Taylor-Weiner, Amaro N

Richter's syndrome (RS) arising from chronic lymphocytic leukemia (CLL) is a striking example of an aggressive malignant histology that emerges from indolent cancer. A major barrier to disease control in CLL, RS is associated with poor clinical outcomes and limited survival. The genetic basis of RS is poorly understood and its relationship to antecedent CLL remains incompletely characterized. Notable challenges to the genomic study of RS includes those of sample acquisition, the distinction between true tumor events rather than sequence artifacts in archival fixed tissue, and the limitations of available computational techniques for deconvoluting admixtures of CLL and RS DNA within the same biopsy specimen. To address these challenges and characterize the genetic profile of RS, we performed whole-exome sequencing (WES) on samples collected from 42 patients with RS of diffuse large B cell lymphoma (DLBCL) histology. For this genomic characterization, samples from 37 patients were analyzed as 'trios' (matched germline, CLL and RS tissue DNA) and those from 5 as 'duos' (matched CLL and RS DNA). CLL diagnosis preceeded RS diagnosis by a median of 60.6 months (range 0.1-234.5). The median number of prior CLL-directed therapies was 2 (range 0-10). 8 patients had no prior CLL-directed therapy, while 9 were exposed to novel agents. The median time from most proximal CLL sampling to RS was 2.7 months (range: 82.2 months pre- to 3.8 months post RS diagnosis). Critical analytic innovations applied to this dataset included addressing contamination of CLL DNA in the germline sample (through the tool DeTIN) and generating the ability to discriminate between clones arising from RS or from CLL, even while both histologies were commonly co-existing within originating biopsies (via the tool PhylogicNDT). From this discovery cohort of 42 cases, 36 (86%) revealed RS and CLL to be clonally-related based on WES analysis, with a distinct RS clone emerging from an existing CLL subclone. Of the 6 (14%) cases determined to be clonally unrelated by WES, 4 had been previously examined by IGHV sequencing; only 1 of 4 was categorized as clonally unrelated, likely due to CLL and RS admixture. RS displayed mutational signatures reflecting aging (CpG), canonical AID, and non-canonical AID processes. Through deconvoluting clonal composition using PhylogicNDT in related sample trios (n=31), we established several notable differences compared to antecedent CLL. First, RS clones presented higher rates of additional mutations than the ancestral CLL clones from which they developed (2.47 vs. 0.86 Mut/Mb, p<0.0001). Second, the frequency of CLL-associated driver mutations in the RS clones was altered:TP53 mutation (n=21, 50%), NOTCH1 mutation (n=17, 40%) NFKBIE (n=5, 12%), EGR2 (n=6, 14%), XPO1 (n=5, 12%), and RPS15 (n=3, 7%). Third, the clonal transition to RS was marked by a diversity of additional driver mutations and particularly increased copy number variants (CNVs). RS biopsies had recurrent arm level events, including del(17p) in 44%, del(4p) in 27%, del(4q) in 27%, del(9p) in 22%, del(17q) in 22% and del(9q) in 20% (Q<0.05, GISTIC). The top focal alterations in RS biopsies, as identified by tool GISTIC included (Q value <= 0.05): amp(7q21.2) - CDK6,amp(8q24.3) - RECQL4, amp(13q31.3) - ERCC5, amp(19p13.3), amp(19q13.42), del(8p12), del(17p13.1) - TP53, del(13q14.3), del(7q35), and del(16q12.2). Finally, whole genome doubling was observed in 6 cases upon transition to RS. To further investigate RS and CLL clonal evolution at high resolution, we performed single-cell RNA-sequencing (10x Genomics), on biopsies at the time of RS diagnosis in 5 individuals with clonally related transformation. Data analysis and clustering was conducted using Seurat(v3) with doublet removal (DoubletFinder). We identified CNV in single-cell transcriptomes that matched the WES copy-number profiles of individual subclones of the RS and CLL populations and thus linked subclones identified by WES to single-cell expression clusters and states, revealing CLL, RS and intermediate evolutionary cell states. In conclusion, we identify that RS arises from CLL subclones through distinct mutational trajectories. Further molecular subclassification of RS, including genetic characterization of additional cases, and linking mutational data with clinical outcomes is ongoing and has potential to alter clinical classification and prognostication of RS. Disclosures Guieze: abbvie: Honoraria, Other: advisory board, travel funds; janssen cilag: Honoraria, Other: advisory board, travel funds; roche: Other: travle funds; gilead: Honoraria, Other: travel funds; astrazanecka: Honoraria, Other: advisory board. Leshchiner:PACT Pharma, Inc.: Consultancy. Tausch:Roche: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Research Funding. Davids:Genentech: Consultancy, Research Funding; Janssen: Consultancy; Gilead Sciences: Consultancy; Novartis: Consultancy, Research Funding; MEI Pharma: Consultancy, Research Funding; Surface Oncology: Research Funding; AbbVie: Consultancy; Adaptive Biotechnologies: Consultancy; Merck: Consultancy; Pharmacyclics: Consultancy, Research Funding; TG Therapeutics: Consultancy, Research Funding; Verastem: Consultancy, Research Funding; Syros Pharmaceuticals: Consultancy; Sunesis: Consultancy; Zentalis: Consultancy; AstraZeneca: Consultancy, Research Funding; Ascentage Pharma: Consultancy, Research Funding; Eli Lilly: Consultancy; Research to Practice: Honoraria; Celgene: Consultancy; BeiGene: Consultancy; Bristol Myers Squibb: Research Funding. Elagina:AbbVie: Current Employment. Jain:TG Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Servier: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Precision Bioscienes: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Research Funding; Pfizer: Research Funding; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Fate Therapeutics: Research Funding; Verastem: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Research Funding; Cellectis: Research Funding; BeiGene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Aprea Therapeutics: Research Funding; Genentech: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive Biotechnologies: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; ADC Therapeutics: Research Funding; AstraZeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Kipps:Oncternal Therapeutics, Inc.: Other: Cirmtuzumab was developed by Thomas J. Kipps in the Thomas J. Kipps laboratory and licensed by the University of California to Oncternal Therapeutics, Inc., which provided stock options and research funding to the Thomas J. Kipps laboratory, Research Funding; Celgene: Honoraria, Research Funding; Gilead: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Genentech/Roche: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; VelosBio: Research Funding; Pharmacyclics/ AbbVie, Breast Cancer Research Foundation, MD Anderson Cancer Center, Oncternal Therapeutics, Inc., Specialized Center of Research (SCOR) - The Leukemia and Lymphoma Society (LLS), California Institute for Regenerative Medicine (CIRM): Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Ascerta/AstraZeneca, Celgene, Genentech/F. Hoffmann-La Roche, Gilead, Janssen, Loxo Oncology, Octernal Therapeutics, Pharmacyclics/AbbVie, TG Therapeutics, VelosBio, and Verastem: Membership on an entity's Board of Directors or advisory committees. Broséus:Novartis: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; AstraZeneca: Consultancy, Honoraria; Gilead: Honoraria. Kay:MEI Pharma: Research Funding; Cytomx: Membership on an entity's Board of Directors or advisory committees; Abbvie: Research Funding; Tolero Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Bristol Meyer Squib: Membership on an entity's Board of Directors or advisory committees, Research Funding; Acerta Pharma: Research Funding; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Juno Theraputics: Membership on an entity's Board of Directors or advisory committees; Dava Oncology: Membership on an entity's Board of Directors or advisory committees; Oncotracker: Membership on an entity's Board of Directors or advisory committees; Rigel: Membership on an entity's Board of Directors or advisory committees; Agios Pharma: Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Membership on an entity's Board of Directors or advisory committees; Sunesis: Research Funding; Morpho-sys: Membership on an entity's Board of Directors or advisory committees. Purroy:AstraZenica: Current Employment. Utro:IBM: Current Employment. Rhrissorrakrai:IBM: Current Employment. Levovitz:IBM: Current Employment. Parikh:GlaxoSmithKline: Honoraria; Pharmacyclics: Honoraria, Research Funding; AstraZeneca: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; MorphoSys: Research Funding; TG Therapeutics: Research Funding; Merck: Research Funding; AbbVie: Honoraria, Research Funding; Ascentage Pharma: Research Funding; Genentech: Honoraria; Verastem Oncology: Honoraria. Brown:Abbvie, Acerta, AstraZeneca, Beigene, Invectys, Juno/Celgene, Kite, Morphosys, Novartis, Octapharma, Pharmacyclics, Sunesis, TG Therapeutics, Verastem: Consultancy; Gilead, Loxo, Sun, Verastem: Research Funding; Janssen, Teva: Speakers Bureau. Parida:IBM: Current Employment. Neuberg:Madrigak Pharmaceuticals: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding; Celgene: Research Funding. Stilgenbauer:Novartis: Consultancy, Honoraria, Other, Research Funding; Mundipharma: Consultancy, Honoraria, Other, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Other: travel support, Research Funding; Gilead: Consultancy, Honoraria, Other: travel support, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Other: travel support, Research Funding; Genentech: Consultancy, Honoraria, Other: travel support, Research Funding; Genzyme: Consultancy, Honoraria, Other: travel support, Research Funding; Pharmacyclics: Consultancy, Honoraria, Other, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Other: travel support, Research Funding; Celgene: Consultancy, Honoraria, Other: travel support, Research Funding; F. Hoffmann-LaRoche: Consultancy, Honoraria, Other: travel support, Research Funding; Amgen: Consultancy, Honoraria, Other: travel support, Research Funding; AbbVie: Consultancy, Honoraria, Other: travel support, Research Funding. Getz:Scorpion Therapeutics: Consultancy, Current equity holder in publicly-traded company, Other: Founder; IBM: Research Funding; Pharmacyclics: Research Funding; Broad Institute: Patents & Royalties: MuTect, ABSOLUTE, MutSig, MSMuTect, MSMutSig, POLYSOLVER and TensorQTL. Wu:Pharmacyclics: Research Funding; BionTech: Current equity holder in publicly-traded company.

PURPOSE Smoldering multiple myeloma (SMM) is a precursor condition of multiple myeloma (MM) with a 10% annual risk of progression. Various prognostic models exist for risk stratification; however, those are based on solely clinical metrics. The discovery of genomic alterations that underlie disease progression to MM could improve current risk models. METHODS We used next-generation sequencing to study 214 patients with SMM. We performed whole-exome sequencing on 166 tumors, including 5 with serial samples, and deep targeted sequencing on 48 tumors. RESULTS We observed that most of the genetic alterations necessary for progression have already been acquired by the diagnosis of SMM. Particularly, we found that alterations of the mitogen-activated protein kinase pathway ( KRAS and NRAS single nucleotide variants [SNVs]), the DNA repair pathway (deletion 17p, TP53, and ATM SNVs), and MYC (translocations or copy number variations) were all independent risk factors of progression after accounting for clinical risk staging. We validated these findings in an external SMM cohort by showing that patients who have any of these three features have a higher risk of progressing to MM. Moreover, APOBEC associated mutations were enriched in patients who progressed and were associated with a shorter time to progression in our cohort. CONCLUSION SMM is a genetically mature entity whereby most driver genetic alterations have already occurred, which suggests the existence of a right-skewed model of genetic evolution from monoclonal gammopathy of undetermined significance to MM. We identified and externally validated genomic predictors of progression that could distinguish patients at high risk of progression to MM and, thus, improve on the precision of current clinical models.

Abstract Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous disease characterized by multiple low-frequency alterations including somatic mutations, copy number alterations (CNAs) and chromosomal rearrangements. We sought to identify previously unrecognized low-frequency genetic events, integrate recurrent alterations into comprehensive signatures and associate these signatures with clinical parameters. For these reasons, our multi-institutional international group assembled a cohort of 304 primary DLBCLs from newly diagnosed patients, 87% of whom were uniformly treated with state-of-the-art therapy (rituximab-containing CHOP regimen) and had long term followup. Tumors were subjected to whole exome sequencing with an extended bait set that included custom probes designed to capture recurrent chromosomal rearrangements. In this cohort, 47% of samples had available transcriptional profiling and assignment to associated disease subtypes. Analytical pipelines developed at the Broad Institute were used to detect mutations (MuTect), CNAs (Recapseq+Allelic Capseq) and chromosomal rearrangements (dRanger+Breakpointer) and assess clonality (Absolute). To analyze formalin-fixed paraffin-embedded tumors without paired normals we developed a method which utilized 8334 unrelated normal samples to stringently filter recurrent germline events and artifacts. Significant mutational drivers were identified using the MutSig2CV algorithm and recurrent CNAs were assessed with GISTIC2.0. In addition, we utilized a recently developed algorithm, CLUMPS2, to prioritize somatic mutations which cluster in 3-dimensional protein structure. With this approach, we identified > 90 recurrently mutated genes, 34 focal amplifications and 41 focal deletions, 20 arm-level events and > 200 chromosomal rearrangements in the DLBCL series. Of note, 33% of the mutational drivers were also perturbed by chromosomal rearrangements or CNAs, underscoring the importance of a comprehensive genetic analysis. In the large DLBCL series, we identified several previously unrecognized but potentially targetable alterations including mutations in NOTCH2 (8%) and TET2 (5%). The majority of identified chromosomal rearrangements involved translocations of potent regulatory regions to intact gene coding sequences. The most frequently rearrangements involved Ig regulatory elements which were translocated to BCL2, MYC, BCL6 and several additional genes with known roles in germinal center B-cell biology. After identifying recurrent somatic mutations, CNAs and chromosomal rearrangements, we performed hierarchical clustering and identified subsets of DLBCLs with comprehensive signatures comprised of specific alterations. A large subset of tumors shared recurrent alterations previously associated with follicular lymphoma including mutations of chromatin modifiers such as CREBBP, MLL2, and EZH2 in association with alterations of TNFRSF14 and GNA13 and translocations of BCL2. This cluster was enriched in GCB-type DLBCLs and contained a subset with select genetic alterations associated with an unfavorable outcome. An additional cohort of tumors was characterized by alterations perturbing B-cell differentiation including recurrent BCL6 translocations or alterations of PRDM1. A subset of these DLBCLs had alterations of NOTCH2 and additional pathway components or mutations of MYD88 in association with TNFAIP3, CD70 and EBF1, a master regulator of B-cell differentiation. An additional group of DLBCLs exhibited frequent MYD88 mutations in association with alterations of CD79B, PIM1, TBL1XR1 and ETV6 and BCL2 copy gain; these tumors were highly enriched for ABC-type DLBCLs. This coordinate signature and additional alterations of p53 pathway components were associated with outcome. We explored bases for the identified genetic alterations in DLBCL by performing an in silico mutational signature analysis. The most frequent mutational signatures were those of spontaneous deamination (aging) and AID with rare cases of microsatellite instability. We also assessed the clonality of identified genetic features to define cancer cell fraction and establish the timing of specific genetic events. The comprehensive genetic signatures of clinically annotated DLBCLs provide new insights regarding approaches to targeted therapy. Disclosures Link: Kite Pharma: Research Funding; Genentech: Consultancy, Research Funding. Rodig:Perkin Elmer: Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding. Pfreundschuh:Boehringer Ingelheim, Celegene, Roche, Spectrum: Other: Advisory board; Roche: Honoraria; Amgen, Roche, Spectrum: Research Funding. Shipp:Gilead: Consultancy; Sanofi: Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Bayer: Membership on an entity's Board of Directors or advisory committees, Research Funding.