Abstract: Introduction: Multiple Myeloma (MM) is an incurable plasma cell malignancy commonly preceded by the asymptomatic stage smoldering multiple myeloma (SMM). MM is characterized with significant genomic heterogeneity of chromosomal gains and losses (CNVs), translocations, and point mutations (SNVs); alterations that are also observed in SMM patients. However, current SMM risk models rely solely on clinical markers and do not accurately capture progression risk. While incorporating some genomic biomarkers improves prediction, using all MM genomic features to comprehensively stratify patients may increase risk stratification precision in SMM. Methods: We obtained a total of 214 patient samples at SMM diagnosis. We performed whole-exome sequencing on 166 tumors; of these, RNA sequencing was performed on 100. Targeted capture was done on 48 additional tumors. Upon binarization of DNA features, we performed consensus non-negative matrix factorization to identify distinct molecular clusters. We then trained a random forest classifier on translocations, SNVs, and CNVs. The predicted clinical outcomes for the molecular subtypes were further validated in an independent SMM cohort of 74 patients. Results: We identified six genomic subtypes, four with hyperdiploidy ( & gt;48 chromosomes, HMC, HKR, HNT, HNF) and two with IgH translocations (FMD, CND) (Table 1). In multivariate analysis accounting for IMWG (20-2-20) clinical risk stages, high-risk (HMC, FMD, HKR) and intermediate-risk (HNT, HNF) genetic subtypes were independent predictors of progression (Hazards ratio [HR]: 3.8 and 5.5, P = 0.016 and 0.001, respectively). The low-risk, CND subtype harboring translocation (11;14) was enriched for the previously defined CD-2 MM signature defined by the B cell markers CD20 and CD79A (FDR = 0.003 ), showed upregulation of CCND1, E2F1, and E2F7 (FDR = 0.01, 0.0004, 0.08), and was enriched for G2M checkpoint, heme metabolism, and monocyte cell signature (FDR = 0.003, 0.003, 0.003, respectively). The FMD subtype with IgH translocations (4;14) and (14;16) was enriched for P53, mTORC1, unfolded protein signaling pathways and plasmacytoid dendritic cell signatures (FDR = 0.01, 0.005, 0.008, respectively). The HKR tumors were enriched for inflammatory cytokine signaling, MYC target genes, T regulatory cell signature, and the MM proliferative (PR) signatures (FDR = 0.02, 0.03, 0.007, 0.02, respectively). The APOBEC mutational signature was enriched in HMC and FMD tumors (P = 0.005), while there was no statistical difference across subtypes in the AID signature. The median follow-up for the primary cohort is 7.1 years. Median TTP for patients in HMC, FMD, and HKR was 3.8, 2.6, and 2.2 years, respectively; TTP for HNT and HNF was 4.3 and 5.2, respectively, while it was 11 years in CND patients (P = 0.007). Moreover, by analyzing the changes in MM clinical biomarkers over time, we found that patients from high-risk subgroups had higher odds of developing evolving hemoglobin and monoclonal protein levels over time (P = 0.01 and 0.002, respectively); Moreover, the absolute increase in M-protein was significantly higher in patients from the high-risk genetic subtypes at one, two, and five years from diagnosis (P = 0.001, 0.03, and 0,01, respectively). Applying the classifier to the external cohort replicated our findings where intermediate and high-risk genetic subgroups conferred increased risk of progression to MM in multivariate analysis after accounting for IMWG staging (HR: 5.5 and 9.8, P = 0.04 and 0.005, respectively). Interestingly, within the intermediate-risk clinical group in the primary cohort, patients in the high-risk genetic subgroups had increased risk of progression (HR: 5.2, 95% CI 1.5 - 17.3, P = 0.007). In the validation cohort, these patients also had an increased risk of progression to MM (HR: 6.7, 95% CI 1.2 - 38.3, P = 0.03), indicating that molecular classification improves the clinical risk-stratification models. Conclusion: We identified and validated in an independent dataset six SMM molecular subgroups with distinct DNA alterations, transcriptional profiles, dysregulated pathways, and risks of progression to active MM. Our results underscore the importance of molecular classification in addition to clinical evaluation in better identifying high-risk SMM patients. Moreover, these subgroups may be used to identify tumor vulnerabilities and target them with precision medicine efforts. Figure 1 Figure 1. Disclosures Bustoros: Janssen, Bristol Myers Squibb: Honoraria, Speakers Bureau; Takeda: Consultancy, Honoraria. Casneuf: Janssen: Current Employment. Kastritis: Amgen: Consultancy, Honoraria, Research Funding; Takeda: Honoraria; Pfizer: Consultancy, Honoraria, Research Funding; Genesis Pharma: Honoraria; Janssen: Consultancy, Honoraria, Research Funding. Walker: Bristol Myers Squibb: Research Funding; Sanofi: Speakers Bureau. Davies: Takeda: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Roche: Consultancy, Honoraria; Janssen: Consultancy, Honoraria. Dimopoulos: Amgen: Honoraria; BMS: Honoraria; Takeda: Honoraria; Beigene: Honoraria; Janssen: Honoraria. Bergsagel: Genetech: Consultancy, Honoraria; Oncopeptides: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Patents & Royalties: human CRBN mouse; GSK: Consultancy, Honoraria; Celgene: Consultancy, Honoraria. Yong: BMS: Research Funding; Autolus: Research Funding; Takeda: Honoraria; Janssen: Honoraria, Research Funding; Sanofi: Honoraria, Research Funding; GSK: Honoraria; Amgen: Honoraria. Morgan: BMS: Membership on an entity's Board of Directors or advisory committees; Jansen: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Oncopeptides: Membership on an entity's Board of Directors or advisory committees; GSK: Membership on an entity's Board of Directors or advisory committees. Getz: IBM, Pharmacyclics: Research Funding; Scorpion Therapeutics: Consultancy, Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees. Ghobrial: AbbVie, Adaptive, Aptitude Health, BMS, Cellectar, Curio Science, Genetch, Janssen, Janssen Central American and Caribbean, Karyopharm, Medscape, Oncopeptides, Sanofi, Takeda, The Binding Site, GNS, GSK: Consultancy.

Abstract: Genomic rearrangements in the MYC locus occur in ∼12% of lymphomas with diffuse large B-cell lymphoma (DLBCL) morphology and are associated with inferior outcome. Previous studies exploring MYC rearrangements have primarily used fluorescence in situ hybridization (FISH) assays to characterize break-apart status but have rarely examined breakpoint location, and in some cases have not examined partner identity. We performed targeted sequencing of MYC, BCL2, BCL6, and the immunoglobulin (IG) loci in 112 tumors with DLBCL morphology harboring MYC rearrangement. We characterized the location of the MYC rearrangement at base pair resolution and identified the partner in 88 cases. We observed a cluster of breakpoints upstream of the MYC coding region and in intron 1 (the “genic cluster”). Genic cluster rearrangements were enriched for translocations involving IGH (80%), whereas nongenic rearrangements occurred mostly downstream of the MYC gene with a variety of partners, including IGL and IGK. Other recurrent partners included BCL6, ZCCHC7, and RFTN1, which has not previously been described as a MYC partner. We compared 2 commercially available FISH break-apart assays for the MYC locus and observed discordant results in 32% of cases examined, including some with MYC-IGL and MYC-IGK rearrangements. In cases of high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement (HGBL-DH), so-called “double-hit” lymphomas, the majority of MYC rearrangements had non-IG partners (65%), with breakpoints outside the genic cluster (72%). In patients with de novo HGBL-DH of DLBCL morphology, MYC-IG rearrangements showed a trend toward inferior time to progression and overall survival compared with MYC–non-IG rearrangements. Our data reveal clinically relevant architecture of MYC rearrangements in lymphomas with DLBCL morphology.

Abstract: Abstract 804 Introduction: Follicular lymphoma (FL) and diffuse large B cell lymphoma (DLBCL) are the two most common types of non Hodgkin lymphoma (NHL). It is widely accepted that DLBCL can be divided into two major subtypes using gene expression profiling: germinal center B-cell (GCB) and activated B-cell (ABC). Both FL and the GCB subtype of DLBCL derive from germinal center B cells and have been found to share some common mutational events such as translocations leading to the deregulation of the BCL2 oncogene and mutations affecting a single tyrosine (Y641) in the histone methyltransferase EZH2. In contrast, ABC DLBCL tumors are characterized by mutations leading to the constitutive activity of NFkB. The clear differences in treatment response between subtypes allow this distinction to be used as a prognostic indicator and may ultimately lead to therapies that target individual features of each subtype. However, besides the gene expression and mutational signatures that differentiate the DLBCL subtypes, there is a paucity of molecular prognostic markers in these NHLs. Further, there is limited knowledge about the genetic events that drive the GCB subtype of DLBCL, which, if better understood, may enable the design of targeted therapeutics. Methods: To identify mutations driving lymphomagenesis and in particular, aggressive cases of NHL, we applied Illumina second-generation sequencing technology to the analysis of tumor genomes and constitutional DNAs from a FL and a DLBCL tumor and the exomes from two additional DLBCLs. In these “omes”, we identified somatic protein-altering point mutations in more than 250 genes including genes known to be involved in cancer, for example TP53, FAS and TNFAIP3 (A20). Many of these mutations may represent passenger rather than driver mutations, the latter of which are involved in disease progression. To identify the likely driver mutations, we sought to identify the genes that are recurrent targets of somatic mutation in these cancers. To this end, we further analyzed the transcriptome sequences we generated using RNA-seq from 95 primary DLBCLs,13 FL cases and 10 DLBCL-derived cell lines. Results: 105 of the genes found mutated in the FL and DLBCL genomes were observed to be recurrent targets of somatic mutation in these diseases. Some of these were known targets of aberrant somatic hypermutation (SHM) including BCL2, PIM1, and IRF4 and others have been previously identified as targets of recurrent mutation in lymphoma, such as EZH2, CD79B and CARD11. One of the most frequently mutated genes was MLL2, a histone methyltransferase never before implicated in lymphomagenesis. MLL2 showed a pattern of mutation characteristic of a dosage-sensitive tumor suppressor gene. Another frequently mutated gene was MEF2B, a calcium-regulated transcriptional co-activator/repressor that cooperates with histone modifying enzymes to epigenetically regulate the expression of genes. We found that mutations affecting MEF2B occur in 11.7% of FL and 9% of DLBCL, with the majority (73%) of these mutations affecting three amino acids (K4, Y69, and D83). Analysis of these 105 recurrently mutated genes for prognostic signatures is ongoing. Conclusions: High-throughput sequencing platforms have enabled the identification of recurrent targets of somatic mutations never suspected to be involved in lymphoma. Some of these mutated genes may have prognostic value while others may represent targets for the rational design of novel therapeutics. Disclosures: No relevant conflicts of interest to declare.

Abstract: Abstract 632 Introduction: Non-Hodgkin lymphomas (NHL) are the most common type of lymphoma and can be broadly classified as indolent (slow-growing) diseases, progressing over many years; and aggressive (fast-growing) diseases, which progress rapidly. The latter class includes diffuse large B-cell lymphoma (DLBCL), which accounts for approximately 30% of all NHL diagnoses. Three DLBCL subtypes have been identified based on gene expression profiling, namely: germinal center B-cell (GCB), activated B-cell (ABC) and primary mediastinal B-cell lymphoma (PMBCL). These subtypes show substantial differences in response to treatment and ultimate disease outcome, suggesting that molecular subtyping is an important prognostic indicator and that each subtype may benefit from a distinct treatment regimen. Despite recent advances in cancer genomics revealing molecular and mutational differences between these subtypes, further studies focused on the common NHL subtypes are required to identify critical players in the pathogenesis of DLBCL that may be targeted by pharmacological intervention to improve patient outcome. Methods: Using ultra-high throughput whole genome shotgun sequencing (WGSS) and whole transcriptome shotgun sequencing (WTSS/RNA-seq) we have discovered protein-coding mutations in NHL genomes. With a focus on recurrent and likely gain-of-function mutations we have established procedures to model the three-dimensional structures of mutant proteins and using a computational “molecular docking” pipeline have identified candidate molecules with specificity for the mutant protein. These small molecule compounds are acquired and tested in cell proliferation assays against a suite of DLBCL cell lines characterized for target mutations. Results: Mutations affecting a single key tyrosine in the catalytic site of enhancer of zeste, homolog 2 (EZH2), a member of the Polycomb-group family involved in transcriptional repression were identified (Morin, R. et al. 2010 Nature Genetics 42(2):181-5). This mutation, in a gene previously unknown to be mutated in cancer, is restricted to the GCB subtype of lymphomas and is highly prevalent in patient samples and DLBCL cell lines. Mutations have also been observed in other proteins involved in epigenetic regulation and thus afford potentially novel therapeutic targets. In proof-of-principle experiments small molecule inhibitors were identified using molecular docking approaches to target the effect of EZH2 mutations in both mutant and wild-type DLBCL cell lines. We identified and imported 96 compounds from the Developmental Therapeutic Program NCI/NIH repository. These compounds were tested in alamarBlue cell proliferation assays revealing three with activity at 10uM concentration in EZH2 mutant but not wild-type cells. Computational optimization of these compounds is underway to identify related compounds with improved activities at reduced concentrations. Conclusions: High-throughput sequencing platforms have enabled the identification of recurrent, non-synonymous protein mutations in tumor genomes and transcriptomes. Such a catalogue of mutations provides new avenues of exploration for targeted therapy including small molecule inhibitors. Despite intensive efforts launched in recent years to determine the crystal structure for every human protein, many (including EZH2) do not currently have three dimensional structures. This poses a challenge to novel drug discovery but can be overcome using homology modeling and/or targeting other members of a pathway. Our observations also demonstrate the importance of epigenetic regulation in NHL tumorigenesis and thus provide potential new therapeutic targets. Disclosures: No relevant conflicts of interest to declare.

Abstract: Abstract 439 Introduction: Follicular lymphoma (FL) is the most common indolent lymphoid malignancy in North America with approximately 20,000 new cases of this incurable cancer diagnosed each year. In approximately 85% of patients, FL is associated with the reciprocal translocation t(14;18)(q32;q21), which results in a fusion between IGH and BCL2 genes and consequent over-expression of the anti-apoptotic protein BCL2. This translocation likely represents an initiating event for FL, requiring additional mutational events for the onset of clinical disease. To investigate the relationship between genome rearrangements and FL we identified rearrangement locations in the genome followed by detailed, fine-structure analysis of the rearrangements to ascertain their effects on genes and other features of biological interest. Patients and Methods: We used a whole-genome bacterial artificial chromosome (BAC) fingerprint-based approach, termed Fingerprint Profiling (FPP, Krzywinski, M. et al. 2007), to detect genome rearrangements relative to the reference human genome in neoplastic B cells purified from 24 FL patient biopsies. Analysis of 2,640,707 BAC fingerprints revealed 721 candidate genomic rearrangements. To validate these observations and provide base-pair resolution of the rearrangement breakpoints we performed paired-end massively parallel sequencing, on the Illumina Genome Analyzer II platform, of the breakpoint-containing regions captured in the BAC clones. Sequence reads were assembled into contigs using our in-house de novo assembly algorithm ABySS (Assembly By Short Sequences, Simpson, J. et al. 2009) then aligned to the reference human genome. Following manual annotation of the breakpoint junctions PCR primers were designed to assay patient tumour and matched constitutional DNA and thus determine whether the observed genome rearrangements were somatic (acquired) or germline in origin. Results: 727 BACs with apparent large-scale genome rearrangements, representing 354 distinct genome rearrangements across 20 patients, were sequenced in 95 pools, generating 72 Gbp of sequence. The 354 distinct events include 163 deletions, 71 inversions, 27 insertions, 83 translocations and 10 duplications, ranging in size from 3 kb to 67 Mb. PCR assays for 194 of the distinct events have been performed thus far identifying 80 distinct somatic and 114 germline-derived structural variations at base-pair resolution. Of the somatic events 5 are present in two or more of the 20 patients analyzed including a 720 kb inversion of 3q27.3 that results in expression of a BCL6-ST6GAL1 fusion transcript. Identification at base-pair resolution of breakpoint sequences enabled a detailed study of breakpoint and fusion mechanisms. We classified breakpoint junctions into 4 groups; those with microhomology (48%), those with sequence additions (28%), those with blunt fusions (20%) and those with flanking low copy repeats (4%). We were particularly interested in establishing the origin of the observed nucleotide sequence additions in 97 breakpoint junctions. The sequence additions ranged in size from a single nucleotide to 454 bp. In one case we have unambiguously mapped a 53 bp sequence, lying within one of the 3q27.3 inversion breakpoints, to chromosome 5q12.3. This finding is consistent with the recently proposed fork stalling and template switching (FoSTeS) DNA replication-based mechanism and thus represents a novel mechanism in FL lymphomagenesis. Conclusions: We have successfully employed high-throughput clone fingerprinting and sequencing to identify numerous novel somatic and germline genome rearrangements from FL primary tumour samples. Furthermore, base-pair resolution of rearrangement breakpoints provides mechanistic insights. With the complete inventory of somatic and germline events in hand we will be able to propose recurrent structurally altered genes in FL patients for validation in independent datasets and improve our understanding of FL biology. Pathway analyses to identify emerging themes from somatic mutations are also being performed. The PCR assays we have developed will also be of utility in identifying germline predisposition alleles in larger FL patient cohorts. Disclosures: No relevant conflicts of interest to declare.

Abstract: Introduction: Central nervous system (CNS) relapse is a rare phenomenon in diffuse large B-cell lymphoma (DLBCL), occurring in less than 5% of all patients, but is associated with disproportionate morbidity and mortality. Indeed, the median survival of patients diagnosed with CNS relapse is as low as 2-4 months. Individual risk factors for CNS relapse are well established, and include clinical parameters such as stage, number/type of extranodal sites and elevated lactate dehydrogenase. These and other clinical risk factors have been integrated into a risk score that is reproducible and easy to calculate (CNS International Prognostic Index). Moreover, molecular attributes such as double-hit translocation status, MYC/BCL2 dual protein expression and the activated B-cell-like subtype have been associated with a higher risk of CNS relapse. However, while experts recommend prophylactic interventions for high-risk patients, the major shortcoming of available risk tools is their limited sensitivity. Herein, we evaluated whether gene expression and/or mutational profiles can identify those patients that will ultimately experience CNS relapse, and whether intratumoral heterogeneity impedes accurate prognostication. Methods: We accrued diagnostic FFPET samples from 230 newly diagnosed DLBCL patients, selected to fall into 3 clinical groups: 1) cases with CNS relapse/CNS involvement at diagnosis (n=58); 2) cases with systemic relapse but without CNS relapse (n=64) and 3) cases without any relapse (n=108). These 230 samples were subjected to microarray-based gene expression profiling and differential gene expression analysis. Pathway analysis was performed using Gene Set Enrichment Analysis on ranked gene lists. We assembled a partially overlapping dataset with mutation data of 45 genes in 213 diagnostic samples (n=65 with CNS relapse, 62 with systemic relapse and 86 without relapse). Lastly, we performed exome sequencing in 5 pairs (peripheral and CNS parenchymal tumors) of patients with CNS relapse or CNS involvement at diagnosis, and reconstructed clonal phylogenies using PyClone. Results: Focusing on gene expression data at first, we did not observe significant differential expression between CNS relapse and non-relapse cases at the individual gene level. This was in contrast to the comparison between systemic relapse vs. non-relapse cases where 368 genes were differentially expressed (adjusted P 〈 0.05). In terms of pathway analysis, minimal gene set enrichment was seen in CNS relapse cases, whereas functional annotations such as translation, ribosome biogenesis and MYC targets were significantly enriched in cases with systemic relapse. In keeping with these observations, the percentage of cases that were positive for the recently published double hit signature was highest in cases with systemic relapse (64% vs. 39% in CNS relapse cases and 27% in cases without relapse, P=0.012). However, CNS relapsing cases were defined by down-regulation of numerous immune signatures (e.g. interferon and multiple T cell signatures), suggesting that an intact immune response may have a protective effect on CNS relapse. Considering mutation data, we found that TP53 and SGK were most commonly mutated in systemic relapse cases, while TNFRSF14 and KTM2D were most commonly mutated in non-relapse cases (all adjusted P 〈 0.05). The only gene mutation with a borderline significant trend for enrichment in CNS relapse cases was MYD88 (adjusted P=0.05). We then performed exome sequencing of 5 tumor pairs. A subset of high-confidence somatic variants and tumor purity were used as input for PyClone to infer clonal population structures. In all pairs, we documented the existence of common ancestral mutations, as well as significant clonal divergence, with CNS-exclusive mutations not identified in diagnostic specimens. Conclusion: In summary, we have documented that CNS and systemic relapse result from distinct biological processes that, in part, may be associated with the underlying taxonomy of DLBCL. Our findings further show that CNS relapse results from the dissemination of sub-clones that may not be readily sampled at the time of diagnosis, and that intratumoral heterogeneity may limit our ability to predict CNS relapse. Large-scale, integrative analyses and in-depth characterization of clonal trajectories hold the promise to increase our ability to predict dissemination of DLBCL into the CNS. Disclosures Kridel: Gilead Sciences: Research Funding. Villa:Roche, Abbvie, Celgene, Seattle Genetics, Lundbeck, AstraZeneca, Nanostring, Janssen, Gilead: Consultancy, Honoraria. Steidl:Nanostring: Patents & Royalties: Filed patent on behalf of BC Cancer; Juno Therapeutics: Consultancy; Bristol-Myers Squibb: Research Funding; Roche: Consultancy; Tioma: Research Funding; Bayer: Consultancy; Seattle Genetics: Consultancy. Savage:BMS, Merck, Novartis, Verastem, Abbvie, Servier, and Seattle Genetics: Consultancy, Honoraria; Seattle Genetics, Inc.: Consultancy, Honoraria, Research Funding. Scott:Celgene: Consultancy; Roche/Genentech: Research Funding; NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoSting [Institution], Research Funding; Janssen: Consultancy, Research Funding.

Abstract: Abstract 139 Background: Diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) constitute 70% of all non-Hodgkin lymphomas (NHL). Both malignancies derive from germinal center (GC) B-cells and are characterized by clinical and genomic heterogeneity. Chromosomal alterations that deregulate oncogenes as well as mutations in genes involved in cell proliferation and apoptosis have been described in DLBCL. This disease can also be divided into distinct molecular subtypes by gene expression profiling. Differences observed between the activated B-cell (ABC) and germinal center B cell (GCB) subtypes result in part from distinct genomic alterations (Lenz, PNAS 2008) . For example, recent targeted re-sequencing efforts have revealed mutations in various genes in the NFkB signaling pathway, which likely contribute mainly to the ABC subtype (Compagno, Nature 2009). Thus far, few GCB-specific mutations other than t(14;18) have been identified. Methods: Targeted re-sequencing studies are only able to reveal mutations in pre-selected candidate genes and so much of the genome has not yet been investigated in lymphomas. To obtain a more global view of the mutational landscape of NHL, we applied Illumina massively parallel second-generation sequencing to sequence the genomic DNA of a FL tumor sample. In parallel, we sequenced the transcriptomes (i.e. mRNA) of 31 DLBCL tumor samples using the same technology. Results: Genomic sequencing revealed a mutation altering tyrosine 641 (Y641) in the polycomb group oncogene Enhancer of Zeste Homolog 2 (EZH2), a gene responsible for trimethylating lysine 27 on histone H3 (H3K27). Mutations affecting the same codon were also observed in 4 DLBCL samples. These mutations were confirmed to be somatic in nature by Sanger sequencing exon 15 in tumor DNA and germline DNA derived from peripheral blood in these 5 patients. Sanger sequencing all coding exons in EZH2 from an additional 25 FL samples revealed that mutations were restricted to codon 641. These mutations could change the tyrosine residue to Asparagine, Serine, Phenylalanine or Histidine. The frequency of EZH2 Y641 mutations in GCB-derived lymphomas was determined by Sanger sequencing exon 15 in a total of 479 lymphoma samples. EZH2 (Y641) mutations occurred predominantly in lymphomas of the GCB type: 18/80 (22%) GCB-type de novo DLBCL, 6/52 (11.5)% of “transformed” DLBCL derived from FL and 16/225 (7.1%) of pre-treatment FL samples. No EZH2 mutations were found in 42 DLBCL of the ABC subype, 25 mantle cell lymphomas, 30 small lymphocytic lymphomas or 25 T cell lymphomas or 23 reactive tonsils. Introducing each of the four Y641 mutations into wild-type EZH2 resulted in 15-fold reduction in the ability to trimethylate lysine 27 on H3 peptides in-vitro. Discussion: Over-expression of EZH2 is thought to drive malignancy in a variety of solid tumors but mutations in this gene have never been described. The trimethylated H3K27 epigenetic mark is used to silence the transcription of genes involved in differentiation and hematopoiesis. In Drosophila, the phenotypic consequence of mutating the orthologous tyrosine residue in the E(z)(“Enhancer of Zeste”) gene indicates an apparent gain-of-function (Jones, Genetics 1990). Taken together, our mutation frequency and biochemical data are compatible with the notion that alteration of the ability of germinal center B-cells to trimethylate H3K27 may promote the development of FL and the GCB subtype of DLBCL. Disclosures: Zhu: BPS Biosciences: Employment. Kimbara:BPS Biosciences: Employment. Shashkin:BPS Biosciences: Employment. Charlot:BPS Biosciences: Employment. Tcherpakov:BPS Biosciences: Employment.

Abstract: MYC and BCL2 genetic alterations are associated with COO subtype-specific clinical effect in R-CHOP-treated DLBCL.

Abstract: Hodgkin Lymphoma (HL) accounts for 11% of all lymphomas and despite being one of the most curable lymphomas, 20% of HL patients still ultimately die of their disease. Similarly, a proportion of cases of primary mediastinal B cell lymphoma (PMBCL) have refractory disease or early relapse and frequently fail second-line therapy. Development of more targeted therapeutic approaches is impeded by the lack of knowledge about the mutational landscape in the cancer genomes of these lymphomas. PTPN1 is a protein tyrosine phosphatase gene that encodes the protein, PTP1B. PTP1B dephosphorylates tyrosine residues on many activated kinases to maintain cellular homeostasis. As overactive receptor kinases are critical oncogenic events in cancer, we hypothesized that constitutively active Janus kinase-Signal transducer and activation of transcription (JAK-STAT) observed in HL and PMBCL are in part due to a mutated PTPN1 gene with an impaired functional ability to dephosphorylate this constitutive signaling pathway. Methods and samples Biopsies at the time of primary diagnosis were obtained for 49 PMBCL and 30 HL patients from the British Columbia Cancer Agency, Arizona Lymphoma Repository and the Hôpital Henri Mondor Pathology Department. DNA from PMBCL samples, microdissected Hodgkin Reed Sternberg (HRS) cells and 12 lymphoma-derived cell lines were extracted for PTPN1 exonic PCR amplification (nested PCR was used for HRS cell DNA) and Sanger sequencing. PTPN1 was silenced in a HL cell line (KMH2) by lentiviral transduction of a vector expressing shRNA and confirmed by quantitative real time (qRT) PCR. Wild type and mutant PTPN1 cDNA were cloned into the mammalian expression vector pcDNA 3.1 and expressed in HEK-293 cells. Protein expression of clinical samples, silenced and expressed cells were analyzed by immunohistochemistry and western blotting. Comparisons between groups were performed using two-sample student t tests. Results After exclusion of reported single nucleotide polymorphisms (SNPs) and silent mutations, 16 PTPN1 coding sequence mutations were found in our PMBCL cohort, corresponding to 14 mutations (29%) in clinical samples and 2 in PMBCL-dervied cell lines. Twelve additional mutations were discovered in our HL cohort, corresponding to 6 mutations (20%) in HRS cell samples and another 6 in HL-derived cell lines. In total, 14 (54%) missense, 4 (15%) frameshift, 3 (12%) single amino acid deletions, 4 (15%) nonsense mutations, and 1 (4%) promoter mutation were observed. Eight of these mutations were confirmed as somatic by sequencing of matched constitutional DNA. Silencing of PTPN1 resulted in hyperphosphorylation of JAK1, JAK2, STAT3, STAT5, STAT6 and up-regulation of the oncogenes, MYC and BCL6. Ectopic expression of nonsense and missense PTPN1 mutants in HEK-293 cells led to sustained phosphorylation of STAT6 in comparison to the empty vector control (densitometric values Q9* 0.5 vs. 1.0, R156* 0.7 vs. 1.0, M74L 0.4 vs. 1.0 and M282L 0.8 vs. 1.0). Furthermore, no phosphatase activity was observed for the nonsense mutants and moderate phosphatase activity for the missense mutants using a tyrosine phosphatase-specific substrate (fold change Q9* 2.0, R156* 1.9, M74L 46.7, M282L 46.0 and WT 58.3, compared to empty vector control). Immunohistochemical analysis showed that PTPN1 mutations correspond to decreased protein expression in PMBCL (p=0.03). Discussion PTPN1 is recurrently mutated in PMBCL and HL contributing to constitutive JAK-STAT signaling and oncogene dysregulation. These data suggest PTPN1 mutations as novel driver alterations in these lymphomas and might provide a novel, rational therapeutic target for treating HL and PMBCL patients. Disclosures: Savage: Eli-Lilly: Consultancy. Connors:F Hoffmann-La Roche: Research Funding; Roche Canada: Research Funding.

Abstract: Abstract 436 Background: Mantle cell lymphoma (MCL) is an aggressive subtype of non-Hodgkin's lymphoma that is characterized by the hallmark t(11;14)(q13;q32) translocation, as well as a high number of secondary chromosomal alterations. Further, a small number of genes such as TP53, ATM and CCND1 have been reported to be recurrently mutated in MCL, but do not fully explain the biology and do not adequately account for the wide spectrum of clinical manifestations, response to treatment and prognosis. The aim of this study was to discover new somatic mutations that could contribute to our understanding of the pathogenesis of MCL. Methods: In our discovery cohort, we sequenced the transcriptomes of 18 clinical samples (11 diagnostic and 7 progression biopsies) and 2 mantle cell lymphoma-derived cell lines (Mino and Jeko-1). For this purpose, whole transcriptome shotgun sequencing was performed on RNA extracted from fresh frozen tissue. We assembled an extension cohort of 103 diagnostic patient samples and 4 additional cell lines (Rec-1, Z-138, Maver-1, JVM-2), and performed Sanger sequencing of NOTCH1 exons 26, 27 and 34 on genomic DNA. We further exposed the 6 cell lines to 1 μM of the γ-secretase inhibitor XXI (compound E) for 7 days and measured cellular proliferation with an EdU incorporation assay. Survival analysis was carried out in the 113 patients with diagnostic biopsies and available outcome data. Results: NOTCH1 mutations were found in 14 out of 121 patient samples (11.6%) and in 2 out of 6 cell lines, Mino and Rec-1 (33.3%). The majority of these mutations (12 out of 14) lie in exon 34 that encodes the PEST domain of NOTCH1 and consist of either small frameshift-causing indels (10 cases) or nonsense mutations (2 cases). These mutations are predicted to cause truncations of the C-terminal PEST domain. To gain further insight into functional relevance, we treated 6 cell lines with compound E, an inhibitor of the γ-secretase complex that plays a critical role in the release of the intracellular domain of NOTCH1 after ligand-induced activation. In Rec-1, that harbours a NOTCH1 mutation, we observed a significant decrease in proliferation (mean percentage of cells in culture incorporating EdU decreasing from 47.5% to 1.4%, p 〈 .001). No effect of compound E was observed in Mino, the other cell line with a NOTCH1 mutation, nor in the 4 cell lines that are wild type for NOTCH1. Outcome correlation analysis showed that NOTCH1 mutations are associated with poor overall survival (1.56 versus 3.86 years respectively, p=.001), but not with significantly shortened progression-free survival (0.88 versus 1.73 years respectively, p=.07). Discussion: We have identified recurrent mutations in NOTCH1 in a subset of patients with MCL (11.6%). The frequency and the pattern of mutations are strikingly similar to what has recently been reported in chronic lymphocytic leukemia, the other major CD5 positive B-cell malignancy (Nature, 2011 Jun 5, 475:101–105 and J Exp Med, 2011 Jul 4, 208:1389–1401). NOTCH1 mutations are associated with adverse prognosis as evidenced by shortened overall survival. This latter finding, however, should ideally be validated in a larger and uniformly treated cohort. Finally, the sensitivity of the Rec-1 cell line to compound E suggests that NOTCH1 mutations could serve as the target for tailored therapy in mantle cell lymphoma. Disclosures: Sehn: Roche/Genentech: Consultancy, Honoraria, Research Funding. Connors:Roche: Research Funding.