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Supplementary Methods from Genomic Deregulation during Metastasis of Renal Cell Carcinoma Implements a Myofibroblast-Like Program of Gene Expression

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Supplementary Figure 9 from Genomic Deregulation during Metastasis of Renal Cell Carcinoma Implements a Myofibroblast-Like Program of Gene Expression

Supplementary Figure 4 from Genomic Deregulation during Metastasis of Renal Cell Carcinoma Implements a Myofibroblast-Like Program of Gene Expression

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Genomic copy number alterations (CNAs) in diffuse large B-cell lymphoma (DLBCL) have roles in disease pathogenesis, but overall clinical relevance remains unclear. Herein, an unbiased algorithm was uniformly applied across three genome profiling datasets comprising 392 newly-diagnosed DLBCL specimens that defined 32 overlapping CNAs, involving 36 minimal common regions (MCRs). Scoring criteria were established for 50 aberrations within the MCRs while considering peak gains/losses. Application of these criteria to independent datasets revealed novel candidate genes with coordinated expression, such as CNOT2, potentially with pathogenic roles. No one single aberration significantly associated with patient outcome across datasets, but genomic complexity, defined by imbalance in more than one MCR, significantly portended adverse outcome in two of three independent datasets. Thus, the standardized scoring of CNAs currently developed can be uniformly applied across platforms, affording robust validation of genomic imbalance and complexity in DLBCL and overall clinical utility as biomarkers of patient outcome.

Array comparative genomic hybridization (aCGH) has yet to be fully leveraged in a prognostic setting in chronic lymphocytic leukemia (CLL). Genomic imbalance was assessed in 288 CLL specimens using a targeted array. Based on 20 aberrations in a hierarchical manner, all 228 treatment-naive specimens were classified into a group with poor outcome (20.6%) exhibiting at least one aberration that was univariately associated with adverse outcome (gain: 2p, 3q, 8q, 17q, loss: 7q, 8p, 11q, 17p, 18p), good outcome (32.5%) showing 13q14 loss without any of the other 10 aberrations (gain: 1p, 7p, 12, 18p, 18q, 19, loss: 4p, 5p, 6q, 7p) or intermediate outcome (remainder). The three groups were significantly separated with respect to time to first treatment and overall survival (p < 0.001), and validation of the stratification scheme was performed in two independent datasets. Gain of 3q and 8q, and 17p loss were determined to be independent unfavorable prognostic biomarkers. TP53, NOTCH1 and SF3B1 mutations correlated with the presence of one poor outcome aCGH marker, at a considerably higher frequency than when only considering poor risk aberrations routinely detected by fluorescence in situ hybridization (FISH). These data support genomic imbalance evaluation in CLL by aCGH to assist in risk stratification.

Clear cell renal cell carcinoma (RCC) is the most common and invasive adult kidney cancer. The genetic and biological mechanisms that drive metastatic spread of RCC remain largely unknown. We have investigated the molecular signatures and underlying genomic aberrations associated with RCC metastasis, using an approach that combines a human xenograft model; expression profiling of RNA, DNA, and microRNA (miRNA); functional verification; and clinical validation. We show that increased metastatic activity is associated with acquisition of a myofibroblast-like signature in both tumor cell lines and in metastatic tumor biopsies. Our results also show that the mesenchymal trait did not provide an invasive advantage to the metastatic tumor cells. We further show that some of the constituents of the mesenchymal signature, including the expression of the well-characterized myofibroblastic marker S100A4, are functionally relevant. Epigenetic silencing and miRNA-induced expression changes accounted for the change in expression of a significant number of genes, including S100A4, in the myofibroblastic signature; however, DNA copy number variation did not affect the same set of genes. These findings provide evidence that widespread genetic and epigenetic alterations can lead directly to global deregulation of gene expression and contribute to the development or progression of RCC metastasis culminating in a highly malignant myofibroblast-like cell. Cancer Res; 70(23); 9682–92. ©2010 AACR.

The goal of this investigation was to study the regulation of acid-sensing ion channel (ASIC)3 expression by TGFbeta in the nucleus pulposus cells of the intervertebral disc. Analysis of human nucleus pulposus tissue indicated decreased ASIC3 and elevated TGFbeta expression in the degenerate state. In a parallel study, treatment of nucleus pulposus cells with TGFbeta resulted in decreased expression of ASIC3 mRNA and protein. Suppression of ASIC3 promoter activity was evident when the nucleus pulposus cells were treated with TGFbeta or co-transfected with the constitutively active ALK5 or a smad3 construct. On the other hand, co-transfection of dominant negative smad3 or smad7 restored ASIC3 promoter activity. We validated the role of smad3 in controlling ASIC3 expression using cells derived from smad3-null mice. ASIC3 promoter activity in the null cells was 2- to 3-fold higher than the wildtype cells. Moreover, expression of smad3 in null cells decreased ASIC3 promoter activity by almost 50%. Further studies using deletion constructs and trichostatin A treatment showed that the full-length smad3 was necessary, and the suppression involved recruitment of histone deacetylase to the promoter. To determine the mechanism, we evaluated the rat ASIC3 promoter sequence and noted the presence of two smad interacting CAGA box motifs. Gel-shift and supershift analysis indicated that smad3 protein was bound to this motif. Chromatin immunoprecipitation analysis confirmed that smad3 bound both the CAGA elements. Results of these studies clearly show that TGFbeta is highly expressed in the degenerate disc and through smad3 serves as a negative regulator of ASIC3 expression.

STUDY DESIGN To identify and characterize endogenous progenitor cell population from intervertebral disc. OBJECTIVE To determine if progenitor cells exist in degenerate human discs. SUMMARY OF BACKGROUND DATA Back pain, a significant source of morbidity in our society, is directly linked to the pathology of the intervertebral disc. Because disc disease is accompanied by a loss of cellularity, there is considerable interest in regeneration of cells of both the anulus fibrosus (AF) and nucleus pulposus (NP). METHODS To determine if skeletal progenitor cells are present in the disc, samples were obtained from the degenerate AF and NP of 5 patients (Thompson grade 2 and 3, mean age 34 +/- 7.6 years) undergoing anterior cervical discectomy and fusion procedures as well as adult rat lumbar spine. RESULTS Cells isolated from degenerate human tissues expressed CD105, CD166, CD63, CD49a, CD90, CD73, p75 low affinity nerve growth factor receptor, and CD133/1, proteins that are characteristic of marrow mesenchymal stem cells. In osteogenic media, there was an induction of alkaline phosphatase activity and expression of alkaline phosphatase, osteocalcin, and Runx-2 mRNA. When maintained in adipogenic media, a small percentage of cells displayed evidence of adipogenic differentiation: accumulation of cytosolic lipid droplets and increased expression of peroxisome proliferator-activated receptor-gamma2 and lipoprotein lipase mRNA. AF- and NP-derived cells also evidenced chondrogenic differentiation. CD133 (+) cells in the AF were able to commit to either the chondrogenic or adipogenic lineages. The results of the human disc studies were confirmed using cell derived from the NP and AF tissue of the mature rat disc. CONCLUSION The analytical data indicated that the pathologically degenerate human disc contained populations of skeletal progenitor cells. These findings suggest that these endogenous progenitors may be used to orchestrate the repair of the intervertebral disc.

The nucleus pulposus is an aggrecan-rich, avascular tissue that permits the intervertebral disk to resist compressive loads. In the disk, nucleus pulposus cells express hypoxia-inducible factor (HIF)-1α, a transcription factor that responds to oxygen tension and regulates glycolysis. The goal of the present study was to examine the importance of HIF-1α in rat nucleus pulposus cells and to probe the function of this transcription factor in terms of regulating aggrecan gene expression. We found that HIF-1α protein levels and mRNA stability were similar at 20 and 2% O2; there was a small, but significant increase in HIF-1α transactivation domain activity in hypoxia. With respect to HIF-1α target genes GAPDH, GLUT-1, and GLUT-3, mRNA and protein levels were independent of the oxygen tension. Other than a modest increase in 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase reporter activity, the oxemic state did not change GAPDH, GLUT-1, and GLUT-3 promoter activities. Treatment of cells with 2-deoxyglucose (2-DG), a glycolytic inhibitor, resulted in a significant suppression in ATP synthesis in normoxia, whereas treatment with mitochondrial inhibitors did not affect ATP production and cell viability. However, measurement of the rate of fatty acid oxidation indicated that these cells contained functioning mitochondria. Finally, we showed that when HIF-1α was suppressed, irrespective of the oxemic state, there was a partial loss of aggrecan expression and promoter activity. Moreover, when cells were treated with 2-DG, there was inhibition in aggrecan promoter activity. Results of this study indicate that oxygen-independent stabilization of HIF-1α in nucleus pulposus cells is a metabolic adaptation that drives glycolysis and aggrecan expression.

Study design To investigate effects of FGF-2 on nucleus pulposus cell growth and differentiation. Objectives To elucidate the phenotypic changes that occur during expansion of nucleus pulposus cells in monolayer culture, and to investigate the effects of fibroblast growth factor (FGF)-2 on cell growth and differentiation. Summary of background data Nucleus pulposus cells would have a limited application for autologous cell transplantation if phenotypic dedifferentiation takes place during culture expansion. FGF-2 has been shown to retain the differentiation potential of monolayer expanded chondrocytic cells. However, its effect on nucleus pulposus cells is not known. Methods Bovine nucleus pulposus cells were serially passaged in the presence or absence of FGF-2 (1 and 10 ng/mL). After passage numbers 1 and 7, cells were immobilized in alginate beads and treated with transforming growth factor (TGF)-beta1 for 1 week to assess their differentiation. Results During culture expansion in monolayer, nucleus pulposus cells maintained the expression of aggrecan messenger ribonucleic acid (mRNA). However, mRNA levels of collagen type I, collagen type II, Sox-9, and versican decreased with increasing passage number for both control (untreated) cells and FGF-2 treated cells. When grown in alginate with TFG-beta1, passage 7 cells that received FGF-2 during culture expansion restored the mRNA expression of type II collagen, Sox-9, COMP, chondroadherin, and fibromodulin. Moreover, FGF-2 treatment resulted in increased sulfated proteoglycan synthesis and lower aggrecan turnover compared to untreated controls under identical culture conditions. FGF-2 treated cells continued to express HIF-1alpha protein till passage 7, while MMP-2 expression was evident in cells treated with TGF-beta1. In addition, cells pretreated with FGF-2 showed higher induction of phospho ERK1/2 after treatment with TGF-beta1. Also, FGF-2 maintained smad 2/smad 3 mediated signaling in cells after TGF-beta treatment. FGF-2 action resulted in reduced actin stress fiber formation and migratory cell morphology, with no effect on cell proliferation. Conclusions The presence of FGF-2 during culture expansion of nucleus pulposus cells in monolayer can sustain a differentiated cell phenotype by maintaining responsiveness to TGF-beta1. Our results suggest that FGF-2 should be tested for its ability to maintain the reactivity of the nucleus pulposus cells to other morphogenic factors that may be used for cell-based transplantation therapy.

Study design Galectin-3 expression in rat intervertebral disc at different stages in postnatal life is evaluated. Objective To determine if galectin-3 expression is confined to cells of the nucleus pulposus in the postnatal rat intervertebral disc. Summary of background data During embryonic development, the anulus fibrosus is derived from the sclerotome, whereas the nucleus pulposus is notochordal. Many authorities opine that in the postnatal disc, notochordal cells play a central role in controlling the development of degenerative disc disease. Surprisingly, unequivocal evidence supporting the existence of notochordal cells in the nucleus pulposus in postnatal life has yet to be demonstrated. Since the expression of galectin-3 is commonly used to identify notochordal cells, we evaluated its expression in tissues of the rat disc and in cultured cells. Methods Galectin-3 expression was studied in the nucleus pulposus and anulus fibrosus tissue of rat discs (2 days, 9 weeks, and 10 months old), and cultured cells using different biochemical and molecular biology methods. Rat sternal cartilage and cultured sternal chondrocytes were used as controls. Results Immunohistochemical studies indicated that galectin-3 was present in the nucleus pulposus and anulus fibrosus. In both discal tissues and cultured cells, studies confirmed that there was a robust expression of galectin-3 messenger ribonucleic acid and protein. Protein expression patterns were similar in neonatal, young, and mature rats. There was also evidence of intracellular and membrane expression of galectin-3 in the cultured disc cells. Finally, significant levels of galectin-3 were evident in rat sternal cartilage and cultured sternal chondrocytes. Conclusions Results of the study indicate that galectin-3 is expressed in the neonatal, young, and mature rat disc, and its expression is not restricted to the cells of the nucleus pulposus. Because of its ubiquitous expression, this protein cannot be used as a marker of notochordal cells in the postnatal rat disc.

The nucleus pulposus is an aggrecan-rich hydrated tissue that permits the intervertebral disc to resist compressive loads. Adaptation to loading is achieved through an elevation in disc osmolarity mediated by the numerous charged glycosoaminoglycan side chains of the aggrecan molecule. The goal of this investigation was to determine the functional role of the osmo-regulatory protein, TonEBP, in cells of the nucleus pulposus. We found that TonEBP and its downstream target genes were robustly expressed in the tissues of the disc. Above 330 mosmol/kg, cultured nucleus pulposus cells up-regulated target genes TauT, BGT-1, and SMIT; above 450 mosmol/kg, there was raised expression of HSP-70. In hypertonic media there was activation of TauT and heat shock protein-70 (HSP-70) reporter activity and increased binding of TonEBP to the TonE motif. When cells were transfected with the dominant-negative form of TonEBP (DN-TonEBP) there was suppression of TauT and HSP-70 reporter gene expression; pTonEBP enhanced reporter gene expression. Moreover, in hypertonic media, forced expression of DN-TonEBP induced apoptosis. We suppressed TonEBP using small interfering RNA technique and noted a decrease in TauT reporter activity in isotonic as well as hyperosmolar media. Finally, we report that the aggrecan promoter contains two conserved TonE motifs. To evaluate the importance of these motifs, we overexpressed DN-TonEBP and partially silenced TonEBP using small interfering RNA. Both approaches resulted in suppression of aggrecan promoter activity. It is concluded that TonEBP permits the disc cells to adapt to the hyperosmotic milieu while autoregulating the expression of molecules that generate the unique extracellular environment.

Study design Rat lumbar discs comprising nucleus pulposus, annulus fibrosus, and cartilaginous endplates were cultured for 1 week in a specialized media containing either TGF-beta1 or TGF-beta3. Role of TGF-beta isoforms on cell function was evaluated. Objective To develop an in vitro organ culture of rat intervertebral disc and evaluate effects of TGF-beta3 on disc cell function. Summary of background data An in vitro model system is of considerable value in understanding the cell biology of the intervertebral disc. Development of a useful organ culture model would enhance understanding of disc function in health and disease. Materials and methods Rat lumbar intervertebral discs were maintained in organ culture in media supplemented with TGF-beta3 or TGF-beta1 for 1 week. Tissue morphology was studied using routine histologic, histochemical and immunohistochemical techniques. Cell function was assessed by gene expression, sulfate incorporation, and Western blot analysis. Results After 1 week in culture with TGF-beta3 and TGF-beta1, the gross morphology and tissue architecture of the disc were preserved. TUNEL analysis indicated that there was no evidence of cell death in the nucleus pulposus or the anulus fibrosus. The level of Alcian blue staining in the nucleus pulposus was similar to that of the freshly isolated disc. However, when compared with TGF-beta1, TGF-beta3 elevated the expression of critical matrix genes, enhanced [S] incorporation into proteoglycans, preserved the expression of TGF-beta receptors, and decreased aggrecan turnover. There was also increased activation (phosphorylation) of ERK, a critical signaling protein. Moreover, inhibition of ERK activity, in the presence TGF-beta3, resulted in suppression of collagen Type II, aggrecan, TGF-beta-RI, TGF-beta-RII and TGF-beta-RIII mRNA expression. Conclusions TGF-beta3 maintains the phenotype of disc cells in organ culture. It exerts this effect, in part, by elevating the levels of activated ERK1/2, which in turn regulates the expression of TGF-beta-RI and TGF-beta-RII.

N-(4-hydroxyphenyl) retinamide (4-HPR, fenretinide) a synthetic retinoid is in clinical trials for the treatment of several malignancies. However, its biological effects and therapeutic value in childhood brain tumor medulloblastoma (MB) has not been investigated. In this study, we report for the first time that fenretinide (2.5–10 μM) induces apoptotic cell death in human MB cells. We observed significant inhibition of cell survival in four MB cell lines (D425MED, D458MED, D283MED and D341MED) as determined by MTT assays. These results were further supported by inhibition of anchorage-independent colony formation in soft agar. Fenretinide-induced decrease in cell viability was in part due to activation of caspase-3 dependent cell death, which was further supported by the cleavage of poly(ADP-ribose) polymerase-1 (PARP-1), a caspase-3 substrate. Cell death was partially prevented by the antioxidant, l -ascorbic acid suggesting that free radical intermediates might be involved in fenretinide effects. These results suggest that pharmacologically achievable concentrations of fenretinide are effective in killing MB cells and thus show its therapeutic potential to treat human MB.

Nucleus pulposus (NP) cells of the intervertebral disc reside in an environment that has a limited vascular supply and generate energy through anaerobic glycolysis. The goal of the present study was to examine the expression and regulation of HIF-1α, a transcription factor that regulates oxidative metabolism in nucleus pulposus cells. Nucleus pulposus cells were isolated from rat, human, and sheep disc and maintained at either 21% or 2% oxygen for various time periods. Cells were also treated with desferrioxamine (Dfx), a compound that mimics the effects of hypoxia (Hx). Expression and function of HIF-1α were assessed by immunofluorescence microscopy, Western blot analysis, gel shift assays, and luciferase reporter assays. In normoxia (Nx), rat, sheep, and human nucleus pulposus cells consistently expressed the HIF-1α subunit. Unlike other skeletal cells, when maintained under low oxygen tension, the nucleus pulposus cells exhibited a minimal induction in HIF-1α protein levels. Electromobility shift assays confirmed the functional binding of normoxic HIF-1α protein to its putative DNA binding motif. A dual luciferase reporter assay showed increased HIF-1α transcriptional activity under hypoxia compared to normoxic level, although this induction was small when compared to HeLa and other cell types. These results indicate that normoxic stabilization of HIF-1α is a metabolic adaptation of nucleus pulposus cells to a unique oxygen-limited microenvironment. The study confirmed that HIF-1α can be used as a phenotypic marker of nucleus pulposus cells. J. Cell. Biochem. 98: 152–159, 2006. © 2006 Wiley-Liss, Inc.

OBJECTIVE The aim of the present study was to investigate whether activation of MAPK subtypes ERK and p38 influences integrin expression and promotes nucleus pulposus cell survival in hypoxia. SUMMARY OF BACKGROUND DATA We have recently shown that in a low oxygen environment, rat nucleus pulposus cells activate phosphatidylinositol 3-kinase/Akt (PI3K/Akt) and mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) signaling pathways. However, the role of these signaling pathways in regulating cell matrix interactions is not known. METHODS Rat nucleus pulposus cells were cultured in hypoxia (2% O2) or normoxia (20% O2). Western blotting and kinase assay were used to analyze expression of MAPK signaling molecules. Cell attachment to collagen was studied using an adhesion assay, whereas flow cytometry and RT-PCR were performed to quantify integrin receptor expression. RESULTS In a hypoxic environment (2% O2), rat nucleus pulposus cells showed a persistent phosphorylation of p38 and ERK proteins; pERK catalyzed the phosphorylation of Elk1-Gst fusion protein. When ERK activity was blocked, cell adhesion to Type II collagen, one of the major extracellular matrix proteins in the nucleus pulposus tissue, was impaired. A similar inhibitory effect on collagen adhesion was observed when nucleus pulposus cells were treated with an antibody to alpha2 integrin. Furthermore, when ERK activity was inhibited, there was a decrease in alpha2 integrin mRNA expression. In contrast to ERK, inhibition of p38 activity did not modulate alpha2 integrin subunit mRNA expression. Likewise, inhibition of ERK, but not p38, resulted in downregulation of nucleus pulposus alpha2 integrin protein levels and blocked cell survival in hypoxia. CONCLUSIONS Hypoxia activated MAPK signaling pathway activity in nucleus pulposus cells. ERK, but not p38, regulated alpha2 integrin expression and cell survival.

Vitamin D3 analogs are potential anti-cancer agents with theoretically wide therapeutic index, but there have been limited studies directed towards human neuroblastoma. The antiproliferative ability of the novel vitamin D3 hybrid analog QW-1624F2-2 (QW, 1-hydroxymethyl-16-ene-24, 24-F2-26, 27-bishomo-25-hydroxyvitamin D3) was examined in two human neuroblastoma-derived cell-lines. Analog QW inhibited cell-cycle progression of IMR5 cells with accumulation in G1 phase. QW induced the differentiation of CHP134 as evidenced by increased neurite length. These effects were accompanied by decreased expression of MYCN in both the cell-lines treated with QW. Furthermore, QW inhibited the migration of CHP134 cells in matrigel invasion assays, indicating its anti-invasive ability. In athymic nude mice, we found that QW was less calcemic than EB1089 (1α, 25-dihydroxy-22, 24-diene-24, 26,27-trishomovitamin D3). Systemic administration of QW in a mouse xenotransplantation model revealed that it is more effective than EB1089 in suppressing the growth of CHP134 flank tumors. In summary, the low-calcemic hybrid analog QW showed significant anti-tumor activity in vivo and thus exhibits potential as a novel cancer therapeutic. © 2005 Wiley-Liss, Inc.

Chromosomal microarray (CMA) is widely used to detect and refine chromosome abnormalities in both congenital and neoplastic cases. Recently, a blood sample from a newborn male with no apparent dysmorphic features was sent to the Mayo Clinic Cytogenetics laboratory for G-banded karyotype analysis to clarify prenatal findings of a positive trisomy 21 noninvasive prenatal screening (NIPS) result. Chromosome analysis of 20 metaphases revealed 13 were normal (46,XY) and 7 had a satellited supernumerary marker chromosome (47,XY,+mar). To further characterize the marker chromosome, CMA studies were performed, which revealed an 8.6 megabase mosaic duplication from 21q11.2 to 21q21.1. Subsequent metaphase FISH studies demonstrated that the duplicated region was present on the supernumerary marker chromosome, indicating that the marker chromosome is derived from chromosome 21. Interphase FISH studies showed that the marker was present in 68% of interphase nuclei. Despite its large size, the duplicated region contains only 30 known genes. In addition, similar duplications involving this region have not been previously described, making the clinical significance of this duplication uncertain. Importantly, the duplicated interval does not include the Down syndrome critical region (21q22.1 to 22q22.3), consistent with this patient’s lack of dysmorphic features. This report highlights the importance of diagnostic follow-up testing and the clinical utility of conventional and molecular cytogenetic techniques in the setting of abnormal NIPS results.

Background: Recent advancements in comprehensive sequencing technologies has enabled researchers to uncover numerous somatic variants within many disease types, but their respective contributions to disease pathogenesis and potential roles as outcome biomarkers are less well-defined. Even fewer studies have integrated somatic mutation events with genomic gain and loss events of respective genes, mostly due to the need to utilize a second platform to robustly assess genomic copy number. To further understand the roles of these genomic aberrations in the disease biology of mature B-cell neoplasms, we developed a next-generation sequencing (NGS) panel of 220 genes for profiling of Diffuse Large B-cell Lymphoma (DLBCL), Follicular Lymphoma (FL), Mantle Cell Lymphoma (MCL), and secondarily for Chronic Lymphocytic Leukemia (CLL). Methods: The 220 genes represented in the panel included genes based on reported frequency of mutations, targets of therapeutic agents, involvement in disease-enriched pathways, prognostic value, and associated with targeted therapy resistance. Also included were genes that mapped to sites of genomic gain and loss commonly observed in these neoplasms. Of all the genes, 163 were enriched for DLBCL, 144 for FL, 44 for MCL, and 107 for CLL. Probes were designed to cover the coding exons of the 220 genes using a hybrid-capture approach (Nimbledesign, Roche, Inc.), with a total capture size of 0.92 Mb comprising 4086 target regions. Optimization of DNA fragmentation and library preparation was performed for DNA extracted from formalin-fixed paraffin-embedded (FFPE) biopsy material, being the most common intended tissue type and also for which tumor burden could be assessed. Sequencing was performed using a Miseq sequencer (Illumina, Inc.) with the goal to enable detection of somatic variants down to an allele variant frequency (AVF) of 5%. CLC Genomics Workbench (Qiagen, Inc.) was used for alignment and variant calling. Filtering was performed to exclude synonymous, intronic, and untranslated region variants, variants within homopolymer regions (>6), and variants detected below 5% AVF. Results: The average depth of coverage achieved across an initial sample set of over 50 FFPE DLBCL specimens was approximately 350X, with only one sample having more than 10% of the target regions not achieving a coverage of 60X or greater (within 95% of the target region). As part of a proof-of-concept study, we sequenced a cohort of 85 DLBCL FFPE samples from a single institution from patients undergoing biopsy as part of their routine clinical care. Clinical outcome, cell-of-origin subtype (by the Hans method) and genomic gain/loss data by array-CGH were available. All studies were performed with IRB approval. Of the 85 cases, 80 had also been submitted to bi-directional Sanger's sequencing for Exons 5-8 of TP53 to establish accuracy of variant detection. Of cases completed to date, additional TP53 mutations have been detected by NGS due to an AVF below that detectable by Sangers or only detected in one direction. In addition, of the 14 cases completely sequenced and filtered to date, EZH2 variants in four samples have been detected in the GCB subtype while four CD79B variants were in samples of the non-GCB subtype, consistent with previously reported associations. Furthermore, six of the eight samples which harbored an EZH2 or CD79B variants had mutations within the catalytic domain at Y646 (EZH2) or the ITAM residue Y196 (CD79B), both of which have clinical implications. Initial assessment of the ability of the panel to infer copy number showed concordance with aCGH in detecting large chromosomal aberrations. The sensitivity and specificity of this approach is currently being optimized. Conclusion: Overall then, a hybrid-capture NGS panel has been developed, targeting genes enriched for involvement in the most frequent subtypes of mature B-cell neoplasms and optimized for application to FFPE biopsy specimens. While emerging pathogenomic patterns observed in the cases sequenced to date have confirmed previously observed patterns, completion of the NGS analysis of the 85 DLBCL cohort will permit more complex integrated analysis of somatic variants and genomic gain/loss with pathologic and clinical outcome data. Disclosures Friedman: Cancer Genetics Inc.,: Employment, Equity Ownership. Guttapalli:Cancer Genetics, Inc.: Employment, Equity Ownership. Ma:Cancer Genetics, Inc.: Employment, Equity Ownership. Thodima:Cancer Genetics, Inc.: Employment, Equity Ownership. Kamalakaran:Cancer Genetics, Inc.: Employment, Equity Ownership. Houldsworth:Cancer Genetics, Inc.: Employment, Equity Ownership.

Introduction: Diffuse Large B-cell Lymphoma (DLBCL), exhibits a wide range of clinical and biological heterogeneity. While initially responsive to rituximab based therapy, more than 70% of patients relapse within 5 years. Two distinct subtypes of DLBCLs were previously identified by gene expression profiling, that correlated to the cell of origin (COO); currently an immunohistochemistry (IHC) surrogate (Hans algorithm) is used to identify this COO. However, the value of COO identification by IHC is being questioned in patients treated with rituximab based regimen. As such there is a need for the identification of additional prognostication markers. The purpose of the present study is to systematically characterize a cohort of patients with DLBCL using a variety of methods including COO by IHC, copy number changes by array-based comparative genomic hybridization, and single gene mutations by next generation sequencing. The goal is to identify prognostic molecular biomarkers that predict survival better than current methods such as COO in DLBCL patients treated with rituximab. Methods: Patients diagnosed between 2003 and 2011 and treated with R-CHOP/R-EPOCH at BIDMC were identified. IPI/R-IPI, ECOG performance status, overall survival data were collected from retrospective chart review. Molecular and immunohistochemical studies were performed on formalin-fixed paraffin embedded tissue (FFPE), which was obtained prior to initiation of therapy (at the time of diagnosis). aCGH: Using a previously developed assay for aCGH to detect genomic gain/loss from archival FFPE, we characterized each DLBCL sample for the presence or absence of 50 copy number variations (CNVs) from 32 common regions of overlapping genomic imbalances comprising 36 minimal common regions. The calling criteria were based on GISTIC defined peaks based on copy number data from three publicly available datasets: IS-172, IS-51HR, EMEXP-3463. Gene panels: Next Generation Sequencing (NGS) was performed using a targeted hybrid capture panel and run on a Miseq (Illumina, Inc.). Gene selection for the panel was based on frequently mutated genes reported in DLBCL, Follicular lymphoma (FL), and Mantle Cell Lymphoma (MCL). Also selected for the panel were genes involved in known dysregulated pathways, therapeutic targets, and genes mapped to sites of genomic gains or losses. Cell of Origin: Immunostains were performed for BCL6, CD10, MUM1, FOXP1, GCET and LMO2. The immunostains were blindly scored by three different pathologists. For this study, GCB vs ABC determination was made using the Hans algorithm (CD10, BCL6 and MUM1 expression). Statistics: Kaplan-Meier (KM) survival analysis was performed using R (version 3.2.1). Results: Data on an initial subset of 49 patients with comprehensive molecular, COO and clinical information is presented (and an additional ~100 case analysis is in progress). Average age of patients at the time of diagnosis was 63, with 23 males and 26 females. By univariate analysis, the COO was not significantly associated with survival in the patients treated with rituximab based regimen (KM p=0.678). By contrast, three of the CNVs were associated with survival by Kaplan Meier analysis (Table 1). Also four, gene mutations were significantly associated with poor survival by univariate analysis (Table 1). Table 1.Markers significantly associated with survival in rituximab treated patients with DLBCL. Ab28 predicted for better survival, whereas the presence of the other mutations or CNVs predicted for poor survival.Gene / CRp value (KM)Ab29 (D1p13.1)0.00787PIK3C2G0.00126PIM10.00499CD79B0.00567DTX10.0102Ab3(A1q21.1-q25.1(3))0.0193Ab28 (D1p36.32-p36.31)0.0211 Conclusions: Our systematic analysis of DLBCLs using multiple immunohistochemical and molecular methods identified mutational and copy number biomarkers predictive of survival in DLBCL patients, treated with rituximab in univariate analysis. Multivariate analysis and data from additional cases will reveal whether these molecular biomarkers can better predict patient survival, compared to current methods (such as COO by IHC). Disclosures Friedman: Cancer Genetics Inc.,: Employment, Equity Ownership. Guttapalli:Cancer Genetics, Inc.: Employment, Equity Ownership. Thodima:Cancer Genetics, Inc.: Employment, Equity Ownership. Kamalakaran:Cancer Genetics, Inc.: Employment, Equity Ownership. Houldsworth:Cancer Genetics Inc.,: Employment, Equity Ownership.

Earlier studies have shown that intervertebral disc cells express TonEBP, a transcription factor that permits adaptation to osmotic stress and regulates aggrecan gene expression. However, the mechanism of hyperosmotic activation of TonEBP in disc cells is not known. Results of this study show that hypertonic activation of ERK signaling regulates transactivation activity of TonEBP, modulating its function. Introduction: In an earlier report, we showed that tonicity enhancer binding protein (TonEBP) positively regulates aggrecan gene expression in disc cells, thereby autoregulating its osmotic environment. Although these studies indicated that the cells of the nucleus pulposus were optimally adapted to a hyperosmotic state, the mechanism by which the cells transduce the osmotic stress was not delineated. The primary goal of this study was to test the hypothesis that, in a hyperosmotic medium, the extracellular signal-regulated kinase (ERK) signaling pathway regulated TonEBP activity. Materials and Methods: Nucleus pulposus cells were maintained in isotonic or hypertonic media, and MAPK activation and TonEBP expression were analyzed. To study the role of MAPK in regulation of TonEBP function, gel shift and luciferase reporter assays were performed. ERK expression in cells was modulated by using expression plasmids or siRNA, and transactivation domain (TAD)-TonEBP activity was studied. Results: We found that hypertonicity resulted in phosphorylation and activation of ERK1/2 proteins and concomitant activation of C terminus TAD activity of ELK-1, a downstream transcription factor. In hypertonic media, treatment with ERK and p38 inhibitors resulted in downregulation of TonE promoter activity of TauT and HSP-70 and decreased binding of TonEBP to TonE motif. Similarly, forced expression of DN-ERK and DN-p38 in nucleus pulposus cells suppressed TauT and HSP-70 reporter gene activity. Finally, we noted that ERK was needed for transactivation of TonEBP. Expression of DN-ERK significantly suppressed, whereas, WT-ERK and CA-MEK1 enhanced, TAD activity of TonEBP. Experiments performed with HeLa cells indicated that the ERK signaling pathway also served a major role in regulating the osmotic response in nondiscal cells. Conclusions: Together, these studies showed that adaptation of the nucleus pulposus cells to their hyperosmotic milieu is dependent on activation of the ERK and p38- MAPK pathways acting through TonEBP and its target genes.

428 Background: About one-third of patients with clear cell renal cell carcinoma (ccRCC) exhibit metastasis at the time of diagnosis and show poor prognosis. The genetic and epigenetic alterations associated with metastasis in ccRCC have variably been studied, and their role in the metastatic process is unclear. The goals of the current study were to identify genomic copy number alterations (CNAs) associated with ccRCC metastasis and examine their clinical utility. Methods: In this IRB-approved study, genome-wide copy number profiling was performed on DNA from 144 ccRCC (81 primary and 63 metastatic lesions). Differential CNAs between primary and metastatic lesions and between different metastatic sites were identified using Fisher’s exact test. Associations between CNAs and overall survival (OS) were tested using the log rank statistic and Kaplan-Meier method. Genomic profiling data of 437 and 240 primary ccRCC (TCGA and PMID: 23797736, respecitively) were used for verification. Results: Between primary and metastatic lesions, 25 CNAs were significantly different (p

Despite excellent initial responses of diffuse large B-cell lymphoma (DLBCL) patients to current frontline immunotherapy (RCHOP), only about 40% of patients are ultimately cured, with most relapses occurring within the first 2-3 years. Apart from clinical features, very few biomarkers are available and validated for risk stratification of DLBCL patients, other than cell-of-origin (COO) subtyping and MYC rearrangement. Genomic copy number changes identified using a variety of genomic profiling technologies including massively parallel sequencing, have variously been reported to have prognostic value in DLBCL. Our previous studies used a common analytical approach across three different clinical datasets to identify and define 32 common regions (CR) of overlapping genomic imbalance (17 gain, 15 loss), comprising 36 minimal common regions (MCR) observed in newly-diagnosed DLBCL. We now report the establishment of standardized calling criteria for a total of 50 aberrations within the 32 CR, taking into consideration GISTIC-defined peaks based on copy number data from three publicly available datasets: IS-172 (GSE11318, n=170), IS-51HR (E-MEXP-3463, n=51 with high IPI), and one similarly analyzed dataset IS-180 (GSE34171, n=180). As a form of validation of the scoring criteria, the frequencies of the aberrations detected in IS-172 in the known GCB and ABC COO subtypes were compared with those previously reported (PMID:18765795). The relative imbalance of the aberrations between the subtypes were re-capitulated including six occurring at higher frequency in the GCB subtype and five in the ABC subtype. Integration of the expression profiles of 162 samples of IS-172 by univariate t-test with the 50 aberrations revealed 569 unique positively-correlated Refseqs mapping to 24 of the MCRs with at least 1.2 fold change in expression (Univariate t-test with P ≤ 0.05 after Benjamini-Hochberg false discovery rate [FDR]). Of these, 27 were located within overlapping peaks of gain/loss. Ingenuity Pathway Analysis determined five significant pathways (P ≤ 0.001, FDR Association of each of the defined 50 aberrations with overall survival (OS) was performed with the Kaplan-Meier method and log-rank statistic in three RCHOP datasets: IS-124 (GSE15127, n=124), a subset of 70 of IS-180 (IS-70), and a dataset of 41 for which array-CGH was performed in-house using a targeted oligonucleotide (Agilent Technologies) with DNA extracted from sections of formalin–fixed paraffin-embedded de novo DLBCL (IH-41). Ten aberrations significantly associated (P ≤0.05) with poor outcome in at least one of the datasets: gain of 12q (12q13 and 12q14), 16q24, 19q13, and loss of 2q24, 2 sites at 6q21, 8p22, 9p21, 15q15, and 17p13. Of these 10 aberrations, loss of 17p significantly associated with gain of 16q, and losses of 6q, 8p, and 15q (P Genomic complexity was assessed by two methods. In the first, the median number of MCR aberrations was determined to be 1, across three datasets (IS-172, IS-180, and IS-124). Specimens in RCHOP-treated datasets IS-124 and IS-70 were then called “complex” if 2 or more MCR aberrations were detected: 31% and 67% respectively. In both datasets, a complex genome was significantly associated with overall unfavorable outcome (P=0.037, 0.006 respectively). Specimens in IS-172 and IS-70 were additionally classified as “complex” based on the presence of at least one of nine aberrations involving the CDKN2A-TP53-RB-E2F axis (PMID:22975378) where 33% and 57% of cases were scored as complex respectively. Using this approach, significant association with outcome was only found for IS-70 (P In summary, establishment of robust scoring criteria for copy number changes afforded correlative analyses with clinical features to reveal that genomic complexity is indeed associated with overall inferior survival in DLBCL and that integrated expression analysis identified biological pathways in DLBCL that may represent potential therapeutic targets. Disclosures Dias: Cancer Genetics,Inc: Employment. Thodima:Cancer Genetics,Inc: Employment, Stock option holder Other. Guttapalli:Cancer Genetics, Inc: Employment, Stock option holder Other. Mendiratta:Cancer Genetics,Inc: Employment. Houldsworth:Cancer Genetics, Inc.: Employment, Stock and stock option holder Other.

Objective Because mesenchymal stem cells can differentiate into chondrocyte-like cells, we ask the question, can mesenchymal stem cells commit to the nucleus pulposus phenotype? Background Back pain, a significant source of morbidity in our society, is linked to degenerative changes of the intervertebral disc. Absence of suitable graft tissue limits therapeutic approaches for repair of disc tissue. For this reason, there is considerable interest in developing "tissue engineering" strategies for the regeneration of the nucleus pulposus. Methods Rat mesenchymal stem cells were immobilized in 3-dimensional alginate hydrogels and cultured in a medium containing transforming growth factor-beta1 under hypoxia (2% O2) and normoxia (20% O2). Mesenchymal stem cells were examined by confocal microscopy to evaluate their viability and metabolic status after labeling with Celltracker green, a thiol sensitive dye, and Mitotracker red, a dye sensitive to the mitochondrial membrane potential. Flow cytometry, semiquantitative reverse transcription polymerase chain reaction and Western blot analysis were carried out to evaluate phenotypic and biosynthetic activities and the signaling pathways involved in the differentiation process. Results Under hypoxic conditions, mesenchymal stem cells formed large aggregates and exhibited positive Celltracker and Mitotracker signals. Glucose transporter-3, matrix metalloproteinase-2, collagen type II and type XI, and aggrecan mRNA and protein expression was upregulated, whereas there was no change in the levels of decorin, biglycan, fibromodulin, and lumican. Hypoxia maintained the expression of CD44 (hyaluronan receptor), ALCAM (CD166), and endoglin (transforming growth factor-beta receptor). Likewise, expression of beta3 and alpha2 integrin was upregulated. Transforming growth factor-beta treatment increased MAPK activity and Sox-9, aggrecan, and collagen type II gene expression. Basal levels of the phosphorylated MAPK isoform ERK1/2, but not p38, were higher under hypoxic conditions than normoxia, and its activation was further augmented by treatment of cells with transforming growth factor-beta. In hypoxia, transforming growth factor-beta sustained phosphorylated p38 expression for an extended time period. Pharmacological inhibition of ERK1/2 and p38 enzymatic activity resulted in a decrease in Sox-9, aggrecan, and collagen type II mRNA levels. Conclusions Our results indicate that hypoxia and transforming growth factor-beta drive mesenchymal stem cell differentiation towards a phenotype consistent with that of the nucleus pulposus. Measurement of selected signaling molecules and response to specific inhibitors suggest involvement of MAPK signaling pathways. It is concluded that mesenchymal stem cells could be used to repopulate the damaged or degenerate intervertebral disc.

Cancer Cytogenomics Microarray Consortium Third Annual Meeting, August 6e7, 2012 SESSION1:HEMATOLOGICMALIGNANCIES Clinical Laboratory Implementation of the Detection of Genomic Aberrations in Formalin-Fixed ParaffinEmbedded Small Lymphocytic Lymphoma Specimens by Array-CGH Charles Ma, Asha N. Guttapalli, Lizalynn M. Dias, Lynnette M. Cahill, Lan Wang, Jane Houldsworth Cancer Genetics Inc., Rutherford, NJ Due to the highly variable course of the disease, risk stratification is essential for the management of chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL) patients. For CLL, assessment of prognostic molecular markers including IGHV mutation status and specific genomic aberrations by either FISH and/or, more recently, array-CGH is routinely performed. The same molecular markers have been shown to offer similar prognostic value in SLL. However, the clinical diagnostic evaluation of these markers in SLL is hampered by the solid tissue type. Indeed, formalin-fixed, paraffin-embedded (FFPE) material is often the only available specimen for analysis. Using over 300 FFPE samples, we have established appropriate laboratory procedures and QC matrices for the clinical implementation of array-CGH for FFPE samples. In brief, DNA is extracted from 5 ten micron FFPE sections, and then a minimum of 1ug of DNA is heat fragmented, labeled enzymatically, and hybridized with a similarly fragmented commercial reference DNA to a custom-designed DNA oligonucleotide microarray representing genomic regions that are commonly altered in mature B-cell neoplasms. For ten SLL FFPE samples, adequate DNA was isolated and found to be of varied quality. Using ADM-2, the same genomic aberrations as commonly found in CLL (13q14 loss (MIR15A/16-1), 17p13 loss (TP53), and 11q22 loss (ATM)) were detected in the SLL specimens with high reproducibility and accuracy. DNA dilution studies indicated an analytical sensitivity of 60%70% while FISH in the specimens for detected aberrations revealed sensitivity closer to 30%-40%. All aberrations detected by array-CGH were independently validated by quantitative PCR for genes mapped within the respective regions. Thus, our data indicated that array-CGH is suitable for the detection 2210-7762/$ see front matter a 2012 Elsevier Inc. Elsevier Inc. http://dx.doi.org/10.1016/j.cancergen.2012.07.004 of prognostic genomic aberrations in SLL in a clinical diagnostic setting that could be implemented in patient risk stratification. Conflict of Interest: These authors are employees of Cancer Genetics, Inc., Rutherford, NJ. Array-Based Karyotyping Post Plasma Cell Enrichment for the Detection of Genomic Abnormalities in Multiple Myeloma Barbara K. Zehentner , Luise Hartmann , Krystal Johnson , Christine Stephenson , Douglas Chapman , Monica de Baca , Denise A. Wells , Michael R. Loken , Budi Tirtorahardjo , Shelly R. Gunn , Lony Lim b HematoLogics Inc., Seattle WA; Combimatrix, Irvine, CA Multiple myeloma (MM) is a hematopoietic neoplasm characterized by malignant plasma cells. The discovery of genomic abnormalities present in the monoclonal plasma cells has diagnostic, prognostic, as well as disease monitoring implications. However, technical and disease-related limitations hamper the detection of these abnormalities by metaphase cytogenetic analysis or FISH. In this study, we tested 28 bone marrow specimens with known plasma cell neoplasm for the presence of genomic abnormalities using microarray analysis post plasma cell enrichment and compared the results with other laboratory findings. Metaphase cytogenetic studies were performed on 15 of the 28 samples and identified disease-related genomic aberrations in only 3 of the 15 cases (20%) due to the low proliferative rate of plasma cells; 84.6% of specimens tested positive by MACS-FISH and 89.3% by array comparative genomic hybridization (aCGH). Furthermore, aCGH detected additional abnormalities in 24 cases as compared with FISH alone. We conclude that the combination of plasma cell enrichment and genomic copy number assessment using CGH microarray is a valuable approach for routine clinical use to achieve a more complete genetic characterization of multiple myeloma patients. Conflict of Interest: Employment, stock ownership.

Abstract 1773 Risk stratification in chronic lymphocytic leukemia (CLL) is highly desirable and should comprise not only evaluation of clinical features but also molecular prognostic markers. Currently such molecular markers include loss of 17p13, 11q22, 13q14, 6q22, and gain of chromosome 12 as assessed by fluorescence in situ hybridization (FISH) and mutation status of the variable region of the IGH gene (IGHV) by sequencing. In recent years, genome-wide scanning technologies such as array-comparative genomic hybridization (array-CGH) have revealed novel and refined known copy number alterations (CNAs) in the CLL genome. In order to evaluate the potential of array-CGH in prognostication in mature B-cell neoplasms, including CLL, and implement array-CGH in a clinical diagnostic laboratory, a targeted oligonucleotide-based microarray was custom designed to represent genomic regions exhibiting gain/loss in these lymphoid neoplasms. The 4 × 44K formatted array included 2 × 17,348 probes for the 80 selected genomic regions (average resolution of 34kbp), and recommended controls including a 1Mbp genome backbone. DNA extracted from two CLL datasets were submitted to array-CGH using an equimixture of commercially available male/female DNA as a reference. CNAs were detected using Genomics Workbench Lite (Agilent Technologies, Inc.) with the ADM2 algorithm. Analytical sensitivity was assessed by cell line DNA dilution and by FISH (116 specimens) and was 30–40% and 20–25%, respectively. Recurrent CNAs in previously untreated patients, greater than 1.5Mbp in size, were analyzed for association with time to first treatment (TTFT) and overall survival (OS) by the log rank test. Association with IGHV mutation status was tested using the Fisher's two-sided exact test. In both datasets for untreated specimens, unmutated IGHV negatively correlated with both TTFT and OS significantly (p < 0.05). Gain of chromosome 12 was detected in 11–12% of untreated specimens in both datasets and as expected did not associate with outcome. Loss of 13q14 as a sole abnormality (excluding copy number changes arising at known sites of normal variation) was associated with an overall favorable outcome, but specimens with loss of both loci (MIR15A/16-1 and RB1) versus one locus (MIR15A/16-1) did not display significantly different outcomes. As expected loss of 17p13 associated with shorter TTFT and OS, and was observed at higher levels in treated specimens. A similar result was observed for 11q22 loss but not in the second dataset, perhaps due to the relatively short follow-up time. Importantly, four additional copy number changes (gain of 2p, 3q, and 8q, and loss of 8p) were found to associate with shorter TTFT and/or OS, and also occurred at higher frequency in treated specimens. Notably, all but one specimen exhibiting two of these CNAs, were Rai Stage 0-II. After multiple comparisons correction, gain of 2p and 3q, and loss of 8p remained significantly associated with an unfavorable outcome. Gain of 2p25.3-p15 was observed exclusively in unmutated IGHV specimens. Loss of 18p and gain of 17q24 were not considered further for testing due to low frequency or lower frequency in treated specimens (data not shown). Uniquely, these data demonstrate in low-intermediate risk CLL cohorts the prognostic value of genomic gain/loss at multiple sites and support implementation of array-CGH into a clinical setting for risk stratification in CLL where genomic gain or loss of multiple clinically relevant genomic regions can be assessed simultaneously. Dataset 1 Untreated n = 81 TTFT p-value OS p-value Treated n = 38 Dataset 2 n = 169 TTFT p-value OS p-value Treated n = 28 Median TTFT 87.6 mo 24.1 mo Median OS 117.7 mo 37.2 mo Rai Stage 0 25 77 I-II 42 48 III-IV 5 1 na 9 43 Unmutated IGHV 46% (n=80) 0.0003 0.0004 38% (n=163) 0.002 0.044 13q14 loss (sole abnormality) 52.5% 0.038‡ 0.087‡ 33.7% 0.144‡ 0.008‡ MIR15A/16-1, RB1 27.5% 0.77 0.337 11.2% 0.011 1 MIR15A/16-1 25.0% 22.5% 11q22 loss (ATM) 12.3% 0.125 0.009 23.7% 8.3% 0.393 0.977 14.3% 17p13 loss (TP53) 2.5% 0.010 0.012 15.8% 4.7% 0.006 Disclosures: Houldsworth: Cancer Genetics, Inc.: Employment. Guttapalli:Cancer Genetics, Inc.: Employment. Ma:Cancer Genetics, Inc.: Employment. Chen:Cancer Genetics, Inc.: Employment. Patil:Cancer Genetics, Inc.: Consultancy.