Mutations In Multiple Myeloma Research Articles

Clinical Application of Epigenetic Modifier Mutations in Myeloma

Epigenetic deregulation is one of the key mechanisms leading to the development of multiple myeloma (MM). While one of the most commonly discussed mechanisms is the deregulation of MMSET by the t(4;14); recent studies have identified a range of other mechanisms that exert important effects and are also potentially amenable to therapy. Methylation patterns are important in MM progression and are characterized by global hypomethylation and gene specific hypermethylation. Interestingly, while this pattern is globally true, the etiologic variants of MM have distinct patterns arguing for their pathologic relevance of acquired methylation change. Identifying epigenetic mutations in MM has proven difficult because of their low frequency but recently a set of key mutated driver genes has been identified, which include a number of important epigenetic genes, of which are therapeutically tractable. RNA splicing has been identified as an important mechanism in AML/MDS but it is also important in MM. SF3B1 mutation occurs at lower frequency but by analogy are also potential therapeutic targets. Furthermore, abnormal splice patterns are more common than can be explained by mutation alone consistent with their being other events, which impact this pathway making it more relevant as a therapeutic target. The analysis of the coding sequence of MM has yielded many potential targets but little work has been done to date to characterize the non-coding sequences. A feature of the non-coding MM genome pointing to a key tractable epigenetic mechanism is structural genomic rearrangement that involves superenhancers. The etiologic translocations that involve the immunoglobulin gene superenhancers are the prime examples of this mechanism and it is now realized that other genes also contain superenhancers that are recurrently involved in structural events. The net results of such structural rearrangement is altered gene expression mediated by transcriptional deregulation making it a key therapeutic target in MM. Another feature of the non-coding sequence that can be used to define targetable mutations is the identification of mutations within non-coding RNA. Despite having looked for recurrent events within these genomic variants we haven't as yet been successful in identifying a key variant. Targeting epigenetic variables in MM is likely to be a growing therapeutic area beyond the use of histone deacetylase inhibitors already approved for use in MM. We can learn a lot about how to use these agents from the work already being done in AML/MDS aimed at manipulating these pathways. Targeting methylation status with hypomethylating agents is possible but is not without risk in MM, given the clinical methylation patterns we have identified. Given the prevalence of transcriptional deregulation in MM the development agents aimed at manipulating superenhancers such as bromodomain inhibitors could be of particular relevance. However, in MM it will be essential to use epigenetic agents within the correct biological context to maximize their clinical value. This approach will require the development of greater biological knowledge that is translated into diagnostic testing strategies, which identify the cases where there is the greatest likelihood of having a clinical impact. DisclosuresMorgan:Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; BMS: Consultancy, Honoraria.

Genomic and Immune Profiles of Multiple Myeloma Revealed By Whole Genome and Transcriptome Sequencing

Introduction:We analyzed genomic profile in line with immune checkpoint molecule expression in multiple myeloma using whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) data.Methods:We performed WGS of CD138+ selected tumor and the matched normal from saliva of multiple myeloma patients at 90-60x and 30x respectively from 37 patients. At the same time, we performed WTS using both tumor (CD138+) and immune milieu (CD138-) samples from these patients. Structural variations were called with Delly2 and Manta and the intersect of two call sets were used as the final SV calls. Copy number analysis was done with Sequenza and custom scripts. Somatic single nucleotide variants were identified with Mutect1 and Strelka and filtered against the panel of normal. RNA-seq was aligned using STAR algorithm and gene expression was quantified using RSEM algorithm. We extracted the expression of 21 immune checkpoint-related molecules (LAG3, PD-L1, IDO1, TIM3, CD27, CTLA-4, ICOS, TIGIT, PD-1, PD-L2, VISTA, and their ligands). To compare cell populations within a set of CD138-sorted MM samples, we used CIBERSORT algorithm to estimate predict fractions of leukocyte RNA.Results & Discussion:A total of 1,359 somatic structural variants were identified, with a median of 28 structural variant events per patient. The most common translocation event was t(4;14) (n=6, 16.2%). We identified novel recurrent deletions in CCSER1 (n=5, 13.5%) either deleting exon 10 (n=3) or exon 6 (n=2). CCSER1 has been proposed to a have a role in cell division with defects leading to cytokinetic defects. We observed an enrichment of whole-genome duplicated samples with CCSER1 deleted patients. We propose that CCSER1 deletion may have a role in whole-genome duplication events seen in multiple myeloma. Chromothripsis was also seen in 7 patients (18.9%). A total of 9 chromothripsis events were observed and chromosome 6 was most frequently involved (n=3). Recurrent mutation in IGKV4-1 chr2: 89185484 and 89185485 (p.Ala60) was observed suggesting dysfunctional antigen recognition in myeloma cells.From immune checkpoint perspective, expression of Galectin-9, a ligand of TIM3, was outstandingly high in immune milieu suggesting potential role of TIM3 inhibitor in myeloma. On the other hand, VISTA was highly expressed in tumors. When we matched the transcriptomic profiles with genomic variants, NRAS G61R mutant showed high expression of TIM3/Galectin-9 axis suggesting characteristics immune milieu of RAS mutant myeloma.Conclusions:We could identify novel CCSER1 recurrent deletion and IGKV4-1 mutation in multiple myeloma using WGS. WTS immune milieu analysis suggest potential role of TIM3 inhibitor in myeloma, especially in RAS mutated cases. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Hotspot Mutations in SF3B1 Result in Increased Alternative Splicing in Multiple Myeloma and Activation of Key Cellular Pathways

Introduction: Mutations in the components of the spliceosome have been shown to occur at relatively high frequency in many cancers such as chronic lymphocytic leukemia, myelodysplastic syndromes and breast cancer. One component in particular, encoded by SF3B1, has hotspot missense mutations that result in a significant increase in alternatively spliced transcripts. RNA splicing in Multiple Myeloma (MM) has not been investigated and in particular the extent of mutations in SF3B1 and its effects on the transcriptome.Methods: Using the MMRF CoMMpass dataset (N=1273) of newly diagnosed MM patients, samples with whole exome sequencing (WES) were analyzed for mutations using Strelka and Mutect, and samples with SF3B1 mutations identified. A range of approaches were used to explore the effect of the SF3B1 mutations on the transcriptome and to determine possible downstream effects. Using RNA-seq with matched WES samples (n=615), the splice junction usage of SF3B1 mutants was compared against non-mutated samples which were matched for key MM molecular sub-types. The RNA-seq data was analyzed using a pipeline that included STAR and Salmon, aligning to human reference genome hg38, gene and transcript differential expression analysis tools DESeq2 and StringTie/Ballgown, differential splicing exon usage tools JunctionSeq/QoRTs, DEXSeq, and SUPPA and for Gene Set Enrichment Analysis (GSEA) the R package FGSEA was used.Results: From the WES data 1.7% (22/1273) of samples had mutations in SF3B1 of which 5 had mutations in the hotpot codons of K666 and K700. Differential isoform analysis of the 22 SF3B1 mutant samples compared to non-mutated samples did not identify any transcripts. However, when the analysis was restricted to the 5 samples with hotspot mutations differential gene expression identified 146 genes that were significantly differentially expressed at an adjusted p-value <0.05. Additionally, many genes that did not show an overall gene expression change between the control and the SF3B1 hotspot mutants did at transcriptional level where we observed isoform switching which included the protein coding genes BCL2L1, SNUR, ACKR3 and CRLF2.Results of differential gene analysis between the control and SF3B1 mutants were used in GSEA and significant normalized enrichment scores (NES) identifying increased protein secretion (p-value =0.009, NES= 1.9) and unfolded protein response (UPR) (p-value = 0.02, NES = 1.52) pathways. Conversely GSEA identified decreased apoptosis (p-value = 0.008, NES = -1.76), KRAS signaling (p-value = 0.008, NES = -1.92), TNFA signaling via NF-κB (p-value = 0.008, NES= 2.12) pathways in SF3B1 mutant samples.Investigation of splicing loci revealed that novel splice loci were significantly more abundant in the SF3B1 mutants versus control samples. Differential splicing analysis detected 474 genes to be significantly differentially spliced and of those 311 were not found to be differentially expressed at the gene level, indicating that alternative splicing is as important alternative mechanism to gene expression differences. 59 novel splice sites were identified, as well as 152 known splice sites and 218 exon significant differential usage with a p-value of < 0.05. The genes with most significant levels of alternative splicing and found by more than one approach were DYNLL1, TMEM14C, CRNDE, BRD4 and BCL2L1, several of which are also seen in other cancers with mutated SF3B1.Conclusions: Hotspot mutations in SF3B1 result in alternative splicing of genes as well as the introduction of novel splice sites. The confirmation that SF3B1 hotspot mutations in MM increases alternative splicing as well as the identification of the genes undergoing alternative splicing may present novel therapeutic targets. Gene expression analysis of these samples identifies key deregulated pathways, perhaps in response to alternative splicing, including the UPR and protein secretion pathways. These analyses indicate that disruption of these pathways are potential avenues of therapeutic intervention in patients with SF3B1 mutations. DisclosuresOrtiz:Celgene Corporation: Employment, Equity Ownership. Flynt:Celgene Corporation: Employment, Equity Ownership. Thakurta:Celgene Corporation: Employment, Equity Ownership. Morgan:Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; Janssen: Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria.

Functional Genomic Landscape of Genes with Recurrent Mutations in Multiple Myeloma

During the last two decades, cell lines and patient-derived samples from multiple myeloma (MM) have been extensively profiled for alterations in their genome with the anticipation that those genes with the most recurrent lesions could represent attractive novel therapeutic targets or markers for aggressive disease. Yet for many of these genes, their functional significance for MM cells has not been formally evaluated. With the advent of new CRISPR/Cas9-based functional genomics platforms, it is possible to generate in genome- or subgenome-scale direct quantitative information on the impact that perturbation of these genes exerts on tumor cell survival, proliferation or other phenotypes. We therefore examined the landscape of our CRISPR-based functional genomic data for these recurrently dysregulated genes We specifically curated information from the MMRF CoMMpass study and multiple other publicly available studies, to identify genes which are recurrently identified to harbor nonsynonymous mutation (SNV or indel), DNA copy number loss or gain, or participation in chromosomal translocations. We then examined the patterns of results for these genes in our genome scale CRISPR-based gene-editing studies for loss-of-function in n=18 MM cell lines.We identified a subset of genes (e.g. FAM46C, CDKN2C, RASA2) which are considered targets for recurrent loss-of-function events and indeed exhibit, for large fractions of the cell lines tested enrichment, of their sgRNAs in CRISPR knock-out studies, consistent with a role of these genes as suppressors of tumor cell survival or proliferation. CRISPR KO of TP53 leads to increased survival/proliferation of only a small minority (2/18 of cell lines tested thus far), which reflects the fact that the overwhelming majority of MM cell lines already harbor LOF events for this gene. Interestingly, a substantial number of genes which have been considered to harbor recurrent LOF events in MM patient samples (e.g. NF1, NF2, CYLD) do not exhibit sgRNA enrichment in CRISPR KO screens in the MM cell lines tested so far. In addition, several other recurrently mutated genes for which their loss- or gain-of-function status had not been previously evaluated with extensive functional studies in MM (e.g. SP140, LTB, EGR1, ATM, PARK2, PRKD2, RAPGEF5, DOCK5, TGDS, TNFAIP8) exhibit in the majority of cell lines tested in in CRISPR knockout studies no significant enrichment or depletion of their sgRNAs. In contrast, PTPN11, CREBBP, EP300, KMT2B, KMT2C, SETD2, SF3B1 and UBR5, are notable examples of recurrently mutated genes which represent dependencies for large fractions of MM cell lines in vitro. These results highlight the value of interpreting results from next generation sequencing studies in the context of information provided by the genome scale by use of functional genomic characterization of available cell line models. We envision that, similar sub-genome scale assays were performed at the level of patient derived samples will also provide direct information about the relevance of some of these genes. In addition, functional studies conducted with context of tumor-microenvironemtn compartment interactions and tumor interface will be needed to evaluate several genes identified in the study. DisclosuresLicht:Celgene: Research Funding. Mitsiades:Takeda: Other: employment of a relative; Janssen/ Johnson & Johnson: Research Funding; Abbvie: Research Funding; EMD Serono: Research Funding; TEVA: Research Funding.

High-Throughput Copy Number Profiling by Digital Multiplex Ligation-Dependent Probe Amplification in Multiple Myeloma

Multiple myeloma (MM) is a genetically heterogeneous disease with a diverse clinical outcome. Copy number alterations (CNAs), including whole chromosome and subchromosomal gains and losses, are common contributors of the pathogenesis and have demonstrated prognostic impact in MM. We tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA), a novel technique combining MLPA and next-generation sequencing, to detect disease-related CNAs. Copy number status at 371 genomic loci was simultaneously analyzed in 56 diagnostic bone marrow samples, which were also examined by conventional MLPA and interphase fluorescence in situ hybridization (iFISH). On average, digitalMLPA identified 4.4 subchromosomal CNAs per patient. The increased number of probes compared with conventional MLPA allowed a detailed mapping of CNAs, especially on chromosome 1, where 24 different patterns were observed in 38 patients harboring loss(1p) and/or gain(1q). iFISH, MLPA, and digitalMLPA results at loci investigated by multiple methods showed a congruency of 95%. Besides precise characterization of hyperdiploid karyotypes not efficiently achievable by iFISH or MLPA, digitalMLPA unraveled 156 CNAs not detected by the other two methods in 45 patients (80%). In addition, we provide proof of principle that digitalMLPA can detect known point mutations, in this case the BRAFV600E. Our study demonstrates the robustness of digitalMLPA to profile CNAs and to screen point mutations in MM, which could efficiently be used in myeloma diagnostics.

Spectrum and functional validation of PSMB5 mutations in multiple myeloma.

Despite an increasing number of approved therapies, multiple myeloma (MM) remains an incurable disease and only a small number of patients achieve prolonged disease control. Some genes have been linked with response to commonly used anti-MM compounds, including immunomodulators (IMiDs) and proteasome inhibitors (PIs). In this manuscript, we demonstrate an increased incidence of acquired proteasomal subunit mutations in relapsed MM compared to newly diagnosed disease, underpinning a potential role of point mutations in the clonal evolution of MM. Furthermore, we are first to present and functionally characterize four somatic PSMB5 mutations from primary MM cells identified in a patient under prolonged proteasome inhibition, with three of them affecting the PI-binding pocket S1. We confirm resistance induction through missense mutations not only to Bortezomib, but also, in variable extent, to the next-generation PIs Carfilzomib and Ixazomib. In addition, a negative impact on the proteasome activity is assessed, providing a potential explanation for later therapy-induced eradication of the affected tumor subclones in this patient.

Complementary Activation of Ccnd, MYC, RAS and NFkB By Mutations in Multiple Myeloma

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. [Display omitted] DisclosuresStewart:Bristol Myers Squibb: Consultancy; Celgene: Consultancy; Takeda Oncology: Consultancy; Janssen Pharmaceuticals: Consultancy.

Aberrantly Expressed APOBEC3B Induces Mutations in Multiple Myeloma

Multiple myeloma (MM) is a malignant plasma cell tumor that arises secondarily from monoclonal gammopathy of uncertain significance (MGUS) due to accumulation of genetic abnormalities. Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) is a family of DNA cytosine deaminases that play critical roles in innate and acquired immunity. APOBEC proteins catalyze cytosine to uracil deamination and eventually induce C to T mutations in DNA. Recent genome-wide analysis revealed that APOBEC-induced signature DNA mutations accumulate during progression of MM and are associated with poor prognosis (Bolli et. al., Nat Commun. 2014). We previously found that one of the APOBEC3 proteins, APOBEC3B (A3B), induces genomic DNA mutations in a human cell culture model (Shinohara et. al., Sci Rep. 2012) and hypothesized that A3B might induce DNA mutations during onset and progression of MGUS and MM.A deletion polymorphism that removes the entire A3B gene is reported to affect breast cancer prognosis, therefore we first investigated the frequency of A3B deletion allele in 88 Japanese MM/MGUS patients and in healthy controls. 41 patients (46.6%) showed wild type, 42 patients (47.7%) heterozygous, and 5 patients (5.7%) had homozygous deletion allele. We could not detect a significant difference between MM/MGUS patients and healthy controls, suggesting that A3B may not contribute to disease initiation. In contrast, real-time PCR analysis revealed a considerably high expression of A3B mRNA in 23 bone marrow specimens from MM/MGUS patients, except for two samples with homozygous deletion allele. We sorted myeloma cells using anti-CD138 beads and the enriched myeloma cell samples exhibited even higher A3B mRNA expression in 9 MM/MGUS patients (relative quantity to peripheral blood cells [PBMC]: range 1.06 to 55.14, median 7.67).Next, we investigated the APOBEC3 family protein expression profile in six myeloma cell lines: U266, RPMI8226, SKMM1, AMO1, OPM2 and THK72. As expected, all of these cell lines demonstrated remarkably high levels of A3B expression by real-time PCR analysis (relative quantity to PBMC: range 1.22 to 489.4, median 62.47). Western blot analysis using an anti-A3B antibody that we newly generated also confirmed the high A3B protein expression in these myeloma cell lines. In addition, fluorescent immunostaining analysis confirmed high expression of A3B protein localized in the nucleus. Because previous studies showed that A3B expression is activated via the NF-kB signaling pathway, we investigated the regulation of A3B transcription in myeloma cells by p65 knockdown through shRNA lentivirus, resulting in suppression of A3B at protein level.To investigate the mutagenic potential of aberrantly expressed A3B in myeloma cell lines, we evaluated somatic mutations in genomic DNA by differential DNA denaturation PCR (3D-PCR) using stable A3B knock-down cells by shRNA lentivirus simultaneously transduced with a fluorescent gene, mCherry. Interestingly, we detected that scramble shRNA-transduced cells lost fluorescence much faster than those transduced with shRNA against A3B. 3D-PCR amplified mCherry fragments more efficiently at a lower denaturation temperature, indicating that these fragments include more AT-rich sequences. We cloned these DNA fragments and sequenced about 4000 bp in total, and detected prominently more TC > TT mutations in the mCherry sequences from control shRNA-transduced cells (C to T mutation, 3.001%) than in those from A3B shRNA-tranduced cells (C to T mutation, 0.0024%). Additionally, the amplified mCherry sequences from scramble shRNA-transduced cells contained various deletions which may be repaired by microhomology-mediated end joining. Since DNA double strand breaks (DSB) are constitutively activated in myeloma cells, we also examined whether aberrantly expressed A3B can induce DSBs. A3B knockdown in RPMI8226 decreased gH2AX signals by fluorescent immunostaining and Western blot analysis, suggesting that A3B induces DSBs.The present study clearly shows that myeloma cells express aberrantly high levels of A3B and suggests that A3B might play crucial roles in clonal evolution or genomic instability of MM/MGUS albeit A3B may not contribute to initiation of MGUS/MM. Whether A3B accelerates chemoresistance or disease progression remains to be elucidated, however, A3B might be a potential therapeutic target in MM/MGUS. DisclosuresIida:Janssen Pharmaceuticals: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Takaori-Kondo:Mochida Pharmaceutical: Research Funding; Takeda Pharmaceutical: Research Funding; Pfizer: Research Funding; Kyowa Kirin: Research Funding; Astellas Pharma: Research Funding; Eisai: Research Funding; Alexion Pharmaceuticals: Research Funding; Chugai Pharmaceutical: Research Funding; Janssen Pharmaceuticals: Speakers Bureau; Merck Sharp and Dohme: Speakers Bureau; Bristol-Myers Squibb: Speakers Bureau; Shionogi: Research Funding; Toyama Chemical: Research Funding; Cognano: Research Funding.

In Vitro JAK1/2 Inhibition, in Association with Bortezomib and Lenalidomide, Is Comparable with Bortezomib, Lenalidomide and Dexametasone: An Alternative for Multiple Myeloma Patients with JAK2 overexpression?

Background: Despite the absence of JAK1 and JAK2 mutations in multiple myeloma (MM), high levels of IL-6 constitutively activate the JAK/STAT pathway promoting survival and proliferation of tumor cells. Therefore, pharmacological inhibition of JAK proteins can be a potentially therapeutic strategy for myeloma treatment. Aims: 1) to identify expression of JAK1 and JAK2 in MM cell lines and in recently diagnosed MM patients; 2) to perform functional in vitro studies in MM cell lines treated with JAK/STAT pathway inhibitor (ruxolitinib), associated with drugs currently used in MM first line treatment (bortezomib, lenalidomide and dexamethasone), with and without co-culture with normal stromal cells; 3) to evaluate global gene expression of JAK/STAT pathway in cell lines treated with ruxolitinib to elucidate its mechanism of action in MM. Methods: JAK1 and JAK2 expression were analyzed in four cell lines (RPMI-8226, U266, SKO-007 and SKM-M2) and in bone marrow samples from 30 MM patients and 3 healthy controls by real time PCR. After IC50 calculation, drugs concentrations were: bortezomib (B) 10 nM for both RPMI-8226 and U266 cell lines; ruxolitinib (R) 30 µM for RPMI-8226 and 40 µM for U266 cell lines; lenalidomide (L) 10 µM for both cell lines; and dexamethasone (D) 1 µM for both cell lines. Apoptosis and cell cycle were evaluated by flow cytometry. PCR array for 92 JAK/STAT pathway related genes (Taqman® Array Human JAK/STAT Pathway, Applied Biosystems, Foster City, CA, USA) was performed in RPMI-8226 and U266 wild type and B+R treated cell lines, in duplicates. Results: Among the four cell lines, U266 presented the highest expression of JAK1 and JAK2 genes. JAK1 was overexpressed in 27% and JAK2 in 57% of 30 MM patients (considering at least 2-fold increase). After B+R treatment, RPMI-8226 showed increased number of cells in SubG0 phase (p<0.001) with reduction of cells in S (p<0.01) and G2/M (p<0.001) phases. In U266 cell line, there is a slight increase of cells in SubG0 phase (p<0.05). Also, after B+R treatment, both RPMI-8226 and U266 presented 50% of cells in late apoptosis, which was accompanied by reduction of expression levels of BCL-2 and BCL-XL anti-apoptotic genes. The expression profile of JAK/STAT pathway after B+R treatment showed that many JAK/STAT, Ras/Raf/MAPK and PI3K/Akt/mTOR pathways genes lost their expression, mainly in RPMI-8226, with insignificant changes in U266 expression pattern. Co-culture of RPMI-8226 with normal stromal cell line HS5 protected tumor cells from apoptosis, as the number of cells in late apoptosis decreased from 50% to 32% (p<0.001). The addition of immunomodulatory drug lenalidomide to the schedule (B+R+L) increased tumor cell death from 32% to 73% in co-culture (p<0.001). Despite the impressive results, B+R+L schedule was equivalent to currently used treatment for standard risk MM patients B+L+D (67% of cell death, p>0.05), in co-culture. Conclusion: B+R combination induced cell cycle arrest and apoptosis in U266 and RPMI-8226. The new drug combination B+R+L has in vitro results comparable with B+L+D and presents an alternative for MM treatment of almost 60% of cases bearing JAK2 overexpression. Our results support future studies using JAK inhibitors as an alternative for MM treatment in a Precision Medicine approach. Financial support: FAPESP 2010/17668-6 and CNPq. DisclosuresNo relevant conflicts of interest to declare.

Parallel Evolution of Multiple PSMB5 mutations in a Myeloma Patient Treated with Bortezomib

Introduction:Proteasome inhibition is the backbone of various Multiple Myeloma (MM) treatment regimens, leading to durable responses and high quality remissions. However, under prolonged therapy patients eventually develop drug resistance and the underlying mechanisms have been poorly understood. Proteasome inhibitor resistant cell lines were generated by continuous exposure to proteasome inhibiting drugs. In these cell line models a number of variants within the PSMB5 gene were observed. This includes single point mutations, leading to conformational changes of the _5 subunit within the 20S proteolytic core of the proteasome, impairing its chymotryptic catalytic function and the binding of inhibitory drugs. However, no PSMB5 mutations could, so far, be identified in human disease, leaving the functional relevance of such mutations to be determined.Methods:We applied the MM Mutation Panel (M3P) and used the Personal Genome Machine (Life Technologies) to sequence CD138+ purified bone marrow plasma cells and peripheral blood germ line control from a MM patient in third relapse that had been previously treated by various proteasome inhibitor containing therapies (VTD-PACE, VCD, PAD-Rev). This patient was subsequently treated with a pomalidomide, bortezomib, adriamycin and dexamethasone combination therapy (Pom-PAD) and achieved a partial remission after 4 cycles of therapy. When being exposed to VCD at earlier relapse a complete remission was induced within 6 cycles of therapy, demonstrating excellent response to proteasome inhibition at this earlier disease stage.Results:We identified clonal missense mutations in this patient at known NRAS hotspot location (p.Gln61Arg) and in MAX (p.Arg35His). Most notably we found and validated four subclonal single point mutations in PSMB5, each of them in subclonal frequencies with variant reads (VR) ranging from 1.9%- 5.9% (average read depth 750X). All PSMB5 mutations occurred in a highly conserved region in exon 2 of the gene (p.Cys122Tyr, p.Met104Ile, p.Ala86Pro, p.Ala79Thr), with three of them being located within the proteasome inhibitor drug binding site. Our 400bp amplicon design allowed us to observe that each mutation identified in PSMB5 is exclusively present on a different sequencing read and no reads are shared between the mutations. This implies that the mutations are present on different subclones of the tumor, which means that, despite low VR frequencies of the single mutation, in sum more than a quarter of the whole tumor might be affected by mutated PSMB5. At a disease stage when the patient was well responsive to proteasome inhibitor treatment (at diagnosis and at first relapse), of note, none of the mutations in PSMB5 is detectable.Conclusion:Here we report the first in human PSMB5 mutation in a MM patient. These mutations evolved in parallel within different subclones of the disease under the selective pressure of bortezomib- containing treatment regimens, representing branching evolution. It is to speculate whether previous investigations negating the existence of PSMB5 mutations in proteasome inhibitor treated patients might not have sequenced deep enough or did set up a sensitivity cut-off too rigid to detect such subclonal mutations. Our finding suggests that the mutations identified may contribute to the development of proteasome inhibitor resistance, emphasizing the need for more detailed genomic characterization of tumors, including minor subclonal mutation detection. Functional analysis of the mutations is ongoing and results will be presented at the meeting. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Patient-Specific Mutation-Derived Tumor Antigens As Targets for Cancer Immunotherapy in Multiple Myeloma

Multiple myeloma (MM) is an incurable plasma cell malignancy accounting for more than 10,000 deaths in the US each year. Novel therapeutic approaches for relapsed MM are urgently needed. Tumor-specific mutations are ideal targets for cancer immunotherapy as they can be potentially recognized as neo-antigens by mature T-cells. Targeting tumor-specific antigens harboring somatic mutations presented on major histocompatibility complex class I molecules (MHC-I) with peptides could personalize the therapeutic approach for relapsed patients. To test this possibility, we examined 6 relapsed MM tumor samples from Mount Sinai, NY to predict in silico patient-specific tumor mutations that may activate the patient's immune systems. This is the first study to utilize Whole-Exome Sequence data (WES) from relapsed MM patients to show the feasibility of using exome sequencing to identify mutation derived neo-antigens that are patient-specific.DNA and RNA from six MM patients were extracted from sorted CD138+ cells from bone marrow aspirates. At the time of sample collection all patients had relapsed following at least five lines of therapy including Autologous Stem Cell Transplantation. The exome capture for DNA sequencing was carried out using the Agilent human whole-exome SureSelect assay. RNA-seq libraries were prepared using Illumina mRNA-seq protocol. All libraries were sequenced on an Illumina HiSeq2500 to generate 100 nucleotide reads. RNA reads were aligned to human reference genome (hg19) and assembled into transcripts using Bowtie-TopHat-Cufflinks. WES data was mapped to reference genome by BWA and then processed by MuTect to detect somatic mutations. Patient-specific alleles were determined using Seq2HLA. The identified mutations lead to candidate antigenic peptides that were filtered by tumor expression level (FPKM >2) using RNA sequence data. Candidate peptides of 8-11 character long were then ranked based on peptide-MHC binding affinity prediction (IC50nM) performed in silico using NetMHCpan.We identified a total of 340 tumor-specific nonsynonymous somatic mutations expressed in the context of patient specific HLA type. 263 (77%) genes were strong binders (IC50<150nM) and 77 (23%) genes were moderate/weak binders (IC50150-500nM). The number of mutated genes that were immunogenic per patient ranged from a minimum of 6 genes to 147 genes. Further, Database for Annotation, Visualization and Integrated Discovery (DAVID) tool was used to identify potentially enriched biological processes among the 340 genes using Gene Ontology (GO) terms. Enrichment analysis of 263 genes showed that they are mainly involved in myeloid cell activation during immune response (eg.LAT2, MYO1F), cell cycle process (CDK1, CHEK2, DNM2, EP300, SETD8), cellular response to stress (RAD21, HDAC2, MAT2B), chromatin silencing (SIRT2, SMARCA4), cell apoptosis and signal transduction (KRAS, NLRP1, ING4, IGF2R). Similarly enrichment analysis of 77 genes revealed their involvement mainly in B cell activation and leukocyte differentiation (LRRC8A, CD3E, PRKDC). Examples of some of these significantly mutated genes with binding affinity and predicted peptides are shown in Table 1.In this study, we show for the first time a correlation between tumor mutations and the epitope landscape by in silico data, suggesting that somatic mutations in MM are immunogenic and could potentially confer antitumor vaccine activity. Our results support an approach in creating cancer vaccines that use tumor-specific immunogenic mutations for the development of personalized vaccines for MM patients.Table 1Immunogenic mutations in Multiple Myeloma#Patient Specific allelesPeptidesIC50Mutated GenesEffectPatient#11HLA-C*14:02CYGHTMVAF57.75LZTR1p.R284C2HLA-C*14:02LYFFGMHVQEY29.75EP300p.C1372Y3HLA-C*14:02TFNEPSSEYF114.21SMARCA4p.G1146SPatient#24HLA-B*15:01MSLHNLGTVF26.2BCRp.A1160G5HLA-A*31:01SIISDSPR149.38FcRL5p.V269I6HLA-A*31:01HYFMHLLK37.16SIRT2p.R116HPatient#37HLA-C*05:01ITDFGHSEIL25.18CHEK2p.K344EPatient#48HLA-A*11:01VVGARGVGK121.47KRASp.G12R9HLA-B*41:01LEIDQLFRI132.84CDK1p.S208LPatient#510HLA-A*31:01AVGCGFRRARR106.68MAT2Bp.P65RPatient#611HLA-A*30:01HQRVLYIEI93.61HDAC2p.D145E12HLA-A*30:01FTRCLTPLL63.19RAD21p.V397L DisclosuresChari:Array Biopharma: Consultancy, Other: Institutional Research Funding, Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Millennium/Takeda: Consultancy, Research Funding; Biotest: Other: Institutional Research Funding; Novartis: Consultancy, Research Funding; Onyx: Consultancy, Research Funding. Jagannath:BMS: Honoraria; Janssen: Honoraria; MERCK: Honoraria; Novartis Pharmaceuticals Corporation: Honoraria; Celgene: Honoraria. Dudley:NuMedii, Inc: Patents & Royalties; Janssen Pharmaceuticals: Consultancy; GlaxoSmithKline: Consultancy; Personalis: Patents & Royalties; Ayasdi, Inc: Other: Equity; Ecoeos, Inc: Other: Equity. Hammerbacher:Cloudera: Membership on an entity's Board of Directors or advisory committees; Bay Sensors: Other: Equity; Cambrian Genomics: Other: Equity; Genome Compiler Corporation: Other: Equity; Science Exchange: Other: Equity; Transcriptic: Other: Equity; Pymetrics: Other: Equity. Schadt:Pacific Biosciences: Consultancy; Berg Pharma: Other: Scientific Advisory Board; GNS Healthcare: Other: Scientific Advisory Board; Clinical Gene Networks AB: Other: Equity. Bhardwaj:Dynavax Technologies Corporation: Consultancy; Crucell: Other: Equity; Dendreon Corporation: Other: Scientific Advisory Board; Merck & Co., Inc.: Other: Scientific Advisory Board; Neostem, Inc.: Other: Equity.

Vemurafenib (VEM) in Relapsed Refractory Multiple Myeloma Harboring BRAFV600 Mutations (V600m): A Cohort of the Histology-Independent VE-Basket Study

Background: Whole-genome sequencing has identified a 4-6% incidence of BRAF mutations in multiple myeloma (MM). We undertook a histology-independent, "basket" study of VEM in BRAF V600m-positive cancers (NCT01524978). Six disease cohorts were prespecified; remaining tumors were classified in a 7th "all-comers" cohort. Here we present preliminary efficacy and safety data for the MM cohort.Methods: A multicenter, Simon, 2-stage adaptive design in patients with relapsed refractory BRAF V600m-positive MM who were receiving VEM (960 mg bid) until disease progression (PD) or unacceptable toxicity was used. Primary end point is investigator-assessed response rate (RR) at week 8 by International Myeloma Working Group criteria. Secondary objectives include overall RR, clinical benefit rate, duration of response, progression-free survival, overall survival, and safety. Stage 1 was complete after the 7th patient received a minimum of 8 weeks of treatment, died, or withdrew early from the study.Results: Eight patients had been enrolled in the MM cohort at the time of the data cutoff (December 3, 2014). Data are presented on patients in stage 1. Twelve patients were screened, of which 4 patients did not meet eligibility criteria. Of the 8 patients enrolled in the study, 6 were men and 2 were women, with a median age of 64 years (range, 55-68). High-risk features were seen in 3 patients by cytogenetics and fluorescence in situ hybridization (FISH). Prior treatment included immunomodulators (IMiDs) in 100% of patients, proteasome inhibitors in 75%, and chemotherapy (melphalan, bendamustine, cytoxan, doxorubicin, etoposide, and cisplatin) in 87.5%. Patients had received between 2 and 7 lines of treatment before enrolling in the BASKET trial, and 5 were refractory to IMiDs or proteasome inhibitors, or both. Median duration of treatment was 3.3 months (range, 1-5) at the time of data cutoff; 3 patients continue to be treated and 5 patients discontinued study drug. Response data were available for 7 patients at the end of 2 cycles. One patient achieved partial response (PR); 4 patients had stable disease; 1 patient had progressive disease; and 1 patient response was reported as not evaluable (objective response rate [ORR] week 8, 14%; 95% confidence interval [CI], 0.4-57.9). Of the patients enrolled, 71% (95% CI, 29.0-96.3) had clinical benefit with single-agent VEM. Responses occurred beyond 2 cycles: 1 patient went on to achieve very good PR (after cutoff date, January 2015). Three patients experienced disease progression between study days 57 and 85, and 1 of these patients died as a result of progressive disease. Single-agent VEM was well tolerated, with a safety profile similar to that observed in melanoma patients. Seven patients (88%) had at least 1 adverse event (AE) of grade 3 or 4, and 3 patients (38%) had at least 1 serious AE, including sepsis and lower respiratory tract infection, that was attributable to the underlying disease. Toxicity was manageable, and 1 patient discontinued treatment because of lower respiratory tract infection and skin lesions. Dose modification was necessary in 5 of 8 patients because of toxicity.Conclusions: This is the first mutation-specific clinical trial in MM. VEM has promising activity in patients with BRAF V600m-positive MM despite these patients being heavily pretreated. Because obvious clinical benefit for patients has been observed, the decision to recruit additional patients was made, and recruitment is ongoing. Updated efficacy results from all patients currently participating in the study will be presented. DisclosuresRaje:Amgen: Consultancy; Celgene: Consultancy; Astra Zeneca: Research Funding; Eli Lilly: Research Funding; BMS: Consultancy; Roche: Consultancy; Takeda: Consultancy; Onyx: Consultancy. Off Label Use: Vemurafenib is a potent inhibitor of BRAF mutated at codon 600 (BRAFV600). Here we explored the efficacy of vemurafenib in multiple myeloma patients with BRAFV600 mutations.. Chau:Roche: Research Funding. Hyman:Chugai Pharma: Consultancy; Biotherapeutics: Consultancy; Atara: Consultancy, Honoraria. Ribrag:Gilead: Membership on an entity's Board of Directors or advisory committees; Esai: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Research Funding; Servier: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmamar: Honoraria, Membership on an entity's Board of Directors or advisory committees. Blay:roche: Research Funding. Tabernero:Taiho: Consultancy; Millennium: Consultancy; Merck: Consultancy; Amgen: Consultancy; Imclone: Consultancy; Chugai: Consultancy; Merck Serono: Consultancy; Boehringer Ingelheim: Consultancy; Eli Lilly: Consultancy; Celgene: Consultancy; Sanofi: Consultancy; Roche: Consultancy; Novartis: Consultancy; Symphgen: Consultancy. Wolf:Roche: Consultancy, Equity Ownership, Honoraria, Research Funding. Sirzen:F. Hoffmann-La Roche: Employment, Equity Ownership. Faris:Merrimack Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Roche: Research Funding; N-of-One-Therapeutics: Consultancy. Kaiser:Bristol-Myers Squibb: Consultancy; Amgen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Janssen: Honoraria; Chugai: Consultancy. Veronese:F. Hoffmann-La Roche: Employment. Makrutzki:F. Hoffmann-La Roche: Employment. Lasserre:F. Hoffmann-La Roche: Employment, Other: Unspecified, Patents & Royalties. Puzanov:Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Baselga:Roche: Consultancy.

Anti-Tumor Phagocytic Cell Activation in Multiple Myeloma By the IAP Antagonist LCL161: Results of a Phase II Clinical Trial

Dexamethasone is a powerful anti-inflammatory, immunosuppressive agent widely used in the treatment of MM with pleiotropic effects on both the tumor, and host immune cells. We report on a completely novel approach to immune modulation using an agent with almost directly opposite effects to glucocorticoids on innate immune cells. LCL161 is an IAP antagonist targeting the cellular inhibitor of apoptosis proteins cIAP1 and -2 (cIAP1/2) that in a phase I study in solid tumors was well tolerated with a cytokine release syndrome as the dose limiting toxicity. We previously reported that loss of cIAP1/2 in MM cells results in the stabilization of NIK and activation of the non-canonical NFkB pathway, a pathway we found frequently activated by a promiscuous array of mutations in multiple myeloma (MM). As expected, we found that LCL161 has no direct anti-tumor activity against MM cells in vitro and ex vivo. However, the non-canonical NFkB pathway is also a key activator of the innate immune response. Remarkably, we found that in vivo LCL161 has dramatic, apoptosis-independent activity associated with marked phagocytosisagainst MM that develops spontaneously in an immunocompetent genetically engineered mouse model of MM (Vk*MYC). Cyclophosphamide (Cy), which has been shown to induce an acute secretory activating phenotype in tumor-associated macrophages, markedly potentiated the anti-tumor effects of LCL161. We show that phagocytes (depleted by liposomal clodronate), but not adaptive immune cells, are required for the anti-tumor effect. Consistently we show that LCL161 activates dendritic cells and macrophages in vitro, and in vivo, and upregulates production of inflammatory cytokines.A phase 2 clinical trial of LCL161 was conducted in 24 patients with relapsed MM previously exposed to both IMiDs and PIs, but less than 5 prior lines of therapy. Patients received LCL161 1200mg po weekly, with Cy 500mg po weekly added for progressive disease or lack of response. Single agent LCL161 was well-tolerated, with grade 3 or 4 non-hematologic toxicity in four patients, and following the addition of cyclophosphamide in 9 patients. No patients responded to single agent LCL161, and the best response was stable disease in 6/24. In 21 patients, Cy was added after a median of 2 cycles, in whom the best response was stable disease or better in 18/21 (p<0.001 compared to LCL161 alone), and a PR or better (including 1 VGPR and 1 CR) in 5/21 (p<0.001 compared to LCL161 alone). Six months following the initiation of Cy, 35% of patients remain event-free. Two patients had stable disease for more than nine months after stopping treatment. One, relapsing after VDT-PACE, HDM200, RVd x 3 years with t(11;14) and del17p, received only three months of LCL161, the last month in combination with Cy. He then achieved a PR, reconstitution of his uninvolved IgG to normal levels for the first time in more than 3 years and still has not progressed one year after stopping therapy. Similar changes in serum and bone marrow inflammatory cytokines and gene expression were observed in patients following treatment with LCL161 to those observed in the mice. We conclude that LCL161 is able to modulate the tumor microenvironment to exert long-term disease control in combination with Cy, and deserves further study in combination with agents that more directly depend on phagocytic cell activity (e.g., monoclonal antibodies, inhibitors of "Don't eat me" signals). DisclosuresBergsagel:Novartis: Research Funding; Constellation Pharmaceuticals: Research Funding; Incyte: Consultancy; Jannsen: Consultancy; Mundipharma: Consultancy. Off Label Use: Use of LCL161 to treat multiple myeloma. Kumar:Celgene: Research Funding; Millenium/Takeda: Research Funding; Onyx: Research Funding; AbbVie: Research Funding; Janssen: Research Funding; Sanofi: Research Funding; Celgene, Millenium, Sanofi, Skyline, BMS, Onyx, Noxxon,: Other: Consultant, no compensation,; Skyline, Noxxon: Honoraria. Stewart:Oncospire Genomics: Research Funding.

Redefining Mutational Profiling Using RNA-Seq: Insight into the Functional Mutational Landscape of Multiple Myeloma

Whole genome and exome sequencing (WGS, WES) have enabled the identification of mutational signatures in Multiple Myeloma (MM) and other cancer types. In studies that assess the impact of coding mutations on protein structure and function, only reads mapping to the exome are pertinent. Thus, WES is typically preferred over WGS, as it provides deeper coverage given the same amount of total reads. However, exome enrichment - a necessary step in WES, limits the ability to call mutations, as coverage is restricted to the capture regions and affected by their GC content. Furthermore, without transcriptional information, it is not possible to determine which coding mutations found by WGS or WES are expressed and, therefore, more likely to be relevant. As an alternative, RNA-seq data directly targets the transcriptome, providing deep coverage, not requiring an enrichment step and intrinsically omitting non-expressed mutations. Moreover, when RNA-seq data is already available for evaluation of gene expression profiles, one can further leverage the data to explore expressed mutational profiles. However, limitations in pipelines to analyze RNA-seq data have restricted their applicability so far.Using paired WES and RNA-seq data from MM patient samples, we have observed that the majority of recurrent mutations in MM occur within genes with very low or no detectable expression (only 27% of mutated genes express). Here, we have further analyzed a large RNA-seq sample set to describe a comprehensive transcriptional mutational landscape in MM and identify potential mutational driver genes. Specifically, we performed RNA-seq on CD138+ MM cells from 292 newly-diagnosed patients and 16 normal bone marrow plasma cell (NBM) samples. The unstranded 50bp paired-end reads were mapped to the human genome using MapSplice followed by a workflow for variant analysis based on GATK. Output was filtered for germline variants and technical artifacts, then evaluated computationally for functional impact, and finally further filtered at the gene level. Using this workflow we were able to identify most reported recurrently mutated genes in MM, including but not limited to TP53 (14%), NRAS (14%), KRAS (11%), ACTG1 (4%), CCND1 (4%), TRAF3 (3%), FAM46C (3%), CYLD (3%) and DIS3 (2%). Importantly, we were also able to identify novel putative mutational driver genes of lower frequency, including several genes involved in the NF-κB pathway (BCR, TAOK2, NFKBIA, PIM1) and genes coding for proteins forming the mTORC2 complex (SIN1, RICTOR, MTOR). We observe that the average mutational frequency, which is a convolution of clonality and relative allelic expression, is slightly below 0.5. Yet, we find diverse mutational frequencies across samples for each given gene. For instance, FAM46C shows a pattern representative of highly subclonal mutations, whereas CCND1 presents mostly bi-allelic and clonal mutations, and others such as TRAF3 show a wide spectrum of mutational frequencies. Further developments will be needed to deconvolve these frequencies.We also applied the workflow to 10 of the samples for which we reported mutations at the DNA level, and observe CCND1, TP53 and KRAS to be recurrently mutated using either WES or RNA-seq. Nevertheless, some mutations are not shared, including 3 WES-exclusive BRAF mutations and one seen in CCND1 through RNA-seq only.In conclusion, we report the first computational analysis to identify mutational driver genes using RNA-seq data, providing additional insight into the mutational landscape of MM. Our findings demonstrate that RNA-seq of unpaired tumor samples can suffice to characterize the most salient characteristics of cancer mutational landscapes. DisclosuresCampbell:14M genomics: Other: Co-founder and consultant. Munshi:celgene: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; novartis: Membership on an entity's Board of Directors or advisory committees.

Targeted Genomic Mutation Panel (M3 P) Results from 504 Multiple Myeloma (MM) Patients

Introduction: Customized gene panel sequencing is an attractive approach to genomic tumor characterization in clinical care. Based on published MM exome data we developed a MM Mutation Panel (M3 P) that includes the most commonly mutated genes, actionable drug targets, genes targeted by current standard of care (SOC) therapies and which allows tracking of clonal evolution, copy number and sample purity. Methods and Material: M3 P (v3.0) covers 88 genes (1327 amplicons, 181kb). MM samples from 504 patients (pts) have been analyzed (corresponding germline in 81%) through collaborations between Mayo Clinic and Hospital-12-de-Octubre (Madrid, Spain), the DSMM and GMMG (Wurzburg, Ulm, Freiburg and Heidelberg, Germany) and the HOVON trial groups (Rotterdam, The Netherlands). The investigated cohort includes 410 untreated pts (81%), which includes a high risk cohort of 72 pts with del17p, 25 paired samples with later follow up from the same cohort, and 94 relapsed patients, of which 50 were relapsed and refractory. Results: Overall coverage per mutation averaged >500x depth. We identified 945 variants (1.9 per pt) and in 83% of the pts a mutation was found. Clonal heterogeneity was assessed with mutations ranging from 3%-100% variant reads suggesting the presence of a significant number of subclones (e.g. 21% of mutations were in Significant differences in DIS3 and FAM46C mutation incidences were observed across cohorts: DIS3 mutations are more common in untreated pts with a 1.7 fold increased predominance (14% untreated and 8% treated). FAM46C has an expected incidence of 8% but was rarely mutated in untreated del17p high risk disease with only one of 100 patients harboring both mutations. The significance of this finding needs to be determined but implies a possible overlap in function. Finally we assessed impact on survival of the mutation variants identified in 142 untreated Mayo patients and found STAT3 mutations negatively impacting PFS (p=0.034) and OS (p=0.001). This gene is rarely mutated in MM (2% of the total cohort) thus the sample size was small and this finding needs further validation. Conclusion: We here describe 504 MM patients sequenced using the M3 P gene panel, which identified mutations in >80% of investigated patients, overlaps well with published whole exome sequence data and provides clinically relevant information. New findings were the high frequency of minor clones, the relative lack of overlap of del17 and FAM46C mutation, a higher frequency of DIS3 mutation at diagnosis compared to relapse, the prognostic significance of STAT3 mutation and the frequent presence of CRBN pathway mutation in drug resistant relapsed patients. Disclosures Sonneveld:Janssen-Cilag, Celgene, Onyx, Karyopharm: Honoraria, Research Funding; novartis: Honoraria. Mai:Janssen-Cilag: Other: Travel Grant; Onyx: Other: Travel Grant; Mundipharma: Other: Travel Grant; Celgene: Other: Travel Grant. Goldschmidt:Takeda: Consultancy, Membership on an entity9s Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity9s Board of Directors or advisory committees; Onyx: Consultancy, Honoraria, Membership on an entity9s Board of Directors or advisory committees, Speakers Bureau; Millenium: Honoraria, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Consultancy, Membership on an entity9s Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Honoraria, Membership on an entity9s Board of Directors or advisory committees, Research Funding, Speakers Bureau; Chugai: Honoraria, Research Funding, Speakers Bureau; Janssen-Cilag: Consultancy, Honoraria, Membership on an entity9s Board of Directors or advisory committees, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Membership on an entity9s Board of Directors or advisory committees, Research Funding, Speakers Bureau. Knop:Celgene Corporation: Consultancy. Kull:Bristol-Myers Squibb: Membership on an entity9s Board of Directors or advisory committees. Martinez-Lopez:Novartis: Honoraria, Research Funding; Bristol-Meyer Squibb: Honoraria; Celgene: Honoraria; Janssen: Honoraria. Einsele:Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau; Amgen/Onyx: Consultancy, Honoraria, Speakers Bureau. Raab:Novartis: Research Funding. Stewart:Oncospire Inc.: Equity Ownership; Celgene: Consultancy; Novartis: Consultancy; BMS: Membership on an entity9s Board of Directors or advisory committees.

Abstract 615: Noninvasive diagnosis of actionable mutations by deep sequencing of circulating tumor DNA in multiple myeloma

Abstract Background: Genome sequencing of multiple myeloma (MM) tumors has revealed recurrent mutations that serve as a fertile ground for targeted therapies. Indeed, activating mutations of KRAS, NRAS and BRAF have been reported in approximately 27%, 24% and 4% of MM cases. Based on this observation, we initiated a Phase II NCI-CTEP sponsored clinical trial of trametinib in patients with MM (PHL-9460). Detection of mutations currently require bone marrow aspirates that are invasive and can yield suboptimal samples. Targeted, ultra-deep sequencing of circulating tumor DNA (ctDNA) is a promising tool for accessing the tumor genome that has not been well studied in MM. We set out to determine the feasibility of detecting ctDNA in MM and of identifying actionable mutations and mutational load using liquid biopsy through ctDNA analysis. Methods: MM patients enrolled onto PHL-9460 or those with heavy tumor burden were identified and consented to have their peripheral blood drawn for analysis. Where possible, matched tumor DNA was also obtained. Cell-free DNA was extracted from 7-15 mL of plasma isolated within ¬1 hour of blood draw using the QIAamp Circulating Nucleic Acid Kit and tagged with barcoded sequencing adapters for subsequent pooling. All exons of KRAS, NRAS, BRAF, PIK3CA and EGFR genes were isolated using a custom hybrid capture panel (IDT xGen Lockdown) and sequenced on an Illumina HiSeq 2000. Reads were aligned to the human genome reference (hg19) using bwa and somatic mutations were detected using muTect. Results: We have collected 25 samples from 23 patients, 7 from patients on PHL-9460, 5 newly diagnosed, and 13 from relapsed patients having received 3.3 median prior lines of therapy (range 1-7). To date, 11 samples from 10 patients have been sequenced. The sample with the lowest DNA yield failed due to low library complexity (range 16.6-3872 ng, median yield: 197 ng). From the remaining 10 samples, the mean target coverage ranged from 31,500 to 32,500. Somatic mutations in KRAS, NRAS, or PIK3CA genes were present in 5 of 9 patients with mutant allele frequencies ranging from 1.1% to 32% (3 KRAS and 2 NRAS of which 2 cases also had a low frequency PIK3CA mutation). We did not uncover mutations in BRAF or EGFR. For patients with matched tumor DNA, mutations in ctDNA concurred with those found in tumor DNA sequencing (4 of 4 tumors with known genotypes). Two patients with NRAS mutations enrolled onto PHL-9460 have responded to trametinib (1 partial and 1 minor response) and remain on therapy. Conclusion: ctDNA analysis in this cohort has identified key mutations in MM. The rate of RAS or RAF mutations in ctDNA compared to matched tumors and correlation to response to trametinib is ongoing and will be presented. Preliminary data suggest that ctDNA may be a reliable method of detecting mutations in MM and an alternative to bone marrow biopsy. Citation Format: Rayan Kaedbey, Olena Kis, Arnavaz Danesh, Mark Dowar, Tiantian Li, Zhihua Li, Jessica Liu, Mark Mansour, Mahadeo Sukhai, Tong Zhang, Suzanne Kamel-Reid, Trevor J. Pugh, Suzanne Trudel. Noninvasive diagnosis of actionable mutations by deep sequencing of circulating tumor DNA in multiple myeloma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 615. doi:10.1158/1538-7445.AM2015-615

Abstract 4248: A long tail of sub-clonal TP53 mutations emerged by ultra-deep sequencing of newly diagnosed multiple myeloma (MM)

Abstract TP53 is rarely reported as being affected either by deletions or mutations in MM, even if chr17p13 copy number (CN) loss defines a samples subgroup with a particularly poor prognosis. Here we aim at retrospectively analyzing by Next Generation Sequencing (NGS) the TP53 gene inactivation in newly diagnosed MM, assessing the mutational events’ frequency and their clinical impact. A cohort of 92 MM, receiving up-front velcade (vel)-based regimens, followed by autologous stem cell transplantation, was included in the study. TP53 gene mutational status was analysed by amplicon-targeted deep NGS approach. An upcoming NGS data analysis software was employed to detect vars (var) and to compare them to IARC database. p53 activity was evaluated by immunoblot assays. Ultra-deep TP53 coding sequence analysis (median depth: 1060) highlighted the presence of a median of 1.8 vars per samples in 73/92 (79%) MM: a total of 131 nucleotide substitutions emerged, with vars allele frequencies (VAF) ranging from 1 to 99% (median 1.3%). TP53 vars, were defined either neutral or deleterious mutations, according to their predicted effect at amino acid level. 36 cases carried 42 deleterious vars (VAF = 1.2%), 67% of which were predicted as non-functional at protein level. 9 samples carried 21 neutral vars (VAF = 1.1%), mainly affecting the DNA binding domain. 28 samples carried 68 SIFT unclassified vars, among which several polymorphisms were counted (VAF = 94.6%). SNPs arrays were performed on 83/92 samples: 14/83 (17%) carried a TP53 CN loss on chr17p13.1. The incidence of TP53 hemizygous deletion was higher among cases carrying deleterious mutations, as compared to cases carrying either neutral or unclassified mutations (25%, 12,5% and 12%, respectively). 2/17 non-mutated samples carried TP53 hemizygous deletion, as well. Interestingly, an Rb1 tumour suppressor gene CN loss on chr13q14.2 significantly characterized samples carrying either mutated (deleterious var) or deleted TP53 (p = 0.006). By immunoblot assay we showed the absence of phosphorilation both in 3 TP53 deleted cases and in 3 MM carrying deleterious vars; on the contrary p-p53 was observed in 4 non-mutated cases. Clinical correlations were performed on 81 MM showing that the presence of either TP53 hemizygous deletions or at least one TP53 deleterious var was more likely associated to the response to vel-based induction therapy (frequencies of ≤partial response: 35% and 64% among samples carrying or not impaired TP53, respectively; p = 0.05). Conversely, the frequency of progression events was slightly higher among MM carrying impaired TP53 (69% vs. 50%). In conclusion, the TP53 coding sequence analysis by ultra-deep NGS of a cohort of newly diagnosed MM highlighted an unexpected, still un-explored, high rate of TP53 vars. The impact of TP53 damage on MM disease course has to be confirmed in randomized clinical trial. Supported by Roche Diagnostics and FP7 NGS-PTL project Citation Format: Marina Martello, Giovanni Martinelli, Angela Flores Dico, Barbara Santacroce, Enrica Borsi, Mauro Procacci, Torsten Haferlach, Flavio Mignone, Igor Saggese, Elena Zamagni, Paola Tacchetti, Lucia Pantani, Anna Maria Brioli, Serena Rocchi, Annalisa Pezzi, Michele Cavo, Carolina Terragna. A long tail of sub-clonal TP53 mutations emerged by ultra-deep sequencing of newly diagnosed multiple myeloma (MM). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4248. doi:10.1158/1538-7445.AM2015-4248

Clinical and Biological Implications of BRAF V600E Mutation in Multiple Myeloma

In a retrospective cohort, seven patients with multiple myeloma carrying the BRAF V600E mutation had significantly shorter overall survival and higher prevalence of extramedullary disease than 251 BRAF wild type (wt) controls (Andrulis et al Cancer Discov 2013). Three case reports are in concordance with this view (Bohn et al and Sharman et al, Clin Lymphoma Myeloma Leuk, 2014). We conducted this study to further investigate the clinical and biological implications of this mutation in multiple myeloma.We used mutation-specific quantitative real-time PCR (qPCR) to screen biopsies from 209 myeloma patients, of which 185 were taken prior to first relapse. The BRAF V600E mutation was detected in 13 (6.2 %) of the patients. 10 of them also expressed the corresponding protein as evaluated by immunohistochemistry (IHC) using the BRAF V600E specific VE1 antibody, and 2 patients had simultaneous mutations in BRAF and NRAS/KRAS. RAS mutations are of particular interest because in vitro studies indicate that their presence may imply a paradoxical effect of BRAF inhibitors (Lohr et al Cancer Cell 2014).Whole exome sequencing (WES) was carried out in three BRAF V600E positive patients from whom we had stored purified myeloma cells. Among the top 11 recurrently mutated genes listed in Lohr et al (Cancer Cell 2014), we found mutations only in BRAF, NRAS, and KRAS. Clonal fraction of BRAF V600E mutated plasma cells as evaluated by IHC and WES varied from 4 to 100 %. There was agreement between detection methods in the patient with a dominating V600E mutated clone, but less so in the patients with small clones.Estimates of BRAF V600E clone size and RAS mutation analysis in 13 patients positive for BRAF V600E by qPCRTable 1IHC (clone size, %)WES (clone size, %)Sanger sequencingNRAS / KRAS mutation75-10086+negative75-100negativenegative75-100+negative50-75+negative50-75+negative25-50negativenegative25-50negativenegative<250negativeKRAS p.G12A (ex2) and p.Q61H (ex3)<25+negative<25+negativenegativenegativenegativenegative4negativeNRAS p.Q61K (ex3)negativenegativenegativeBRAF V600E positive patients presented a variety of clinical phenotypes and no characteristic genotype-phenotype relation could be identified. Progression free and overall survival, and all clinical parameters including the presence of extramedullary disease, were similar in patients with BRAF V600E and BRAF wt. Three patients carried the mutation in > 75 % of tumour cells, and all had indolent disease. One of them died after seven years, whereas the remaining two responded with long lasting CR to broad acting therapy (MP, MPT) and are still in remission after five and seven years. The Regional Ethics Committee approved the study (REK 2165-2012). [Display omitted] In conclusion, we found no evidence supporting a prognostic role or association with a particular clinical phenotype for the BRAF V600E mutation in early multiple myeloma, which is in contrast to earlier reports. Furthermore, the three patients with a high fraction of mutated cells had a relatively benign disease responsive to conventional treatment. This study demonstrates that the role of mutation V600E is more diverse than previously assumed. Presence, and particularly high fraction of BRAF V600E mutated cells as well as translation to protein, are prerequisites for specific inhibitory treatment. However, these characteristics are alone not sufficient to predict outcome or to choose the right treatment. DisclosuresHovig:PubGene Inc.: Equity Ownership; GeneSeque AS: Honoraria, Membership on an entity’s Board of Directors or advisory committees. Vodák:PubGene AS: Research Funding.

Development and Results of a Multiple Myeloma Specific Custom 77-Gene Mutation Panel for Clinical Targeted Sequencing

▪Background:A goal of “post-genomic” cancer care is development of specific, affordable, reliable and rapid next-generation sequencing-based assays determining prognosis, therapeutic selection and minimal disease monitoring, replacing older technologies in the diagnostic and monitoring workup. In this regard, we designed and deployed a custom gene panel for identification of mutations, copy-number changes and clonal frequency in multiple myeloma (MM) samples.Methods: The MM Mutation Panel Version 2.0 (M3P 2.0)1 includes 1271 amplicons from 77 genes that are either mutated in MM (genes with a published mutation incidence ≥3%), represent critical pathophysiological pathways, are targetable with small molecule-based therapies and/or are associated with drug resistance (eg. XBP-1, CRBN, IZKF, IRF4). The amplicons are spread across 21 chromosomes, allowing the identification of copy-number changes in these regions.Results: We have sequenced 38 MM cases (150 will be presented) with paired tumor-germline DNA samples, using only 20ng of DNA for library preparation. Patients (Pts) included 29 untreated and 9 MM pts with multi drug refractory disease. Coverage depth averaged 964X. Hyperdiploid MM was successfully identified in 45% of cases, del(13q) in 34%, del(1p) in 18%, del(17p) in 8% and gain of 1q in 13%. Array CGH in representative cases confirmed concordance with semiconductor sequencing. Overall, 71 exonic missense and 3 nonsense mutations were detected, and 7 frameshift indels. In 89% of the pts a mutation in at least one M3P2.0 gene was identified (range 1-8). 92% of mutations were predicted damaging (Provean, Polyphene-2 or SIFT). Most commonly mutated were KRAS (37%), NRAS (21%), BRAF (13%), TP53, CDKN1B, DIS3 (each 11%), FAM46C, STAT3, and IRF4 (each 8%). The MEK-ERK pathway was mutated in 61% of cases and in 3 cases more than one gene in this pathway (NRAS, KRAS, BRAF) was simultaneously mutated. Six mutations in BRAF were identified in 5 untreated pts, 3 of them known to be activating and targetable (Val600E). Other commonly mutated pathways were the NFKB pathway in 24% of pts and the Cyclin D pathway, mutated in 16% of cases.Genes of the cereblon pathway (CRBN, IRF4, IKZF3), essential for the action of lenalidomide (len) were mutated in 5 Pts. One newly diagnosed and len refractory Pt harbored a subclonal CRBN mutation (Asn316Lys, allelic fraction [AF] 20%) as well as 4 clonal IRF4 mutations within the DNA binding domain of the gene (Lys89Asn (AF 78%), Lys77Glu, Ser48Arg and Cys49Ser (AF 80% each). Another IRF4 mutated (Lys123Arg, AF 90%) hemodialysis dependent Pt was responsive to dose adapted treatment of len and dexamethasone (dex). Mutations in the C2H2-type 3 region of IKZF3 in a len resistant (Gly191Arg, AF 48%) pt occured as well as in a len and dex responsive (Arg242Gly, AF 52%) Pt. Furthermore, we identified a truncating XBP1 mutation (p.Leu232*, 97% AF) in a Pt refractory to bortezomib. One patient harbored a mutation in the steroid receptor NR3C1 (Pro255Leu, 22% variant reads). Finally, integrated mutation and copy-number data identified biallelic deletions of CDKN2C and FAM46C in a multi drug refractory Pt. Mutation and/or copy-number losses in both alleles were found in DIS3 in 4 Pts, in CYLD, TP53 and TRAF3 in 2 Pts and in CARD11, CDKN2A, CDKN1B, RB1and STAT3 in one Pt each.Conclusion: In summary, we report the initial results from 38 MM Pts using a custom MM sequencing panel which employs small amounts of DNA requiring very few cells and providing deep coverage in clinically meaningful timeframes. Our findings frequently include prognostically significant information, actionable targets and mutations in genes related to drug resistance. Targeted mutation profiling will likely become part of the clinical workup in MM and our M3P2.0 mutation panel is a suitable tool to provide information needed to guide precision therapy and to set the basis for individually tailored treatment decisions.1. Kortuem KM. et al. Development Of a 47 Gene Sequencing Panel For Common Mutations Present In Multiple Myeloma: Preliminary Results In 77 p53 Deleted Patients, ASH 2013. DisclosuresStewart:Celgene: Consultancy; Bristol Myers Squibb: Consultancy; Array BioPharma: Consultancy; Sanofi: Consultancy; Takeda Pharmaceuticals International Co.: Research Funding; Novartis: Consultancy. Bruins:OncoSpire: Salary support Other. Vasmatzis:OncoSpire: Salary Support Other. Kumar:Celgene: Consultancy, Research Funding; Millennium: The Takeda Oncology Co.: Consultancy, Research Funding; Onyx Pharmaceuticals: Consultancy, Research Funding; Sanofi-Aventis: Consultancy, Research Funding; Array BioPharma: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Skyline Diagnostics: Membership on an entity’s Board of Directors or advisory committees. Fonseca:Medtronic, Otsuka, Celgene, Genzyme, BMS, Lilly, Onyx, Binding Site, Millennium, AMGEN: Consultancy, patent for the prognostication of MM based on genetic categorization of the disease. He also has sponsored research from Cylene and Onyx Other, Research Funding. Bergsagel:MundiPharma: Research Funding; OncoEthix: Research Funding; Constellation Pharmaceutical: Research Funding; Novartis: Research Funding.

Clinical Grade “SNaPshot” Genetic Mutation Profiling in Multiple Myeloma

Whole genome sequencing studies have identified several oncogenic mutations in multiple myeloma (MM). As MM progresses, it evolves genetically underscoring the need to have tools for rapid detection of targetable mutations to optimize individualized treatment. Massachusetts General Hospital (MGH) has developed a Clinical Laboratory Improvement Amendments (CLIA)-approved, high-throughput, genotyping platform to determine the mutation status of a panel of known oncogenes. Sequence analysis using SNaPshot on DNA extracted from bone marrow and extramedullary plasmacytomas is feasible and leads to the detection of potentially druggable mutations. Screening MM patients for somatic mutations in oncogenes may provide novel targets leading to additional therapies for this patient population.