Abstract: Introduction Patients diagnosed with diffuse large B-cell lymphoma (DLBCL) are treated with standard frontline immunochemotherapy (R-CHOP). However, for cases where R-CHOP fails (relapsed-refractory DLBCL, rrDLBCL), prognosis is extremely poor, with 2-year overall survival of 20-40%. The successful development of new therapies may be hampered by our limited understanding of the genetic and molecular mechanisms underpinning treatment resistance. For example, recent data from our group has highlighted novel mutations that emerge following treatment with R-CHOP. The contribution of copy-number variations (CNVs) towards treatment resistance has not yet been thoroughly explored. A more complete characterization of these genetic alterations may lead to new prognostic biomarkers or treatment strategies. Methods We analyzed exome sequencing data from 59 rrDLBCL cases derived from either tissue biopsies or liquid biopsies collected after relapse, including both unpublished and previously published cases (Schmitz et al. (2018) NEJM 378:1396-1407 and Morin et al. (2016) Clin Can Res 22(9)). We separately performed low-pass whole-genome sequencing (lpWGS, 0.1-1x coverage) on 45 rrDLBCL liquid biopsies with ctDNA levels insufficient for exome-based analysis, for a total of 104 cases with copy-number information. We identified CNVs from exome and lpWGS data using Sequenza and ichorCNA, respectively. Next, we identified significant peaks of recurrent gains and losses using GISTIC2. Comparison of these peaks to CNVs in a previously published diagnostic DLBCL cohort (Schmitz et al. (2018) NEJM 378:1396-1407) enabled the identification of events that were significantly more prevalent in rrDLBCL. Results Overall, the landscape of CNVs in rrDLBCL is reminiscent of diagnostic DLBCL, with recurrent amplifications of chromosome 7 (43/104, 41.3%) and 18q (42/104, 40.4%) and recurrent deletions of 6q (25/104, 24.0%) and 17p13 (39/104, 37.5%). We identified nine regions enriched for recurrent amplifications or deletions among rrDLBCLs. These include deletions of 17p13.1 (20.4% in diagnostic biopsies vs 41.3% of rrDLBCLs, q=8.53x10-5) and recurrent amplifications of 8q24 (18.5% vs 42.3%, q=5.72x10-7) and 7p22 (27.2% vs 57.9%, q=6.29x10-8). Many of these peaks represent focal events that are exceedingly rare in diagnostic DLBCL and do not contain established lymphoma-associated genes, including amplifications affecting 700kb of 6p11.2 (2.03% vs 7.69%, q=0.0178) and 500kb of 19p13.3 (6.7% vs 31.7%, q=9.99x10-10). Notably, the 6p11.2 amplifications were associated with inferior progression-free survival following R-CHOP (p=0.02), with most tumors harboring this alteration relapsing within 12 months. We also identified a novel, recurrent deletion affecting a 20mb region of 5q (2.78% vs 10.6%, q=0.00604) which was significantly deleted in rrDLBCL. For tumors with additional samples collected prior to R-CHOP and following salvage therapy, deletions of 5q appeared to emerge following frontline therapy and persisted after subsequent treatments, suggesting they may contribute to treatment resistance. Discussion The 17p13.1 deletion enriched in rrDLBCL encompasses TP53, which is a common target of somatic point mutations in rrDLBCL and associated with inferior treatment outcomes. The amplification of 8q24 and 7p22 include MYC and GNA12/CARD11, respectively, although these large events encompass numerous additional genes which may be the target of such events. Curiously, the focal 6p11.2 amplification only overlaps a handful of genes including miR_598, which has been predicted to target CD27 and CD38 and whose expression is upregulated in B-cell cell lines (Lawrie et al. (2008) Leukemia 22:1440-2446). Further investigation and validation of these events and their corresponding targets will provide insight into the biology of rrDLBCL and may reveal novel therapeutic targets. Disclosures Michaud: Epizyme: Current Employment. Daigle:Epizyme: Current Employment. Jain:Kite/Gilead: Consultancy; Novartis: Consultancy. Kuruvilla:Merck: Consultancy, Honoraria; Bristol-Myers Squibb Company: Consultancy; Celgene Corporation: Honoraria; AstraZeneca Pharmaceuticals LP: Honoraria, Research Funding; AbbVie: Consultancy; Gilead: Consultancy, Honoraria; Karyopharm: Consultancy, Honoraria; Roche: Consultancy, Honoraria, Research Funding; Seattle Genetics: Consultancy, Honoraria; Janssen: Honoraria, Research Funding; Amgen: Honoraria; Antengene: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; TG Therapeutics: Honoraria. Crump:Servier: Consultancy; Roche: Consultancy; Kite/Gilead: Consultancy. Assouline:BeiGene: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Takeda: Research Funding; Pfizer: Consultancy, Honoraria; AstraZeneca: Consultancy, Honoraria, Speakers Bureau; F. Hoffmann-La Roche Ltd: Consultancy, Honoraria, Research Funding. Steidl:Juno Therapeutics: Consultancy; Seattle Genetics: Consultancy; Roche: Consultancy; Bristol-Myers Squibb: Research Funding; AbbVie: Consultancy; Bayer: Consultancy; Curis Inc: Consultancy. Johnson:AbbVie: Research Funding; Roche/Genentech, Merck: Honoraria; Roche/Genentech, Merck, Bristol-Myers Squibb, AbbVie: Consultancy. Scott:NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoString, Research Funding; Janssen: Consultancy, Research Funding; Roche/Genentech: Research Funding; NIH: Consultancy, Other: Co-inventor on a patent related to the MCL35 assay filed at the National Institutes of Health, United States of America.; Celgene: Consultancy; Abbvie: Consultancy; AstraZeneca: Consultancy. Morin:Celgene: Consultancy.

Abstract: Diffuse large B-cell lymphoma (DLBCL) patients are typically treated with immunochemotherapy containing rituximab (rituximab, cyclophosphamide, hydroxydaunorubicin-vincristine (Oncovin), and prednisone [R-CHOP]); however, prognosis is extremely poor if R-CHOP fails. To identify genetic mechanisms contributing to primary or acquired R-CHOP resistance, we performed target-panel sequencing of 135 relapsed/refractory DLBCLs (rrDLBCLs), primarily comprising circulating tumor DNA from patients on clinical trials. Comparison with a metacohort of 1670 diagnostic DLBCLs identified 6 genes significantly enriched for mutations upon relapse. TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations remained clonally persistent throughout treatment in paired diagnostic-relapse samples, suggesting a role in primary treatment resistance. Nonsense and missense mutations affecting MS4A1, which encodes CD20, are exceedingly rare in diagnostic samples but show recurrent patterns of clonal expansion following rituximab-based therapy. MS4A1 missense mutati ons within the transmembrane domains lead to loss of CD20 in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. In a time series from a patient treated with multiple rounds of therapy, tumor heterogeneity and minor MS4A1-harboring subclones contributed to rapid disease recurrence, with MS4A1 mutations as founding events for these subclones. TP53 and KMT2D mutation status, in combination with other prognostic factors, may be used to identify high-risk patients prior to R-CHOP for posttreatment monitoring. Using liquid biopsies, we show the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens.

Abstract: Introduction Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma and is characterized by its genetic and clinical heterogeneity. Patients can develop DLBCL de novo or as a transformation from other lymphoid malignancies, most commonly follicular lymphoma. For patients with relapsed/refractory DLBCL (rrDLBCL), prognosis is extremely poor with 2-year overall survival of 20-40%. While numerous treatments are under investigation to improve patient outcomes, the success of these treatments has been limited as the genetic mechanisms underpinning treatment resistance are largely unknown. Identifying genomic alterations which contribute to relapse may improve salvage therapy for patients with rrDLBCL or allow patients to be stratified prior to frontline treatment. Methods To identify genomic alterations which contribute to R-CHOP resistance, we previously collected samples from patients enrolled in four clinical trials exploring candidate salvage therapies for patients with rrDLBCL as well as a retrospective rrDLBCL cohort, totalling 193 cases (133 de-novo DLBCL, 60 transformed). Plasma samples were collected from each patient upon relapse along with diagnostic tissue biopsies where available. A combination of exome sequencing and target-panel sequencing of lymphoma associated genes was performed on circulating tumour DNA and tissue biopsies (if available). Mutations implicated in R-CHOP resistance were identified through two complimentary strategies. First, the mutation frequency of recurrently mutated genes across de novo rrDLBCL samples was compared to a cohort of unrelated diagnostic DLBCL cases (n=1691) to identify genes enriched for mutations. Second, the genomic landscape and tumor clonal structure was compared prior to and following R-CHOP to identify mutations in each patient that underwent clonal expansion following therapy. Anti-CD20 antibody binding affinity of MS4A1 mutants was evaluated using flow cytometry on transfected CHO-S cells. Results We have identified five genes enriched for mutations in our rrDLBCL cohort relative to diagnostic DLBCL: KMT2D (Mutated in 49%, Q=0.0385), TP53 (47%, Q=1.07x10-9), FOXO1 (11%, Q=0.0727), NFKBIE (11%, Q=0.0385), and MS4A1 (8%, Q=0.0522). Consistent with its characterization as a poor prognostic marker, mutations in TP53 were typically present at diagnosis and remained stable following R-CHOP therapy for both de novo and transformed DLBCL (23/27 cases, 85%). Recurrent mutations affecting Arg248 of TP53 (6.8%, Q=0.0413) were also clonally stable and have previously been associated with poor overall survival across several cancer types. The histone methyltransferase KMT2D is dominated by nonsense and frameshift mutations which were stable or underwent clonal expansion following R-CHOP (17/19, 89%). Recurrent missense mutations in MS4A1 targeted the small loop and adjacent transmembrane domains of CD20, including several patients with a Tyr86 mutation. Transfected cells carrying Tyr86Cys or Leu66Arg mutations were not bound by rituximab or other anti-CD20 antibodies including obinituzumab and ofatumumab. Subclonal populations containing MS4A1 mutations underwent clonal expansion (6 cases) or were stable (1 case) following treatment, including one case with multiple MS4A1 mutations in distinct subclonal populations which both underwent clonal expansion. In another unique case, a series of ctDNA samples were available prior to and following R-CHOP and salvage therapy, where we again observed convergent evolution of two mutually exclusive clonal subpopulations containing MS4A1 mutations. The first subpopulation underwent clonal expansion following frontline therapy but was extinguished following salvage therapy, while the other subpopulation underwent clonal expansion following salvage therapy and harboured a transmembrane domain mutation. Conclusion Mutations in TP53 and truncating mutations in KMT2D are generally present prior to treatment and will be investigated as biomarkers of treatment failure. Additional mutations are not always present at diagnosis, but their emergence can be detected in ctDNA and relapsed tissue, specifically mutations in MS4A1. As mutations in MS4A1 attenuate rituximab binding and are recurrently associated with clonal expansion, they likely impart a selective advantage and lead to resistance against anti-CD20 antibodies. Disclosures Michaud: Epizyme: Employment. Daigle:Epizyme: Employment. Jain:Kite/Gilead: Consultancy. Kuruvilla:Roche: Honoraria; Astra Zeneca: Honoraria; Novartis: Honoraria; Merck: Honoraria; Karyopharm: Honoraria; Gilead: Honoraria; Celgene: Honoraria; BMS: Honoraria; Amgen: Honoraria; Seattle Genetics: Consultancy; Roche: Consultancy; Merck: Consultancy; Karyopharm: Consultancy; Gilead: Consultancy; Janssen: Research Funding; Roche: Research Funding; BMS: Consultancy; Abbvie: Consultancy; Seattle Genetics: Honoraria; Janssen: Honoraria. Assouline:Abbvie: Consultancy, Honoraria; Janssen: Consultancy, Honoraria, Speakers Bureau; F. Hoffmann-La Roche Ltd: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria, Speakers Bureau. Scott:NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoSting [Institution], Research Funding; Celgene: Consultancy; Roche/Genentech: Research Funding; Janssen: Consultancy, Research Funding. Johnson:BD Biosciences: Other: Provided a significant proportion of the antibodies used in this project free of cost.; Merck: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Abbvie: Consultancy, Employment, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche: Consultancy, Employment, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel fees, gifts, and others, Research Funding; Seattle Genetics: Honoraria; Lundbeck: Employment, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel fees, gifts, and others, Research Funding.

Abstract: Cell-free DNA (cfDNA) has become a comprehensive biomarker in the fields of non-invasive cancer detection and monitoring, organ transplantation, prenatal genetic testing and pathogen detection. While cfDNA samples can be obtained using a broad variety of approaches, there is an urgent need to standardize analytical tools aimed at assessing its basic properties. Typical methods to determine the yield and fragment size distribution of cfDNA samples are usually either blind to genomic DNA contamination or the presence of enzymatic inhibitors, which can confound and undermine downstream analyses. Here, we present a novel droplet digital PCR assay to identify suboptimal samples and aberrant cfDNA size distributions, the latter typically associated with high levels of circulating tumour DNA (ctDNA). Our assay was designed to promiscuously cross-amplify members of the human olfactory receptor (OR) gene family and includes a customizable diploid locus for the determination of absolute cfDNA concentrations. We demonstrate here the utility of our assay to estimate the yield and quality of cfDNA extracts and deduce fragment size distributions that correlate well with those inferred by capillary electrophoresis and high throughput sequencing. The assay described herein is a powerful tool to establish quality controls and stratify cfDNA samples based on presumed ctDNA levels, then facilitating the implementation of robust, cost-effective and standardized analytical workflows into clinical practice.

Abstract: Introduction Animal models of human cancers are an important tool for the development and preclinical evaluation of new treatments. Canine B-cell lymphoma (cBCL) is an appealing alternative to murine preclinical models due to its frequent, spontaneous incidence and its clinical and histological similarity to human B-cell non-Hodgkin lymphoma (NHL). The potential utility of cBCL as a veterinary model of human B-cell lymphomas would be bolstered by a more complete understanding of the genetic features found in cBCL. Methods To study the genetics of cBCL, we obtained fresh frozen and matched plasma/serum from 86 patients from the Canine Comparative Oncology Genomic Consortium(CCOGC) with 65 confirmed as B-cell lymphomas by immunophenotyping. Tumor DNA was prepared into libraries using the QIAseq FX DNA Library Kit (Qiagen). Plasma and serum DNA was prepared into libraries using the NebNext Ultra II DNA Library Prep Kit. Targeted hybridization enrichment was performed on the libraries using our custom baits and sequencing reads were aligned to canFam3.1 using Geneious and each mutation was visually confirmed. Variants were annotated with Variant Effect Predictor and human-dog pairwise alignments were extracted from Ensembl to identify the orthologous human amino acid for all canine variants. Results Our analysis confirmed the previously reported high frequency of mutations in TRAF3 and FBXW7. We also observed mutations in POT1, TP53, and SETD2 at similar frequencies to those reported in previous studies. DDX3X was mutated in 20% of cases, which is substantially higher than previously reported. MYC mutations were also more frequent (13%) than has been previously described in cBCL. In human lymphomas, MYC is commonly deregulated by translocation to a potent enhancer and these events are often associated with point mutations in MYC that are induced by aberrant somatic hypermutation (aSHM). Interestingly, we identified a more focal pattern of MYC mutations in cBCL that implies they do not result from aSHM and are likely functional. This finding implicates the conserved MYC phosphodegron sequence, a motif commonly mutated among additional aSHM-associated mutations, as the target of bona fide driver mutations in both human and cBCLs. Mutations in FBXW7 primarily affected the substrate recognition domain responsible for MYC degradation. The observation that MYC and FBXW7 mutations did not co-occur in any canine patient is consistent with the notion that FBXW7 mutations operate as an alternative path to MYC stabilization which is not frequently observed in human NHL. DDX3X was one of the most frequently mutated genes in our cohort (20%). DDX3X mutations are common in human Burkitt lymphoma and, though less abundant in hDLBCL, tend to be observed in samples with MYC translocations. In Burkitt lymphoma, these mutations display a sex-specific pattern, wherein females show mainly missense mutations, while males are affected by loss-of-function mutations. Interestingly, all DDX3X mutations in cBCL are missense variants and are presumed to be dominant acting. This lack of sex difference in DDX3X mutations is an important distinction between human and canine B-cell lymphomas that warrants further exploration. Conclusions Our study has revealed key differences in the mutational profiles of canine and human B-cell lymphomas and provides an impetus for enhanced genomic characterization of canine lymphomas as a model for human NHL, particularly in clinical trial settings. Disclosures Grande: Sage Bionetworks: Current Employment. Alcaide: GA Diagnostics AB: Current Employment. Morin: Celgene: Consultancy; Foundation for Burkitt Lymphoma Research: Membership on an entity's Board of Directors or advisory committees; Epizyme: Patents & Royalties. Coyle: Allakos, Inc.: Consultancy.

Abstract: A significant proportion of diffuse large B-cell lymphoma (DLBCL) patients treated with immunochemotherapy containing rituximab (R-CHOP) exhibit either primary or acquired treatment resistance. The advancement of therapeutics in the relapse setting has likely been encumbered by our limited understanding of the molecular features that underlie resistance to R-CHOP. Unfortunately, our knowledge of DLBCL genetics is mostly limited to analyses conducted on diagnostic tissue biopsies, which have not been exposed to the selective pressures imposed by therapy. Identifying genetic alterations that contribute to treatment resistance may reveal additional treatment options and lead to biomarkers allowing patients to be paired with appropriate treatments. Genetic subgroups are gaining popularity as a new strategy to implement precision medicine in DLBCL (1). The relevance of these and other biomarkers in the relapse setting remains unclear due to limited genetic exploration of relapsed and refractory DLBCL (rrDLBCL). Progress has been limited, in part, by the requirement of tissue biopsies collected after relapse. It is well established that quantitative genomic techniques such as digital PCR and targeted sequencing can be used to determine the proportion of tumor DNA in plasma from lymphoma patients (2). With a sufficiently broad panel, sequencing affords additional opportunities including the ability to identify subclonal structure and population dynamics over time. This presentation will discuss our recent analysis of a large collection of ctDNA primarily comprising DLBCL patients on various clinical trials (3). Targeted sequencing of these samples and comparison to exome data from a meta-cohort of previously characterized untreated DLBCL biopsies revealed six genes significantly enriched for mutations upon relapse. We found both TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations persisted in the dominant clone following relapse, suggesting a role in primary treatment resistance. By inferring subclonal dynamics, we observed recurrent patterns of clonal expansion and contraction following rituximab-based therapy, with MS4A1 mutations representing the only example of consistent clonal expansion. MS4A1 missense mutations within the transmembrane domains led to loss of CD20 expression in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. Our analysis nominates TP53 and KMT2D mutation status as novel prognostic factors that may facilitate the identification of high-risk patients prior to therapy. Moreover, we have demonstrated the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens. In certain scenarios whole-exome sequencing (WES) or whole-genome sequencing (WGS) can be successfully applied to ctDNA, thereby allowing the identification of mutations, structural variation, and copy number changes. Low-pass sequencing of shotgun libraries can also be used to ascertain course estimates of ctDNA levels as well as the copy number landscape (4). Given the importance of copy number and structural alterations in the inference of genetic subgroups, these methods may allow the exploration of these groups and their stability over time. Through a series of illustrative examples, this presentation will explore the benefits of each of these techniques in the study of tumor evolution and acquired treatment resistance in DLBCL. References: 1. Morin RD, Scott DW. DLBCL subclassification: Divide and conquer? Blood 2020;135:1722–4. 2. Rossi D et al. The development of liquid biopsy for research and clinical practice in lymphomas: Report of the 15-ICML workshop on ctDNA. Hematol Oncol 2020;38:34–7. 3. Rushton CK et al. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv 2020;4:2886–98. 4. Adalsteinsson VA et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun 2017;8:1324. Citation Format: Nicole Thomas, Laura K. Hilton, Neil Michaud, Kevin Bushell, Ryan Rys, Michael Jain, Lois Shepherd, Marco A. Marra, John Kuruvilla, Michael Crump, Koren Mann, Sarit Assouline, Christian Steidl, Mark S. Cragg, David W. Scott, Nathalie Johnson, Ryan D. Morin, Christopher K. Rushton, Sarah E. Arthur, Miguel Alcaide, Matthew Cheung, Aixiang Jiang, Krysta M. Coyle, Kirstie L. S. Cleary. Detecting and quantifying mutations associated with treatment resistance in aggressive lymphomas using ctDNA [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr IA42.