Wier, Scott Van

Abstract Hyperdiploid MM (H-MM), characterized by recurrent trisomies constitute about 50% of MM, yet very little is known about its pathogenesis and oncogenic mechanisms. Studies in leukemia and solid tumors have shown gene dosage effect of aneuploidy on gene expression. To determine the possible gene dosage effect and deregulated cellular program in H-MM we undertook a gene expression study of CD138-enriched plasma-cell RNA from 53 hyperdiploid and 37 non-hyperdiploid MM (NH-MM) patients using the Affymetrix U133A chip (Affymetrix, Santa Clara, CA). Gene expression data was analyzed using GeneSpring 7 (Agilent Technologies, Palo Alto, CA). Genes differentially expressed between H-MM and NH-MM were obtained by t-test (p<0.01). The majority of the differentially expressed genes (57%) were under-expressed in H-MM. Genes located on the commonly trisomic chromosomes were mostly (but not always) over-expressed in H-MM and constitute 76% of over-expressed genes. Chromosome 1 contained the most differentially expressed genes (17%) followed by chromosome 12 (9%), and 19 (8%). To examine the relationship of gene copy number to gene expression, we examined the expression of genes on chromosomes 9 and 15 in subjects with 2 copies (15 normal control and 20 NH-MM) and 3 copies (12 H-MM) of each chromosome as detected by interphase FISH. We then derived a ratio of the mean expression of each gene on these chromosomes between patients with 3 copies and 2 copies of the chromosome. If a simple relationship exists between gene expression and gene copy number, one would expect the ratio of expression of most genes on these two chromosomes to be about 1.5 in H-MM compared to NH-MM. However, many genes have ratios either higher than 2 or lower than 0.5. Furthermore, when the heterogeneity of cells with underlying trisomies is taken into consideration by correcting the ratio for the number of cells with trisomies, the actual ratio is always lower than the expected ratio. When the expression of genes on a chromosome was compressed to a median value, this value was always higher in the trisomic chromosomes for H-MM compared to NH-MM. The data suggests that although gene dosage influence gene expression, the relationship is complex and some genes are more gene dosage dependent than others. Amongst the differentially expressed genes with known function, 33% are involved in mRNA translation/protein synthesis. Of note, 37 of the top 100 differentially expressed genes are involved in these processes. In particular, 60 ribosomal protein (RP) genes are significantly (p<0.05) upregulated in H-MM. This signature in H-MM is not associated with increase proliferation as measured by PCLI. This predominant signature suggests that deregulated protein synthesis may be important for the biology of H-MM. Many of these RPs are involved in the synthesis of product of oncogenic pathways (e.g. MYC, NF-KB pathways) and may mediate the growth and survival of tumor cells. It is therefore possible that these tumor cells may be sensitive to the disruption of mRNA translation/protein synthesis. Targeting the mTOR pathway with rapamycin may therefore be useful for treatment of H-MM.

Abstract Introduction: Molecular cytogenetic studies have revealed that, to a great extent, the heterogeneity of myeloma is largely dictated by the underlying genetic and cytogenetic aberrations present in the clonal plasma cells. Most recently the group from the University of Arkansas identified strong prognostic associations with an increased level of gene expression of a cell cycle associated gene, CKS1B. CKS1B favors cell cycle progression by promoting degradation of p27 with release of the cyclin dependent kinases and entry into mitosis. Patients and methods: To further test this hypothesis we studied: a) via FISH for CKS1B amplification in a cohort of patients treated at the Mayo Clinic with high dose chemotherapy and stem cell support, as well as a group of patients with cytogenetically defined hypodiploidy, and b) a cohort of myeloma patients that were studied by gene expression profiling. Gene expression analysis was performed on CD138-enriched plasma-cell RNA using Affymetrix U133A chips (Affymetrix, Santa Clara, CA). Results: Of 159 patients studied 46 exhibited FISH abnormalities consistent with increase number of signals for CKS1B (30%): amplification was marginal or low in 44 cases, and in only two cases the ratio between CKS1B and control probe was greater than 2.0. Therefore, the predominant pattern is one of gene duplication rather than amplification where gene copy usually exceeds 10 and ratio with control probe exceeds 5 (e.g. HER-2/neu amplification). Patients with CKS1B duplication had a higher prevalence of chromosome 13 deletion (72%), and t(4;14) (29%). The presence of CKS1B duplication was more frequent (53%) among 19 patients with hypodiploidy. Using gene expression data for CKS1B, we found a positive association with t(14;16)(q32;q23). The level of CKS1B gene expression positively correlated with the PCLI (p<0.0001) but there was heterogeneity in this relationship (r2 = 0.34). We found no correlation between the expression level of CKS1B and p27 (r2 = 0.008, p = 0.37). While CKS1B gene duplication had a negative effect on survival this effect was weak (29.9 versus 38 months, p = 0.124. Median follow-up is 55 months) and disappeared when the variable was entered into the multivariate model including PCLI, B2-microglobulin and all the major genetic abnormalities by FISH. Likewise the level of expression of CKS1B determined by gene expression only carried prognostic significance when extreme levels of expression were utilized as a prognostic variable. Discussion: In this study we show that increase copy number of CKS1B is present in one third of patients with MM (majority of these being gene duplication) and seem to be associated with a shorter overall survival, but the net effect of this is rather weak in our series. Further study is needed to understand its potential role as a progression factor in the plasma cell neoplasms.

Abstract H-MM affects about 40–50% of patients, and a similar proportion of MGUS/SMM. The genetic evolution of the disease and the clinical implications of the co-existence of 13q- or t(14q32) are unknown. We conducted a global survey of genetic abnormalities in H-MM in order to describe genetic evolution pathways. H-MM cases from the Mitelman cancer genetic database were combined with cases from the Mayo Clinic MM genetic database. All abnormalities (regional/whole chromosome gains/losses, breakpoints and translocations) were plotted against a 344-chromosome band profile created in a matrix format, and the number of genetic abnormalities per tumor (NAPT) logged. The abnormalities present in more than 5% of tumors were considered recurrent and each karyotype was scored for the presence or absence of each of the recurrent abnormalities. To investigate the temporal pattern of acquisition of genetic abnormalities, all tumors with a given abnormality were selected and the distributions of NAPT plotted. The modes of these distributions were used as a value of ‘lateness’, referred to as time of occurrence (TO). The impact of co-existence of 13q- and t(14q32) on progression free survival (PFS) and overall survival (OS) in H-MM was determined for MM patients entered into an Eastern Cooperative Oncology Group chemotherapy trial. Four hundred and sixty-nine H-MM patients were included in the karyotypic analysis. The median chromosome number was 53 (range 48–74) and the median NAPT was 10 (range 1–25). The distribution of NAPT revealed a normal distribution, suggesting an obligatory acquisition of a given number of genetic abnormalities. The most common abnormalities were trisomies of chromosomes 3,5,7,9,11,15,19 and 21 affecting a third or more of the patients. Deletions and abnormalities of even-numbered chromosomes occur in 20% or less of patients. None of the more than 300 specific translocations detected were recurrent. However, 5 translocation breakpoints were recurrent including 14q32, 8q24 and 11q13. TO analysis suggest that for H-MM, the trisomies are early genetic events, translocations occur midway and deletions tend to be later events. Amongst the trisomies, correlation analysis does not suggest a particular order of acquisition. Clustering analysis using principal component analysis suggests that in H-MM, IgH translocations are secondary events associated with disease evolution rather than defining unique biological entities. Consistent with this, survival of H-MM patients is not affected by 13q- status but is negatively impacted by the presence of t(14q32) especially those with unknown partners (p<0.05). The data presented suggest that H-MM fit a proposed aneuploid model of cancer due to auto-catalytic chromosome reassortment (Duesberg et al Cell Cycle2003:2:202–210). The presence of tumor specific trisomies and the apparent similar phenotype induced by various combinations of trisomies are consistent with this model.

Abstract Waldenström’s macroglobulinemia (WM) is an incurable low-grade lymphoproliferative disorder characterized by bone marrow (BM) infiltration of a clonal population of small B-lymphocytes, plasmacytoid lymphocytes and plasma cells that secrete monoclonal IgM antibody. Because it is difficult to obtain tumor metaphases for karyotype studies, few recurrent chromosomal abnormalities have been reported and the genetic basis of the disease remains poorly defined. Therefore, we performed a comprehensive high-resolution study to identify genomic abnormalities involved in WM pathogenesis. Fifty-seven WM patients were analyzed using a combination of array-based comparative genomic hybridization (aCGH)(N=42); gene expression profiling (GEP)(N=22), DNA sequencing (N=24) and cIgM-FISH (N=57). Agilent 244A and Affymetrix U133 platforms were used in the aCGH and GEP experiments, respectively. An NF-κB index was calculated from GEP data, as a surrogate marker of NF-κB transcription activity. NFKB2 sub cellular localization was determined by immunofluorescence staining. Overall, 83% of samples have aCGH defined chromosomal abnormalities, with a median of 3 abnormalities per patient (range 0 to 27). We identified 16 recurrent regions of copy number change found in >5% (3 or more patients); 10 deleted and 6 amplified regions. The most common abnormality was the entire or partial deletion of 6q, identified in 40% of cases. Four nonoverlapped minimal deleted regions were identified on 6q (MDR1 to MDR4), each of them being present in at least 14 of 17 patients with the abnormality. Gain of 6p was the second most common abnormality (17%) and its presence was always concomitant with 6q loss. Other recurrent deletions were 13q14 (10%) and 7q22, 8p, 11q22-q23, 11q23-q24 and 17p11-p13 (7% each). Copy gains were identified as partial or entire gains of chromosomes 18 (17%), 4 (12%) and 3 (10%), 8q (10%) and Xq27.1-q28 (10%). Three patients had either homozygous deletions or LOH with mutations affecting both alleles of TRAF3 on 14q32. TRAF3 inactivation was correlated with an increased NF-kB transcriptional signature and it was associated with activation of the non-canonical NFkB pathway. Additionally, we identified the inactivation of TNFAIP3, another negative regulator of the NF-kB pathways, in one of 24 patients. Finally, interstitial deletions identified in 4 patients at 13q14 identified a 1.1 Mb MDR, including MIRN15A and MIRN16-1. These findings confirm that focal 13q14 deletion is not restrict to B-CLL and that the MIRN15A/MIRN16-1 abnormalities might be common to several indolent B-cell diseases. Overall, we identified TRAF3 and TNFAIP3 inactivation in 5.3% and 2.4%, respectively. To our knowledge, this is the first study showing the inactivation of bona fide tumor suppressor genes in WM patients. Furthermore, these genes are negative regulators of NF-kB signaling pathway, highlighting its biologic importance in sustaining and limiting growth in WM. Mutational activation of this pathway, which is normally activated by ligand-receptor interactions within the BM microenvironment, suggest a therapeutic role for inhibitors of NF-KB pathway activation in the treatment of WM.

Abstract Background: The free light chain (FLC) assay allows a nephelometric measurement of this free kappa and lambda light chains that circulate as monomers or dimers, not bound to the immunoglobulin heavy chain. Estimation of the free light chain levels and their ratio has utility in screening, prognostication and treatment response assessment in multiple myeloma, and is particularly useful in light chain myeloma. Previous studies have suggested that absence of a functional rearrangement on at least one of the IgH allele is the basis of light chain myeloma. Translocations involving the immunoglobulin heavy chain (IgH) locus on chromosome 14 can be detected using FISH in over half of the patients with myeloma. We hypothesized that presence of an IgH translocation may be associated with compromised production of heavy chains and leads to unbalanced, excess production of clonal light chain. Methods: From February 1988 to May 1992, 653 patients with previously untreated multiple myeloma were enrolled on the phase III clinical trial E9486. Serum free light chains were run on stored sera obtained at baseline in 495 patients as part of a previous study. Among these patients, 314 patients were previously studied using FISH for presence or absence of IgH translocations, p53 abnormalities and deletion 13 and were included in the current analysis. Results: The median difference between the involved and uninvolved FLC (FLCdiff) was higher among the group of patients with any IgH translocation abnormality compared to those with none (Figure 1). This was particularly evident among the patients with a t(14;16) who had the highest FLCdiff. In a multivariate analysis, we examined if the prognostic value seen with FLCdiff was independent of the presence of IgH translocations t(4:14) and t(14;16), which are associated with a worse outcome. The presence of t(4;14) or t(14;16) was associated with FLCdiff groups using a cutoff point of 185, with 13% of those with FLCd ≤185 and 27% of those with FLCd > 185 having the translocations (P= 0.008). At the cutoff value of 185, the prognostic value of the FLC-diff on progression free and overall survival appears to be independent of these high risk IgH translocations (P-value=0.03 and 0.003, respectively for PFS and OS) We then examined the prognostic value of the FLC-diff in the group of patients without these two high risk abnormalities and were able to confirm that they remained prognostic for PFS (P=0.009) and OS (p=0.005). However, among the group of patients with either of the two high risk IgH abnormalities, FLCdiff estimate added little to assessment of their outcome (P=0.97 and 0.20, respectively for PFS and OS). Conclusion: Elevated free light chain levels are associated with presence of IgH translocations and these patients are more likely to harbor the high risk genetic abnormalities. Routine FISH testing for patients with newly diagnosed myeloma will allow us to confirm these and allow better risk stratification of the patients. Additional work needs to be done to help us better understand the molecular basis for unbalanced light chain excretion by myeloma cells and the current finding of the association with IgH translocation abnormalities should form the basis for this work. Figure 1. Distribution of FLC ratio (inv vs. uninv) and FLC difference (inv − uninv) among patients. Solid squares represent patients with t(4;14) or t(14;16) or t(11;14) or other 14q32 translocation; open circles represent patients without t(4;14), t(14;16), t(11;14) and any other 14q32 translocations. The horizontal dashed lines refer to FLC ratio original values of 100 and 1000, and vertical dashed lines refer to FLC difference original values of 10 and 100. Solid line indicates significant association (P<=0.05) between the dichotomized FLC groups and translocation status. Figure 1. Distribution of FLC ratio (inv vs. uninv) and FLC difference (inv − uninv) among patients. Solid squares represent patients with t(4;14) or t(14;16) or t(11;14) or other 14q32 translocation; open circles represent patients without t(4;14), t(14;16), t(11;14) and any other 14q32 translocations. The horizontal dashed lines refer to FLC ratio original values of 100 and 1000, and vertical dashed lines refer to FLC difference original values of 10 and 100. Solid line indicates significant association (P<=0.05) between the dichotomized FLC groups and translocation status.

Abstract Table 1. Samples to p53 deletions p 53 deletion FISH aCGH FISH and aCGH MGUS 142 - - SMM 108 - - Newly diagnosed MM - 182 - Relapsed/refractory MM 62 156 19 HMCLs - 48 - Total 312 386 19 Background: Inactivation of p53 by mutation or allelic loss is a rare event in multiple myeloma (MM) at the time of disease diagnosis and believed to be more common in the late stages of the disease. Here we defined the prevalence of p53 deletions in monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), newly diagnosed MM, relapsed MM and human myeloma cell lines (HMCLs). Indirect mechanisms of p53 inactivation such as amplification of MDM2, or deletion of CDKN2A (p14ARF) were also investigated. Patients and Methods: A total of 631 MM samples and 48 HMCLs were analyzed for p53 abnormalities (Table 1) and compared with a cohort of plasma cell leukemia (PCL) previously published by us. Interphase fluorescence in situ hybridization (FISH) and highresolution array-based comparative genomic hybridization (aCGH) were used to detect p53 deletions. MDM2 amplification and p14ARF loss were evaluated by aCGH. Overall survival (OS) was estimated through Kaplan Meier method. Results: The prevalence of p53 deletions was 1.4%, 3.7%, 8.9%, 20% and 87.5% in MGUS, SMM, newly diagnosed MM, relapsed MM and HMCLs respectively (Figure 1). Of interest patients in first relapse showed a p53 deletion prevalence of 18% in comparison with 33% for patients in second relapse or more. We obtained p53 deletion status in 8 patients noted to have deletion at the time of relapse and in whom we had previous samples stored. In 7 of 8 cases deletions had been acquired (absent in the previous samples). The median OS for relapsed MM patients with or without p53 deletion were 4.2 months and 37.8 months respectively (p <0.001). MDM 2 amplification and p14ARF loss was detected in 0.4% and 2% of new diagnosed MM, 0.6% and 5.1% of relapsed MM and 2% and 29% of HMCLs respectively. Discussion: Emergence of p53 deletion/mutations denotes progression genetic events in MM. Importantly we show for the first time the overriding importance of p53 deletions as prognostic markers in relapsed MM. A molecular staging system that is based on the presence of p53 inactivation may be more powerful than classifying patients based on the loss of p53. Other abnormalities involving p53 pathway regulators like MDM2 gain and p14ARF loss are infrequent events in MM, even in advanced disease. Figure 1. Prevalence of p53 deletions Figure 1. Prevalence of p53 deletions

Abstract Constitutive activation of NF-κB signaling pathways has been identified in a variety of malignancies, however the molecular basis has remained largely unknown. Recently, we have shown mutations in 10 genes encoding positive and negative regulators of NF-κB signaling pathways in 20% of multiple myeloma (MM) patients, with TRAF3 being the most commonly affected gene. TRAF3 is a negative regulator of NF-κB signal and its inactivation results in the constitutive activation of the alternative or noncanonical NF-κB signaling pathway. With the exception of two recent studies in MM, there is no available data regarding the mechanisms that dysregulate NF-κB in other B-cell malignancies. The aim of this study was to analyze the TRAF3 status in a cohort of Waldenström’s macroglobulinemia (WM) patients. Forty-nine WM were analyzed by using a combination of array-based comparative genomic hybridization (aCGH) and cIgM-FISH. Genome sequencing from 28 of these patients was performed on all coding exons of TRAF3 and the adjacent intron-exon junctions. A NF-κB index, as a measure of NF-κB transcription activity, was calculated from 21 patients with gene expression data. The index is the mean expression level of four probe sets differentially expressed between human myeloma cell lines with identified mutations compared to those without identified NF-κB pathway mutations (CD74, IL2RG and 2x TNFAIP3). By performing aCGH we identified a small monoallelic deletion (∼460 Kb), including the TRAF3 locus in one of 22 patients. Genome sequencing identified a missense mutation (D483N) in the remaining allele. This substitution affects a highly conserved amino acid throughout vertebrate evolution, suggesting its functional relevance. We used cIgM-FISH to screen 27 patients with no available aCGH data and we found one biallelic TRAF3 deletion and one chromosome 14 monosomy. In the later case, no DNA was available to sequence the remaining allele. Both samples with biallelic inactivation of TRAF3 possess the two highest NFKB index values of our WM cohort, suggesting NF-κB transcription activity. Moreover, the case with biallelic deletion showed the lowest level of TRAF3 gene expression. Additionally, the entire TRAF3 coding region was sequenced in 28 of these 49 patients and one homozygous nonsense mutation (K286X) was identified. No GEP was available in this sample to calculate the NF-κB index. TRAF3 was only recently implicated in a malignant process, when inactivating mutations and biallelic deletions were reported in approximately 13% of MM patients, making it the most frequently inactivated tumor suppressor in MM. Our study has identified biallelic TRAF3 inactivation in at least 3 of 49 WM patients, suggesting that the constitutive activation of NF-κB signaling pathways may be involved in the pathogenesis of WM. Recent findings showing an association between TRAF3 loss of function and good response to bortezomib in MM patients suggest that proteasome inhibitor-based therapy may be an attractive option in the treatment of the WM patients with constitutive activation of NF-κB signaling pathways. Additional mutational screening of TRAF3 and other regulators of these pathways are ongoing to determine the extent of constitutive activation present in WM and other B-cell malignancies.

Abstract The use of high-resolution aCGH allows for whole genome screening for copy number changes even in tumors that rarely produce metaphase spreads. The aim of this study was to characterize the aCGH findings in B-CLL, lung MALT lymphoma, Waldenström’s Macroglobulinemia (WM), Multiple Myeloma (MM) and human myeloma cell lines (HMCLs). This study includes 301 B-cell malignancy samples (19 B-CLL, 19 MALT, 20 WM, 48 HMCLs and 195 MM) and an additional 76 melanoma samples. We found MM to have the highest number of abnormalities per karyotype, with 15.8±7.5 (mean ± SD) and 20.6±17.0 in hyperdiploid (H) and non-hyperdiploid MM (NH), respectively. The remaining diseases have a significantly lower number of abnormalities: 5.5±4.5 in B-CLL, 3.5±1.96 in MALT and 4±3.5 in WM. Aneuploidy and biallelic deletions were rare events in these three diseases. B-CLL has two highly recurrent abnormalities involving 11q22-q23 (29%) and 13q14.3 (33%). A minimal deleted region (MDR) of ∼108Kb was identified at 11q comprising ACAT1, NPAT and ATM. In 13q, a 280Kb MDR was recognized, including TRIM13, KCNRG, mir-15a and mir-16. The subgroup of MALT patients with t(11;18) had very few abnormalities and the majority are a consequence of unbalanced translocations (MALT, BIRC2 and BIRC3 deletions). In the remaining MALT samples, trisomy 3 and 18q gain were the most common abnormalities (31% each). The 6q16.3-q26 deletion was the most common abnormality in WM (45%). In 4 of 9 patients with 6q deletion there was an associated 6p gain. The same observation was found in 2 of 3 patients with 8p loss and concomitant 8q gain. Interestingly, 6p and 8q gain were not identified in patients without 6q and 8p deletions. Deletion of 17p was the most common recurrent abnormality observed in our panel of B-cell cancers, being identified in MM, WM and B-CLL. In B-CLL and WM, small mono and biallelic deletions of the NF-kB negative regulators, TRAF3 and NFKBIA, were identified, suggesting a potential involvement of this pathway in the pathogenesis of these diseases. Hierarchical clustering of the aCGH data in MM identified 3 distinct groups, NH-MM, H-MM and MM with deletions of chromosome 13 and 14. Interestingly, MGUS and SMM were more commonly clustered with H-MM. Several sub-clusters were observed in the H-MM group, the most prominent being made up exclusively of patients from TC class D1. This cluster was characterized by the presence of trisomy 11 and 21. The 11q13 TC group clustered and was highly associated with 11q amplifications due to unbalanced t(11;14). The 6q deletion defined a cluster with WM, MM and Melanoma patient with that abnormality. In the case of B-CLL and MALT, the only identifiable clusters were observed in cases with 13q loss and trisomy 3, respectively. These results highlight both, the common and unique aCGH findings in several B-cell cancers. By hierarchical clustering, MM was significantly divergent from the rest of the B-cell diseases. Due to the limited number of abnormalities in B-CLL/MALT/WM, the clustering of these groups was exclusively based on the common abnormalities. The use of aCGH has refined the MDRs of 11q and 13q in B-CLL. Additionally, the identification of deletions affecting the NF-kB pathway in B-CLL and WM has prompted us to hypothesize on the importance of constitutive NF-κB activation in these diseases.

17516 Background: The p53 tumor suppressor is commonly inactivated by mutations. Even in tumors without mutations, there are defects in the response to p53 activation. In MM, the prognostic significance of p53 mutation is unknown, while there has been no systematic study of p53 function. We seek to address these issues in this study. Methods: p53 mutation was studied by conformation sensitive gel electrophoresis with primers encompassing exons 1 to 10 followed by sequencing of DNA fragments with altered electrophoretic pattern in newly diagnosed MM patients entered into ECOG E9486 trial where patients were randomized to receive variations of melphalan-based conventional chemotherapy (VBMCP). Fisher’s exact tests were used to compare variables between patients. Kaplan-Meier survival curves were compared using the log-rank test. To investigate p53 function, we analyzed the expression of p53, and 3 of its transcriptional targets, APAF1, p21 and MDM2, in a separate cohort of 15 normal plasma cells (PC), 14 MGUS, 13 smoldering myeloma (SMM) and 101 MM (73 new and 28 relapsed) from the Mayo Clinic who had gene expression profiling performed on the Affymetrix U133A chip (Santa Clara, Ca). Results: Two hundred and sixty-eight patients had enough materials for study and were included in the analysis. The prevalence of p53 mutation was 3% (n = 9). Five of the 9 patients (56%, p = 0.001) with mutations also had p53 deletion (studied by fluorescent in-situ hybridization) resulting in bi-allelic loss of p53. Soft tissue plasmacytomas (37% v 7%, p = 0.018), and among the common translocations, t(4;14) and t(14;16) (50% v 18%) were more common in patients with p53 mutations. Despite similar response to treatment, those with p53 mutation had very short OS (16.7 v 41.4 months, p < 0.001). There was induction of p53 expression in MGUS and SMM with concurrent induction of APAF1, p21 and MDM2 whereas loss of this pattern was frequent in MM (45% in new MM and 60% in relapse MM compared to 15% in MGUS/SMM (p = 0.03)). Conclusions: p53 mutations are relatively rare in newly diagnosed MM patients but portend a short survival. However, functional abnormalities of p53 are prevalent and may be important in progression from MGUS/SMM to MM. [Table: see text]

Abstract MYC expression is frequently dysregulated in multiple myeloma (MM). In one comprehensive study, MYC structural variations (SV) were found in nearly half of MM cases (Affer et al. Leukemia 2014). The prevalence was higher in hyperdiploid (HRD) tumors (65%) compared to non-hyperdiploid (NHRD) tumors (36%). The large amount of tumor DNA required for all of the genomic studies performed may have biased the samples analyzed (e.g., to those with higher tumor burdens). To validate the findings of recurrent MYC SV in another dataset, we analyzed the CoMMpass data. We analyzed long-insert whole genome sequencing (WGS) data from diagnostic samples in 420 patients from the IA7 release (dbGAP phs000748) for SV. The results of clinical data, processed WES (SNV), RNASeq (gene expression) and WGS (copy number) data from IA8 (http://research.themmrf.org) were used to calculate survival, RAS and NFKB pathway mutation (WES), TC class (RNA), NFKB index (RNA) and hyperdiploid index (WGS). MYC SVs were identified in 38% of tumors. They were present in 53% HRD and 28% NHRD, and by TC in 55% D1, 43% D2, 36% MMSET, 26% MAF, 13% CCND. Juxtaposition of an Ig enhancer (IgH, IgK, IgL) close to MYC was the most common MYC SV, representing ~40% of the MYC SV. Other enhancers identified have mostly been reported previously, with the most frequent being NSMCE2 (12% of SV) and TXNDC5 (5% of SV). Intrachromosomal SV (deletions, inversions, duplications) not associated with any known enhancer were also frequent (18% of SV). As expected, MYC expression was higher in tumors with MYC SV compared to those without (~2.4 fold, p-value<0.0001). We used Gene Set Enrichment Analysis (GSEA) to identify activated pathways that might substitute for MYC in HRD patients without MYC SV and observed significant activation of the NFkB pathway. Interestingly, examining patients with RAS/MAPK pathway (NRAS, KRAS, BRAF, FGFR3 - abbreviated RAS) mutations (identified in 50% of all patients) the same pattern was observed: in the absence of RAS mutation, there was a significantly higher NFkB index. In general, the HRD tumors seem to have either activation of RAS and/or MYC, or activation of NFkB (Figure). There was no difference in overall survival in patients with versus those without MYC SV. We developed a clinically applicable sequencing platform to identify MYC SV, which cannot be reliably identified by FISH. We sought to validate this targeted capture approach, where in addition to the coding exons of 81 interesting genes described previously (M3P), we also pulled down the region surrounding MYC (2 Mb), IgH (0.5 Mb), IgK (50 kb) and IgL (100 kb) allowing us to additionally identify SV in MYC and Ig loci. Using this approach we identified IgH translocations in 29/30 samples with translocations previously identified by FISH (97%). Moreover, we identified MYC SV in 19/22 patients with SV previously identified by mate-pair WGS (86%). Importantly, sequencing identified the precise translocation breakpoint, and identity of the enhancer dysregulating MYC, which may be important variables. In one informative patient two different MYC SV were present at diagnosis, only one of which was still present following a partial response to four cycles of lenalidomide and dexamethasone. This suggests that the two MYC SV are in different subclones, one of which was much more sensitive to the treatment. Interestingly, the enhancer dysregulating MYC in the sensitive subclone harbors 5 strong Ikaros binding sites identified by ChIPseq, suggesting one intriguing mechanism for sensitivity to lenalidomide. To summarize, we verified in a large dataset that MYC expression is frequently dysregulated by SV in MM (38%), and the RAS/MAPK (50%) and NFKB (23%) pathways are frequently activated by mutations. Surprisingly, given their generally good prognosis, nearly half of HRD tumors seem to be MYC driven, while this is true for only a quarter of NHRD tumors. HRD tumors not driven by MYC or RAS appear to be driven by NFKB. Remarkably, the pathways most commonly activated by mutation in MM: CCND, MYC, RAS, NFKB are common to many cancers and have been studied extensively individually. To understand their clinical impact in MM we have developed a comprehensive custom capture sequencing panel that identified 97% of IgH translocations, 86% of MYC SV, and as well as SNV and CNV of 81 recurrently mutated genes. It will be important to include such a comprehensive genetic analysis to complement clinical trials in the future. Figure. Figure. Disclosures Stewart: Bristol Myers Squibb: Consultancy; Celgene: Consultancy; Takeda Oncology: Consultancy; Janssen Pharmaceuticals: Consultancy.