Baker, Angela

Abstract Abstract 606 Multiple myeloma is a complex malignancy with multiple underlying genetic events. Our group has spent considerable effort over the last 15 years to elucidate the genetic underpinnings of myeloma. Most recently, we used array-based comparative genomic hybridization (aCGH) as a discovery tool in 62 myeloma patients and 46 myeloma cell lines. In that preliminary screen using the Agilent 44B aCGH platform (∼70kb resolution) we identified a diverse array of abnormalities, which resulted in constitutive activation of the NF-kB pathways. That initial analysis concentrated on the 43 genes we identified as potential targets of the 13 homozygous deletion events detected in the patient samples. A pathway analysis of these genes revealed a single pathway involving TRAF3, TRAF2, BIRC2, BIRC3, and CYLD. This first analysis focused exclusively on abnormalities present in the patient samples as we worried some abnormalities identified exclusively in the cell lines might not be relevant to the pathogenesis of myeloma in patients. However, several abnormalities were equally or more frequent overall but occurred exclusively in cell lines including CDKN2C (14 samples), CDKN1B (4 samples), KDM6A/UTX (4 samples), RB1 (3 samples), TP53 (3 samples). Given the fact that KDM6A/UTX deletions were as frequent as many of the best-described tumor suppressors it seemed like a good candidate but in the absence of patient events or a known function at the time it was not prioritized for further study. Recently, as part of the Multiple Myeloma Research Consortium (MMRC) Genomics Initiative, we have completed the analysis of a cohort of 250 myeloma patient samples by aCGH using the Agilent 244A aCGH platform (∼15kb resolution) and gene expression profiling using the Affymetrix U133Plus2.0 genechip. In this cohort with a significantly improved aCGH platform we identified 17 genes that are recurrently inactivated by homozygous deletions including DIAPH2 (15 samples), CDKN2C (14 samples), TRAF3 (11 samples), CYLD (8 samples), BIRC2/3 (7 samples), KDM6A/UTX (6 samples), and RB1 (5 samples). Based on the significant improvement in resolution and data quality achieved with the Agilent 244A aCGH platform we rescreen all of the cell lines on this improved platform. This significantly changed the frequency of several homozygous deletions in this population with the most frequently targeted genes now being CDKN2C (20 samples), KDM6A/UTX (13 samples), DIAPH2 (7 samples), RB1 (4 samples), TP53 (4 samples), CDKN1B (4 samples), and TRAF3 (4 samples). Moreover, as part of the genomic characterization of a spontaneous myeloma mouse model that we have developed, Vk*-Myc, we have identified recurrent (∼50%) homozygous deletions of Kdm6a/Utx. Therefore, one of the genes most commonly targeted by a homozygous deletion in human and mouse myeloma is KDM6A/UTX. In late 2007 after we had identified the first patients with KDM6A/UTX deletions it was shown that UTX is a functional histone demethylase that removes methyl groups from histone H3 lysine 27 (H3K27me). Given the high incidence of deletions and the fact that MMSET, the overexpressed target gene of t(4;14) in myeloma, is predicted to methylate H3K27, H3K36, and/or H4K20 by evolutionary conservation we developed the hypothesis that myeloma is characterized by abnormalities that result in excessive H3K27me (typically a repressive chromatin mark). Given the extensive whole genome sequencing occurring in the MMRC genomics initiative we elected to focus our resequencing efforts on the cell lines exclusively. These studies identified an additional 4 samples with LOH and an inactivating mutation bringing the total percentage of inactivated cell lines to 33%. Clearly, in the expanded patient and cell line cohorts the inactivation of KDM6A/UTX is not independent of MMSET overexpression suggesting they may act independently or synergistically. We are currently attempting to identify the genes controlled by KDM6A/UTX inactivation to better understand the functional consequences of this highly recurrent event. However, in the mouse model unlike the patient or cell lines, the gene expression profiling has identified a gene expression signature that differentiates UTX inactivated and functional samples suggesting an oncogenic function of inactivation. Disclosures: No relevant conflicts of interest to declare.

Abstract Waldenström macroglobulinemia (WM) is a lymphoid neoplasm associated with accumulation of lymphoplasmacytic cells in the bone marrow and an elevated monoclonal IgM in the serum. Although the genetic and molecular mechanisms behind the pathogenesis of WM are not well understood, losses of the long arm of chromosome 6 have been found as the only recurrent genomic aberration. These deletions, mostly starting at 6q21, are observed in upwards of 50% of patients and involve the majority of the clonal cells. To better characterize pathologic gene expression signatures in different types of WM at the molecular level (6q deleted versus not), we examined gene expression level changes of more than 20000 human gene probes in bone marrow tissues of clinically proven WM patients. We used Affymetrix HG-U133A v2 chips (n = 24). Clonal cells were purified using a combination of anti-CD138 and anti-CD19 Miltenyi™ magnetic microbeads. Based on cIgM-FISH results, we classified samples into two groups - 6q normal (ND) group and 6q deletion (D) group. We then proceeded to identify genes that showed differential expression between the two groups. We selected 165 differentially expressed genes (DEG) using SAM, and underwent further investigation of biological annotations of them using Gene Ontology™ (GO) terms. Among165 DEG, only 32 showed high level of expression in ND group compared to D group while 133 showed high level of expression in D group. As expected, all genes that reside in 6q region showed under-expression in D group, constituting 53% (17 genes) of genes under-expressed in D group (32 genes). According to GO analysis, the 6q-deletion-induced under-expression affects many biological processes, and is associated with a transcriptional upregulation of downstream genetic cascades. This likely indicates release of regulatory control by a tumor suppressor gene. Genes involved in cell growth and maintenance, cell communication and morphogenesis are also over-expressed in D group. Interestingly, a gene that is involved in innate immune response and inflammatory response shows under-expression in D group but is not accounted for by other mechanisms. In similar vein, a gene that is involved in negative regulation of cytokine biosynthesis showed over-expression in D group. We think these transcriptional characteristics can provide basic framework for differentiating subtypes of WM and search for genes associated with WM pathogenesis

Abstract Abstract 604 We have conducted a pilot study to interrogate both CpG hyper- and hypomethylation in Multiple Myeloma (MM) using the Illumina GoldenGate (GG) BeadArrayTM high-throughput assay. Specifically, we utilized the Illumina Methylation Cancer Panel I, which spans 1,505 CpG loci selected from 807 genes including known tumor suppressor genes and oncogenes. To date we have profiled 50 CD138+ MM specimens, 4 MM cell lines and 6 normal CD138+ plasma cell samples (each representing a pool of 3-5 individuals) obtained from the bone marrow of patients who have undergone hip or knee replacement surgeries. We have obtained highly reproducible and reliable DNA methylation profiles with an average r2 of greater than 0.98 when the β values were compared between technical replicates. Further, we generated an internal control panel for the array by performing methylation specific PCR (MSP) to determine the methylation status of several genes found on the array (CDKN2A, E-Cadherin, MGMT, hMLH1) in 4 MM cell lines. A differential methylation analysis was conducted between normal plasma cells and MM samples using the BeadStudio Methylation Module v3.2. Differential scores for each CpG locus on the array were generated that correspond to significant differences between groups. Scores greater than (hypermethylation) or less than (hypomethylation) 13 represent ‘Diff scores' that are statistically significant (p values < 0.05) and this cut-off threshold is used to determine differentially methylated loci. Globally, when comparing MM to normal plasma cells, hypomethylation occurred at 42% of probes on the array, and was more common than hypermethylation, which occurred at only 21% of probes. Interestingly, 77% of probes situated in non-CpG islands were hypomethylated compared to 26% or probes in CpG islands. On the contrary hypermethylation occurred mainly in CpG islands (26% of probes) whereas only 7.4% of probes in non-CpG islands were considered hypermethylated. A total of 946 CpG loci were differentially methylated between normal plasma cells and MM. Among the most significantly differentially methylated CpG loci between normal plasma cells and MM were FZD9, ALOX12, MMP-3, MMP-8, and p16. Array comparative genomic hybridization (aCGH) data availabel for this same sample set was used to generate a hyperdiploid index for each sample by identifying those samples with whole chromosome gains at minimally three odd numbered chromosomes. There were 751 CpG loci that were differentially methylated between hypderdiploid and non-hyperdiploid tumors with WEE1, FRZB, ELK1, CLDN4, and SHH being among the most significant. We also applied the pathway enrichment analysis tool GeneGo v5 (Agilent) to these data, which identified cell adhesion/ECM remodeling, developmental pathways and several immune response pathways as the most significantly enriched pathways between normal and plasma cells with ephrin signaling pathways in the context of cell adhesion as the most significantly enriched pathway between hyperdiploid and non-hyperdiploid tumors. We hope to integrate methylation data with orthogonal datasets including gene expression, aCGH, and DNA sequence data being developed as part of the MMRF Genomics Initiative. Further validation of hits will also be followed up by functional studies to assess the true biological relevance of differentially methylated genes. This study represents one of the first methylome interrogation studies in MM and points towards global hypomethylation as possibly an important mechanism driving myelomagenesis. Our data also suggest that differential methylation of genes may be a significant determinant of hyperdiploid biology. Determining the set of critical genes and pathways based on the myeloma methylome is likely to lead to an improved understanding of biological mechanisms involved in myelomagenesis, ultimately leading to new and improved methods of diagnosing and treating this disease. Disclosures: No relevant conflicts of interest to declare.

Abstract Abstract 1923 Our understanding of the genetic abnormalities associated with the development of multiple myeloma has increased significantly in the last decade. However, very little is known about how, or if, myeloma tumor genomes change with time and if therapeutic interventions influence these events. To address these issues we studied a cohort of 29 patients for whom at least two serial samples (1-65 months, median 19 months) were available for analysis. Each serial pair was analyzed by both array-based comparative genomic hybridization (aCGH) and microarray gene expression profiling (GEP) to identify DNA copy number abnormalities (CNA) at a 25kb resolution and gene expression differences present in the bulk of the tumor mass. Though this does not address the intra-clonal heterogeneity that may exist at a given time point, it does answer if the bulk of the tumor mass is changing with time. This study has unearthed several surprising and clinically relevant findings. First, myeloma tumor genomes are not as unstable as previous cytogenetic analyses suggest. In 40% of patients we observed no detectable CNA changes (1-37 months, median 12 months). In 24% of patients we observed the exclusive acquisition of new CNA (1-12, median 3.5) (3-22 months, median 18 months). In 36% of patients we observed both the loss (1-20, median 3) and gain (1-33, median 21) of CNA (5-43 months, median 20 months). Because time was not a significant influence on the detection of stable or unstable genomes we compared CNA changes with TC class and found patients with the high-risk 4p16 and maf IgH translocations were over-represented in the latter subset of patients. These observations raise the question of what happens between multiple rounds of therapy and if different regimens influence these phenotypes differently. For two patients with no CNA changes between the first two time points there was an additional sample that extended the follow-up by 52 and 12 months. Again no CNA changes were seen between diagnosis and these final samples taken 63 and 50 months later. For one patient with CNA changes (5 shared, 29 lost, and 32 gained) we have a detailed time course of 5 samples from diagnosis through to end-stage plasma cell leukemia. This patient received continuous lenalidomide-dexamethasone (Rd) for 20 months and progessed with a clone containing a BIRC2/3 deletion, which activates the NFKB pathway. The patient received single agent PR-171 and a bortezomib containing regimen and unexpectedly, the tumor genome observed in the third sample was almost identical (32 shared, 2 lost, and 4 gained CNA) to the first time point, including two copies of BIRC2/3. Subsequently, the patient received melphalan-prednisone-bortezomib (MPV) and the tumor genome observed in the fourth and fifth samples, which were identical, were similar to that seen in the second sample (24 shared, 13 lost, and 39 gained CNA). To understand these observations better we performed FISH to ascertain if the observed clones were detectable earlier, albeit at a low frequency. These experiments proved that the two dominant subclones observed at time points 1 and 3 versus 2, 4, 5 were mutually exclusive at the single cell level. Moreover, both of these clones were detectable at diagnosis with 12% of the tumor mass being the second subclone that eventually evolved into plasma cell leukemia. Interestingly, we assayed 5 of the 39 unique CNA observed in the final two samples and only one, the 17p13 deletion, was detectable earlier. This suggests the MPV regimen effectively eliminated a clone that was previously sensitive to Rd and selected for a dramatically evolved subclone that was previously sensitive to two different proteasome inhibitors. Although it is clear that the high-risk patients are enriched in the subset with the most changes, it is not clear if the specific drugs used (Melphalan vs IMID vs proteasome inhibitor) or intervention strategy (Cycled vs continuous/maintenance) and perhaps the response achieved (PR vs CR) influences these events. These observations do highlight two important clinical concepts that need to be considered in the future. First, the meaning of a partial response needs further investigation as this may reflect effective elimination of one subclone but not another. Second, because some patients are not changing or can revert back to a previous subclone we need to consider re-chanllenging patients with previously effective regimens when patients progress. Disclosures: Fonseca: Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties. Stewart:Millennium: Consultancy; Celgene: Honoraria. Bergsagel:Amgen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Genentech: Membership on an entity's Board of Directors or advisory committees; Millennium: Speakers Bureau; Novartis: Speakers Bureau.

Abstract In an attempt to identify novel genetic abnormalities in multiple myeloma (MM) we analyzed 68 MM patient samples and 42 human myeloma cell lines (HMCL) with high-resolution (60kb) array-based comparative genomic hybridization (aCGH). We concentrated on bi-allelic genomic deletions with the expectation that these regions might contain novel tumor suppressor genes and identified a common abnormality at 14q32. Fine mapping of the 14q32 microdeletion by PCR demonstrated a 45 kb minimal deletion encompassing two genes; TRAF3, a negative regulator of the non-canonical NF-kB pathway, and AMN. To determine the frequency of copy number abnormalities of this region a cohort of 161 patients were screened with a FISH probe mapping to the minimally deleted region. This identified 7 (4.4%) patients with bi-allelic deletion and 19 (11.8%) patients with a single copy of the target region. Sequencing of all TRAF3 coding exons in 62 patients and 42 HMCL identified inactivating mutations in 9 patient samples and 4 HMCL. Overall, the incidence of TRAF3 inactivation, bi-allelic deletion or mutation, is 7/42 (16.7%) in HMCL and 12/62 (19.4%) in patients, making it one of the most common genetic abnormalities identified in MM. Importantly, dysregulation of NF-kB pathways is a common event in MM, but the mechanism for this dysregulation is largely unknown. Although TRAF3 is a negative regulator of the non-canonical NF-kB pathway it has not previously been implicated in cancer. Therefore, we tested the tumor suppressor function of TRAF3 by reintroducing TRAF3 into HMCL harboring TRAF3 abnormalities using an adenovirus gene transfer system. Expression of TRAF3 in HMCL with TRAF3 abnormalities rapidly reversed cellular processing of NFKB2 from p100 (an inactive isoform) to p52 (active) and additionally led to a 60% reduction in cellular proliferation (range, 10–89%) associated with Go/G1 cell cycle arrest and induction of cell death by apoptosis. At 48 hrs post infection the proportion of cells entering S-phase or G2/M declined by 31% (range, 8.1–56.1) and the proportion undergoing apoptosis increased by 28% (range 11.7–47.4%). In contrast, over-expression of TRAF3 in control HMCL without TRAF3 abnormalities had no effect. Overall, TRAF3 is identified as a novel tumor suppressor that regulates the non-canonical NF-kB pathway and is inactivated in ~ 20% of MM patients. Given the involvement of the NF-kB pathway in multiple human malignancies and the near constitutive expression of TRAF3 we propose that inactivation of TRAF3, a novel tumor suppressor identified for the first time in this study, may occur in other cancers. In this regard, we have recently identified a Burkitt lymphoma cell line that does not express TRAF3 and thus has constitutive processing of p100 to p52. The clinical and therapeutic consequences of this finding and its frequency in other tumor types are currently the focus of further investigation. In conclusion, the abnormalities identified in this study represent the first mutations identified that cause constitutive NF-kB activation in MM.

Abstract Abstract 832 We hypothesized that new therapeutic targets for multiple myeloma (MM) could be discovered through the integrative computational analysis of genomic data. Accordingly, we generated gene expression profiling and copy number data on 250 clinically-annotated MM patient samples. Utilizing an outlier statistical approach, we identified HOXA9 as the top candidate gene for further investigation. HOXA9 expression was particularly high in patients lacking canonical MM chromosomal translocations, and allele-specific expression analysis suggested that this overexpression was mono-allelic. Indeed, focal copy number amplifications at the HOXA locus were observed in some patients. Outlier HOXA9 expression was further validated in both a collection of 52 MM cell lines and 414 primary patient samples previously described. To further verify the aberrant expression of HOXA9 in MM, we performed quantitative RT-PCR, which confirmed expression in all MM patients and cell lines tested, with high-level expression in a subset. To further investigate the mechanism of aberrant HOXA9 expression, we interrogated the pattern of histone modification at the HOXA locus because HOXA gene expression is particularly regulated by such chromatin marks. Accordingly, immunoprecipitation studies showed an aberrantly low level of histone 3 lysine 27 trimethylation marks (H3K27me3) at the HOXA9 locus. H3K27me3 modification is normally associated with silencing of HOXA9 in normal B-cell development. As such, it appears likely that the aberrant expression of HOXA9 in MM is due at least in part to defects in histone modification at this locus. To determine the functional consequences of HOXA9 expression in MM, we performed RNAi-mediated knock-down experiments in MM cell lines. Seven independent HOXA9 shRNAs that diminished HOXA9 expression resulted in growth inhibition of 12/14 MM cell lines tested. Taken together, these experiments indicate that HOXA9 is essential for survival of MM cells, and that the mechanism of HOXA9 expression relates to aberrant histone modification at the HOXA9 locus. The data thus suggest that HOXA9 is an attractive new therapeutic target for MM. Disclosures: No relevant conflicts of interest to declare.

Abstract The plasma cell malignancy Multiple Myeloma (MM) is a rare but deadly form of cancer with 5 year survival rates of ∼30%. Epidemiological studies have suggested that MM exacts an especially heavy burden on African American (AA) patients. We examined a multi-ethnic cohort of MM tumors to assess potential differences in the frequency of molecular events in tumors derived from either African American (AA) or European American (EA) patients. The frequency of 14q32 translocation breakpoints at the IgH locus was compared among a series of data from 115 AA MM patients from three studies and EA MM from the Eastern Cooperative Oncology Group (ECOG). In addition, we analyzed matching genome-wide copy number and transcriptional data among 45 AA MM tumors and 196 EA MM tumors to determine differences in the frequency of molecular events in tumors from these populations. No differences were found for specific translocation subtypes; however, we detected a statistically significant difference in the overall frequency of IgH translocations between the two groups, which occurred more frequently in EA patients (52% vs. 40%; p = 0.032). When assessing genomic copy number events previously shown to be associated with poor outcome in MM, frequencies of alterations were not significant after correcting for multiple testing. Furthermore, there was not a significant difference in the association of high-risk disease using expression profiling. Our study represents the first comprehensive assessment of the frequency and distribution of molecular alterations in MM tumors from both AA and EA patients and could help shed light on possible biological features associated with population differences in incidence and outcome in MM. Citation Format: Angela S. Baker, Esteban Braggio, Susana Jacobus, Sungwon Jung, Dirk Larson, Terry Therneau, Angela Dispenzieri, Scott A. Van Wier, Gregory Ahmann, Joan Levy, Louise Perkins, Seungchan Kim, Kim Henderson, David Vesole, S. Vincent Rajkumar, Dianne F. Jelinek, John Carpten, Rafael Fonseca. Characterization of myeloma tumors from a multi-ethnic cohort using cytogenetics and genomic analysis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2021. doi:10.1158/1538-7445.AM2013-2021

Key PointsIn this study, African American MM patients have a significantly lower frequency of IgH translocations than European American patients.

Abstract Purpose: Pancreatic adenocarcinoma is among the most lethal forms of all malignancies. While significant research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult. The majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to assess global somatic events across multiple pancreatic tumors by using next-generation sequencing technologies (NGS). Experimental Design: We performed whole genome sequencing (WGS) on paired tumor and normal samples from 3 pancreatic adenocarcinoma patients. Additionally, we performed whole transcriptome sequencing (WTS) on 2 of these patients’ tumors for which tumor RNA was available. Results: We generated on average 132 billion mappable bases across all patients using WGS, and identified 140 somatic coding events including point mutations, insertion/deletions, and chromosomal copy number variants. Data from WGS and WTS were integrated and analyzed to identify the most heavily affected pancreatic cancer pathways across all patients. The KRAS signaling pathway was identified as the most significant map. Unbiased global pathway analysis was also performed to identify processes that may be impacted. Consistent with the previous analysis, the most significant pathway from this analysis is also KRAS signaling. This integrated analysis specifically identifies heavily affected pathways in pancreatic cancer and pinpoints genes and processes that may be considered as targets for more effective therapies. Conclusions: While sequencing of additional patients is necessary to strengthen selection of key pathways, we demonstrate the utility of using NGS to understand the processes driving pancreatic adenocarcinoma so that standardized treatments for patients may be improved. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5104. doi:1538-7445.AM2012-5104