six times denser than the whole genome (P < 6.55 10(-33)). The CAD risk alleles of SNPs rs10811656 and rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines homozygous for the CAD risk haplotype show no binding of STAT1, and in lymphoblastoid cell lines homozygous for the CAD non-risk haplotype, binding of STAT1 inhibits CDKN2BAS (also known as CDKN2B-AS1) expression, which is reversed by short interfering RNA knockdown of STAT1. Using a new, open-ended approach to detect long-distance interactions, we find that in human vascular endothelial cells the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of IFNA21. In human vascular endothelial cells, interferon-γ activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1-binding, long-range enhancer interactions and altered expression of neighbouring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signalling in a vascular cell type and thus demonstrate the utility of genome-wide association study findings in directing studies to novel genomic loci and biological processes important for disease aetiology.

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Sex Chromosome Evolution in Amniotes: Applications for Bacterial Artificial Chromosome Libraries

Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently. These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100-200kb of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced. With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries.

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Autistic and psychiatric findings associated with the 3q29 microdeletion syndrome: Case report and review

The screening of individuals with mild dysmorphic features and mental retardation using whole genome scanning technologies has resulted in the delineation of several previously unrecognized microdeletion syndromes.

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Large Clinically Consequential Imbalances Detected at the Breakpoints of Apparently Balanced and Inherited Chromosome Rearrangements

When a chromosome abnormality is identified in a child with a developmental delay and/or multiple congenital anomalies and the chromosome rearrangement appears balanced, follow-up studies often examine both parents for this rearrangement. If either clinically unaffected parent has a chromosome abnormality with a banding pattern identical to the affected child's study, then it is assumed that the chromosome rearrangement is balanced and directly inherited from the normal carrier parent. It is therefore unlikely that the chromosome rearrangement is responsible for the child's clinical presentation. We present two unrelated cases in which an identical and apparently balanced abnormal chromosome banding pattern was identified in both an affected child and an unaffected parent of that child. Despite the identical banding patterns, molecular characterization through genomic microarray and fluorescence in situ hybridization showed the parent to be balanced whereas the affected child was significantly unbalanced. These two cases emphasize the utility of genomic microarray for further characterization of apparently balanced inherited chromosome rearrangements and caution against the assumption that identical banding patterns between a child and parent represent identical genomic rearrangements.

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Microdeletion of 16p11.2 associated with endocardial fibroelastosis

Endocardial fibroelastosis (EFE) was first described by Weinberg and Himmelfarb [1943] and is characterized by a porcelain-like thickening of the ventricular endocardium. It presents as unexplained heart failure in infants and children; with most patients progressing to end-stage heart failure and death [Nield et al., 2002]. With improvement in prenatal ultrasonography examination, EFE can be suspected in utero on the basis of ventricular enlargement, poor ventricular contractility, and marked echodensity of the endocardial surface.

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A novel microdeletion / microduplication syndrome of 19p13.13

Whole genome interrogation by array-based comparative genomic hybridization has led to a rapidly increasing number of discoveries of novel microdeletion and/or microduplication syndromes. We here describe the clinical and cytogenomic correlates of a novel microdeletion/microduplication of 19p13.13.

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The Structure of the TNFRSF13C Promoter Enables Differential Expression of BAFF-R during B Cell Ontogeny and Terminal Differentiation

The B cell-activating factor of the TNF family receptor (BAFF-R), encoded by the TNFRSF13C gene, is critically important for transitional B cell survival to maturity. Thus, ligation of BAFF-R by BAFF delivers a potent survival signal. Reports implicating the BAFF/BAFF-R signaling axis in the pathogenesis of autoimmune human diseases and B lineage malignancies have largely prompted studies focusing on BAFF expression; however, there is an equally critical need to better understand BAFF-R expression. Initial BAFF-R expression, although characterized in murine B cells, has not yet been reported in human B lymphopoiesis. In this study, we first demonstrate that BAFF-R expression is absent from early precursors and is acquired by bone marrow B cells newly expressing the BCR. We next focused on identifying the specific genomic region that controls BAFF-R expression in mature B cells (i.e., the TNFRSF13C promoter). To accomplish this, we used in silico tools examining interspecies genomic conservation in conjunction with reporter constructs transfected into malignant B and plasma cell lines. DNase protection assays using nuclear extracts from BAFF-Rexpressing cells suggested potential regulatory sites, which allowed the generation of EMSA probes that bound NFs specific to BAFF-Rexpressing cells. With a more stringent analysis of interspecies homology, these assays identified a site at which a single nucleotide substitution could distinctly impact promoter activity. Finally, chromatin immunoprecipitation assays revealed the in vivo binding of the specific transcription factor c-Rel to the most proximal genomic region, and c-Rel small interfering RNA transfections in BAFF-Rexpressing lines demonstrated a coincident knockdown of both c-Rel and BAFF-R mRNA.

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Understanding the molecular genetics of renal cell neoplasia: implications for diagnosis, prognosis and therapy

Renal neoplasms exhibit a wide spectrum of molecular characteristics that are closely associated with their diverse morphologic manifestations and clinical behaviors. A wealth of information has been garnered via methodology ranging from classical cytogenetics to FISH and gene expression profiling; however, the exact mechanisms by which each type of renal tumor develops remain incompletely understood.

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Dual-color, Break-apart FISH Assay on Paraffin-embedded Tissues as an Adjunct to Diagnosis of Xp11 Translocation Renal Cell Carcinoma and Alveolar Soft Part Sarcoma

Both Xp11.2 translocation renal cell carcinoma (RCC) and alveolar soft part sarcoma (ASPS) are characterized by various translocations disrupting chromosome Xp11.2, which result in gene fusions involving the TFE3 transcription factor gene. Diagnostic tools to detect translocations involving the TFE3 gene on chromosome X would be valuable in the evaluation of these tumors. We developed a dual-color, break-apart fluorescence in situ hybridization (FISH) assay to identify the chromosomal break point in paraffin-embedded tissue. This assay was validated using 4 cases of Xp11.2 RCC [proven by karyotype and/or reverse-transcriptase polymerase chain reaction (RT-PCR)], 2 cases of ASPS (proven by karyotype or RT-PCR), the UOK109 cell line carrying the inv(X) (p11;q12), and several negative controls (both neoplastic and non-neoplastic). This break-apart FISH assay is a relatively quick procedure for detecting Xp11.2 RCC and ASPS translocations and can be applied to archival paraffin-embedded tissue.

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Loss of p73 promotes dissemination of Myc-induced B cell lymphomas in mice

Mice engineered to express c-Myc in B cells (Eμ-myc mice) develop lethal lymphomas in which the gene encoding the p53 tumor suppressor is frequently mutated. Whether the p53 homolog p73 also functions as a tumor suppressor in vivo remains controversial. Here we have shown that p73 loss does not substantially affect disease onset and mortality in Eμ-myc mice. However, it does alter the phenotype of the disease. Specifically, p73 loss decreased nodal disease and increased widespread extranodal dissemination. We further found that p53 acted as the dominant tumor suppressor during the onset of Eμ-mycdriven B cell lymphomagenesis, while p73 modulated tumor dissemination and extranodal growth. Immunophenotyping and expression profiling suggested that p73 loss allowed increased maturation of malignant B cells and deregulated genes involved in lymphocyte homing and dissemination of human lymphomas. Consistent with this, p73 expression was frequently downregulated in a large cohort of human mature aggressive B cell lymphomas, and both the incidence and degree of p73 downregulation in these tumors correlated with their extranodal dissemination status. These data indicate that p73 is a modifier of Myc-driven lymphomas in mice, favoring tumor dissemination, and suggest that p73 could be a biomarker for human B cell lymphoma dissemination, a notion that can now be tested in clinicopathologic correlation studies.

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Promiscuous Gene Expression in Thymic Medullary Epithelial Cells: Scope, Phylogenetic Conservation and Regulation at the Single Cell Level

In the thymus a specific subset of thymic stromal cells - medullary thymic epithelial cells (mTECs) - express a highly diverse set of tissue-restricted antigens (TRAs) representing essentially all tissues of the body, which is known as promiscuous gene expression (pGE). This allows self-antigens, which otherwise are expressed in a spatially or temporally restricted manner to become continuously accessible to developing T-cells thus, rendering them tolerant to most self-antigens.

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Array comparative genomic hybridisation of 52 subjects with a Smith-Magenis-like phenotype

Smith-Magenis syndrome (SMS) is caused by del(17)(p11.2), including the retinoic acid induced 1 gene (RAI1), or mutation of RAI1. Haploinsufficiency of RAI1 results in developmental delay, mental retardation, sleep disturbance, self-abusive behaviors, and most features commonly seen in SMS. In this study, 52 subjects were referred for molecular analysis of RAI1 due to the presence of an SMS-like phenotype in each case. For this cohort, deletion and mutation analyses of RAI1 were negative; thus, the clinical diagnosis of SMS could not be confirmed and suggested that at least one other locus was responsible for the phenotype(s) observed.

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Efficient Transposition of Tol2 in the Mouse Germline

Insertional mutagenesis screens play an integral part in the annotating of functional data for all sequenced genes in the postgenomic era. Chemical mutagenesis screens are highly efficient but identifying the causative gene can be a laborious task. Other mutagenesis platforms, such as transposable elements, have been successfully applied for insertional mutagenesis screens in both the mouse and rat. However, relatively low transposition efficiency has hampered their use as a high-throughput forward genetic mutagenesis screen. Here we report the first evidence of germline activity in the mouse using a naturally active DNA transposon derived from the medaka fish called Tol2, as an alternative system for high-throughput forward genetic mutagenesis screening tool.

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Patent: Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product.

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Comprehensive aneuploidy screening in single cells using microarray comparative genomic hybridization methods implications for preimplantation genetic diagnosis

To develop clinically applicable DNA microarray methods for comprehensive identification of genomic imbalances (ie aneuploidy) in isolated cells.

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Efficacy of Wogonin in the Production of Immunoglobins and Cytokines by Mesenteric Lymph Node Lymphocytes in Mouse Colitis Induced with Dextran Sulfate Sodium

We previously examined wogonin, isolated from Scutellaria baicalensis, chemical mediators, and IgE by mesenteric lymph node (MLN) lymphocytes in rats. The present study explores the effect of wogonin on the MLN lymphocyte function of mice given orally at 20 mg/kg for 2 weeks with dextran sulfate sodium (DS)-induced colitis. The results indicate that IgA levels in MLN lymphocytes were high, while IgE was low, in mice given wogonin compared to those given water. Also, fecal IgA concentration of DS in the wogonin group mice was significantly higher than in the DS group. Concentrations of interferon-? and interleukin (IL)-2 of T cells by concanavalin A treatment was significantly higher in the wogonin fed group than in the normal group. Activation-induced IL-4, IL-5 and IL-10 secretion was lower in wogonin fed mice compared control mice after DS-induced colitis. For these reasons, we conclude that wogonin can alleviate the inflammation in DS-induced colitis brought about by an abnormal Th2 response.

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