ALBERT

Description: The Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT0145429) is a longitudinal study of 1000 patients with newly-diagnosed multiple myeloma. The study opened July 2011 and now includes over 650 patients from 91 sites in the United States, Canada and European Union. Each patient is required to receive an approved proteasome inhibitor, immunumodulatory agent, or both. Enriched tumor and matched constitutional samples are comprehensively analyzed using Long-Insert Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES) and RNA sequencing (RNAseq). Clinical parameters, Quality of Life measurements and health care resource utilization values are collected at study entry and every three months for a minimum of five years. Additional bone marrow aspirates are collected and analyzed at each recurrence or progression of disease. An extensive clinical and molecular database, the MMRF Researcher Gateway (https://research.themmrf.org), has been developed to facilitate the rapid dissemination of the results and provides the myeloma community with a mechanism to analyze the data. In this current interim analysis, we report on 195 patients that are fully characterized at the molecular level. We focused this analysis on immunoglobulin translocations and inter-chromosomal fusion transcripts. As expected we detected the classic canonical t(4;14), t(6;14), t(11;14), and t(14;16) translocations targeting FGFR3/MMSET, CCND3, CCND1, and MAF respectively. Seven patients presented with t(8;14) rearrangements correlating with high expression of MYC. Novel translocations were detected targeting MAP3K14/NIK in two patients and NFKB1, TOP1MT, TXNDC2, APOL3, FCHSD2, PRICKLE1, and BCL2L1 in individual patients. Importantly, the matched RNAseq data confirmed the high expression of MAP3K14, NFKB1, TOP1MT, APOL3 and BCL2L1. Moreover, the anti-apoptotic isoform of BCL2L1, Bcl-xL, was the prominent transcript isoform detected. In several patients we detected multiple IgH translocations. For instance the BCL2L1 translocation occurred in a downstream class switch recombination region from one associated with a co-occurring t(11:14). We also analyzed the RNAseq dataset for inter-chromosomal fusion transcripts and leveraged the independent long-insert WGS data to validate the predicted fusions. The only recurrent fusion partner identified was IgH-MMSET created by t(4:14). Fusion transcripts were detected in individual patients between IgH elements and MYEOV and WWOX along with several of the novel IgH translocation partners; NFKB1, TOP1MT, and APOL3. Several genes are involved in multiple fusions but with different partners. Three independent fusions were detected between the highly expressed gene FCHSD2 and MYC, MAP3K14, and ANKRD55. Three additional fusions were detected between MAP3K14 and ELL, PLCG2, and CDC27, which produce hybrid MAP3K14 isoforms lacking the N-terminal negative regulatory domain. We also detected three independent fusions involving BRF1, which is typically not expressed in myeloma tumors. These appear to be markers of translocations occurring just centromeric of the strong 3’ IgH enhancers. Interestingly, two of the partners are located in a region of chromosome 12 harboring MDM2 and spiked expression of MDM2 was observed. Additional genes with multiple fusion events included NEDD9 and ARHGEF12. Integrating the WES and RNAseq datasets, we identified 3518 variants (median 14 per patient) where the variant allele detected by WES, was also detected in the RNAseq data, suggesting it is potentially biologically relevant. Of these, 44 distinct genes were mutated in at least 2% of patients. The most common mutations (〉7 patients) occurred in KRAS, NRAS, IGLL5, DIS3, BRAF, ACTG1, EGR1, FAM46C, TRAF3, DUSP2, FGFR3, and PRR14L. We also identified a deletion of IKZF3/Aiolos in a patient who progressed rapidly on lenalidomide-dexamethasone. Alterations in Ikaros family members like Aiolos have recently been reported as a potential mechanism of resistance to IMiDs. As the study continues to mature, we expect it will provide unprecedented molecular characterization and correlating clinical datasets that will help define the determinants of response to anti-myeloma agents and facilitate future clinical trial designs, thus serving as a stepping-stone toward personalized medicine for myeloma patients. Disclosures Lonial: Millennium: The Takeda Oncology Company: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Onyx Pharmaceuticals: Consultancy, Research Funding.

Description: The Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT145429) is a longitudinal study of 1000 patients with newly-diagnosed multiple myeloma from clinical sites in the United States, Canada, Spain, and Italy. Each patient receives a treatment regimen containing a proteasome inhibitor, immunumodulatory agent, or both. Clinical parameters are collected at study enrollment and every three months through the five-year observation period. To identify molecular determinants of clinical outcome each baseline and progression tumor specimen is characterized using Whole Genome Sequencing, Exome Sequencing, and RNA sequencing. This will be the first public presentation of the interim analysis seven cohort with 760 enrolled patients of whom 565 are molecularly characterized. This cohort of patients includes 14 patients with baseline and secondary samples along with 7 patients with characterized tumor samples from the bone marrow and peripheral blood. Although the median follow-up time for the cohort is only 260 days the patients on proteasome and IMiD based combinations are currently showing a PFS and OS benefit compared to those receiving combinations with each agent alone. From the raw mutational analysis we identified 24 significant genes that are recurrently mutated and the mutated allele is detectably expressed in all but one, DNAH5. Suggesting these mutations are likely contributing to myelomagenesis through an unconventional mechanism. Interestingly, DIS3 mutations are independent of KRAS, NRAS, and BRAF indicating a potential mechanistic link while PRKD2 mutations are associated with t(4;14). To identify events driving the initiation of myeloma we performed a detailed clonality analysis using a bayesian clustering method that corrects for copy number abnormalities and tumor purity to assign mutations into distinct clonal branches versus the initiating trunk mutations. On average 63.8% of mutations are trunk mutations and in 86.7% of patients at least one trunk mutation is associated with somatic hypermutation of an immunoglobulin gene as expected in a late stage B-cell malignancy. This identified many expressed trunk mutations that did not come out in the classic significance analysis like ATM, EGR1, and CCND1. To identify molecular subtypes we performed unsupervised clustering using a consensus clustering approach on independent discovery and validation cohorts, which identified 12 distinct subtypes, using a combination of silhouette score and cumulative distribution of consensus scores. This analysis identified two distinct groups associated with t(4;14) with mutations in FGFR3 and DIS3 being exclusive to one subgroup. In addition, this analysis separates patients with cyclin D translocations into three different groups, with one group having the second lowest PFS proportion. Three patients without CCND1 or CCND3 translocations were found to have IgH translocations targeting CCND2. The MAF subgroup was associated with the lowest OS and PFS proportion, and the three MAF/MAFB translocation negative patients in the subgroup all had MAFA translocations. The remaining 6 subgroups are associated with hyperdiploid copy number profiles and harbor the majority of the IgH-MYC translocation events. Two of the hyperdiploid groups are associated with a low level of NFKB activation compared to the remaining four, one of these is defined by the highest proliferation index but paradoxically the other has the second worst OS proportion. Another group is enriched with FAM46C and NRAS mutations. The genomic profiles of the paired tumors isolated from the peripheral blood and bone marrow are highly similar indicating these are not genetically distinct tumor compartments, at least in this subset of seven patients. Applying our bayesian clustering method to the serial samples resolved additional clonal clusters as mutations with similar cancer cell fractions at diagnosis clearly diverged at later timepoints. These analyses have identified tumor initiating mutations and new subtypes of myeloma, which are associated with distinct molecular events and clinical outcomes. Disclosures Jagannath: Novartis: Honoraria; Bristol Myers Squibb: Honoraria; Celgene: Honoraria; Merck: Honoraria; Janssen: Honoraria. Siegel:Celgene Corporation: Consultancy, Speakers Bureau; Amgen: Speakers Bureau; Takeda: Speakers Bureau; Novartis: Speakers Bureau; Merck: Speakers Bureau. Vij:Takeda, Onyx: Research Funding; Celgene, Onyx, Takeda, Novartis, BMS, Sanofi, Janssen, Merck: Consultancy. Zimmerman:Amgen: Honoraria, Speakers Bureau; Celgene: Honoraria, Speakers Bureau; Millennium: Honoraria, Speakers Bureau; Onyx: Honoraria. Niesvizky:Celgene: Consultancy, Speakers Bureau. Rifkin:Onyx Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millennium Pharmaceuticals, Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Consultancy, Membership on an entity's Board of Directors or advisory committees. Lonial:Millennium: Consultancy, Research Funding; Onyx: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Celgene: Consultancy, Research Funding.