Based on gene expression profiles, diffuse large B-cell lymphoma (DLBCL) is subdivided into germinal center B-cell-like (GCB) and activated B-cell-like (ABC) DLBCL. Two of the most common genomic aberrations in ABC-DLBCL are mutations in MYD88 as well as BCL2 copy-number gains. Here, we employ immune phenotyping, RNA sequencing, and wholeexome sequencing to characterize a Myd88-and BCL2-driven mouse model of ABC-DLBCL. We show that this model resembles features of human ABC-DLBCL. We further demonstrate an actionable dependence of our murine ABC-DLBCL model on BCL2. This BCL2 dependence was also detectable in human ABC-DLBCL cell lines. Moreover, human ABC-DLBCLs displayed increased PD-L1 expression compared with GCB-DLBCL. In vivo experiments in our ABC-DLBCL model showed that combined venetoclax and PD-1 blockade significantly increased the overall survival of lymphoma-bearing animals, indicating that this combination may be a viable option for selected human ABC-DLBCL cases harboring MYD88 and BCL2 aberrations.SignificAnce: Oncogenic Myd88 and BCL2 cooperate in murine DLBCL lymphomagenesis. The resulting lymphomas display morphologic and transcriptomic features reminiscent of human ABC-DLBCL. Data derived from our Myd88/BCL2-driven autochthonous model demonstrate that combined BCL2 and PD-1 blockade displays substantial preclinical antilymphoma activity, providing preclinical proofof-concept data, which pave the way for clinical translation.

The BCL2 inhibitor venetoclax has been approved to treat different hematological malignancies. Since there is no common genetic alteration causing resistance to venetoclax in CLL and B cell lymphoma, we asked if epigenetic events might be involved in venetoclax resistance. Therefore, we employed whole exome sequencing, methylated DNA immunoprecipitation sequencing and genome wide CRISPR/Cas9 screening to investigate venetoclax resistance in aggressive lymphoma and high-risk CLL patients. We identified a regulatory CpG island within the PUMA promoter which is methylated upon venetoclax treatment, mediating PUMA downregulation on transcript and protein level. PUMA expression and sensitivity towards venetoclax can be restored by inhibition of methyltransferases. We can demonstrate that loss of PUMA results in metabolic reprogramming with higher OXPHOS and ATP production, resembling the metabolic phenotype that is seen upon venetoclax resistance. While PUMA loss is specific for acquired venetoclax resistance but not for acquired MCL1 resistance and is not seen in CLL patients after chemotherapy-resistance, BAX is essential for sensitivity towards both venetoclax and MCL1 inhibition. As we found loss of BAX in Richter's syndrome patients after venetoclax failure, we defined BAX-mediated apoptosis to be critical for drug resistance but not for disease progression of CLL into aggressive DLBCL in vivo. A compound screen revealed TRAIL-mediated apoptosis as a target to overcome BAX deficiency. Furthermore, antibody or CAR T cells eliminated venetoclax resistant lymphoma cells, paving a clinically applicable way to overcome venetoclax resistance.

Genomic profiling revealed the identity of at least 5 subtypes of DLBCL, including the MCD/C5 cluster characterized by aberrations in MYD88, BCL2, PRDM1 and/or SPIB. We generated mouse models harboring B cell-specific Prdm1 or Spib aberrations on the background of oncogenic Myd88 and Bcl2 lesions. We deployed whole exome sequencing, transcriptome, flow- and mass cytometry analyses to demonstrate that Prdm1- or Spib-altered lymphomas display molecular features consistent with pre-memory B cells and light zone B cells, whereas lymphomas lacking these alterations were enriched for late light-zone and plasmablast-associated gene sets. Consistent with the phenotypic evidence for increased B cell receptor signaling activity in Prdm1-altered lymphomas, we demonstrate that combined BTK/BCL2 inhibition displays therapeutic activity in mice and in five out of six relapsed/refractory DLBCL patients. Moreover, Prdm1-altered lymphomas were immunogenic upon transplantation into immuno-competent hosts, displayed an actionable PD-L1 surface expression and were sensitive to anti-murine-CD19-CAR-T cell therapy, in vivo.

Purpose of review Recent lymphoma genome sequencing projects have shed light on the genomic landscape of indolent and aggressive lymphomas, as well as some of the molecular mechanisms underlying recurrent mutations and translocations in these entities. Here, we review these recent genomic discoveries, focusing on acquired DNA repair defects in lymphoma. In addition, we highlight recently identified actionable molecular vulnerabilities associated with recurrent mutations in chronic lymphocytic leukemia (CLL), which serves as a model entity. Recent findings The results of several large lymphoma genome sequencing projects have recently been reported, including CLL, T-PLL and DLBCL. We align these discoveries with proposed mechanisms of mutation acquisition in B-cell lymphomas. Moreover, novel autochthonous mouse models of CLL have recently been generated and we discuss how these models serve as preclinical tools to drive the development of novel targeted therapeutic interventions. Lastly, we highlight the results of early clinical data on novel compounds targeting defects in the DNA damage response of CLL with a particular focus on deleterious ATM mutations. Summary Defects in DNA repair pathways are selected events in cancer, including lymphomas. Specifically, ATM deficiency is associated with PARP1- and DNA-PKcs inhibitor sensitivity in vitro and in vivo.

Diffuse large B cell lymphoma (DLBCL) is the most common lymphoid malignancy in adults. Both biologically and clinically, DLBCL represents a highly heterogeneous disease. DLBCL has been subdivided into germinal center B cell (GCB)-like and activated B cell (ABC)-like DLBCL, on the basis of gene expression profiling, which separates DLBCL according to the presumed cell of origin (COO). This COO-based classifier distinguishes sub-entities displaying distinct biological features, pathogenesis and clinical response to frontline therapy. In addition to this classic transcriptome-based stratifier, recent genomic analyses of human DLBCL samples led to the discovery of partially overlapping genetically-defined DLBCL subsets. A study by Schmitz et al. employed a supervised clustering approach, allowing the classification of ~50% of the cases into four genetically-defined DLBCL subtypes, one of which is being characterized by co-occurring MYD88- and CD79B mutations as well as high expression of BCL2 (termed MCD). In a second approach by Chapuy et al., patient samples were clustered in an unsupervised manner. Also in this study, a cluster with recurrent mutations in MYD88 (specifically p.L265P) and CD79B, as well as gains of 18q (the location of BCL2) was identified (termed C5). We previously reported the formation of B cell lymphoma in mice that were engineered to express Myd88 p.L252P in combination with overexpression of BCL2 (Myd88 p.L252P/wt;R26 LSL.BCL2/wt;Cd19 Cre/wt, abbr. MBC) in a B cell-specific manner. While the developing lesions display many features of human ABC DLBCL, their B220 -/CD138 + immunophenotype reflects plasmablastic characteristics. To refine this mouse model, we incorporated additional C5/MCD lesions by engineering a B cell-specific loss of Prmd1 or Spib overexpression generating Prdm1 fl/fl;Myd88 p.L252P/wt;R26 LSL.BCL2/wt;Cd19 Cre/wt (PPMBC) and Myd88 p.L252P/wt;R26 LSL.BCL2/LSL.Spib;Cd19 Cre/wt (SMBC) compound animals. Both, the B cell-specific loss of Prdm1 and Spib overexpression on the MBC background resulted in a marked reduction of CD138 + cells in the spleens of 10 weeks old animals compared to control (Fig. 1A), accompanied by a decrease in serum immunoglobulins, indicative of a plasma cell differentiation block and in agreement with the reported function of PRMD1 and SPIB as transcription factors regulating plasma cell differentiation. Both PPMBC and SMBC mice developed lymphoma significantly earlier than MBC animals. These tumors largely displayed a B220 +/CD138 - immunophenotype. As transcriptional profiling is the gold standard for differentiation between GCB and ABC DLBCL, we generated germinal center- and activated blood B cell gene sets from healthy donors. We then performed gene set enrichment analyses between SMBC/PPMBC tumors and either MBC or Kmt2d fl/fl;VavP-Bcl2;Cɣ1 Cre/wt (KBC) lymphomas, the latter being reminiscent of human GCB DLBCL. While both PPMBC and SMBC samples were enriched for GCB gene signatures when compared to MBC, they enriched for ABC gene sets in comparison to KBC, potentially suggesting a developmental stage between KBC and MBC lesions (Fig. 1B). We next aimed to employ our PPMBC model of C5 DLBCL as a pre-clinical tool, in order to derive therapeutic approaches for this disease. In this regard, we note BCL2 has emerged as a potential therapeutic target in DLBCL. The BCL2 inhibitor venetoclax produces response rates of ~18% in relapsed/refractory DLBCL (Davids et al., 2017). Similarly, in a phase I/II clinical trial involving 80 patients with relapsed/refractory DLBCL, ibrutinib induced complete or partial remissions in 37% of ABC-DLBCL patients, but in only 5% GCB-DLBCL patients (Wilson et al., 2015). Building on these observations, we asked whether single agent or combined venetoclax and ibrutinib treatment might display pre-clinical activity in the PPMBC setting. Indeed, combination treatment with ibrutinib and venetoclax resulted in a significant survival benefit compared to single compound or untreated animals (Fig. 1C). Given this preclinical activity, we treated 6 relapsed/refractory (r/r) non-GCB DLBCL patients (determined by Hans algorithm) in an off-label setting and observed tumor shrinkage in 5 of 6 patients (Fig. 1D). Thus, our clinical data corroborate our preclinical observations and suggest that combined venetoclax and ibrutinib may display clinical activity in a subset of r/r non-GCB DLBCL. Figure 1 Figure 1. Disclosures Hallek: Roche: Honoraria, Speakers Bureau; Gilead: Honoraria, Speakers Bureau; Mundipharma: Honoraria, Speakers Bureau; Janssen: Honoraria, Speakers Bureau; Celgene: Honoraria, Speakers Bureau; Pharmacyclics: Honoraria, Speakers Bureau. Calado: Myricx Pharma: Consultancy, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company, Patents & Royalties: Cancer Treatments. WO patent WO 2020/128475 A1 (2020). Pasqualucci: Sanofi: Research Funding; Astra Zeneca: Research Funding. von Tresckow: Amgen: Consultancy, Honoraria; AbbVie: Other: congress and travel support; Pentixafarm: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; BMS-Celgene: Consultancy, Honoraria, Other: congress and travel support; MSD: Consultancy, Honoraria, Other: congress and travel support, Research Funding; Novartis: Consultancy, Honoraria, Other: congress and travel support, Research Funding; AstraZeneca: Honoraria, Other: congress and travel support; Kite-Gilead: Consultancy, Honoraria; Roche: Consultancy, Honoraria; Takeda: Consultancy, Honoraria, Other, Research Funding. Chapuy: Gilead: Honoraria; BMS: Honoraria; Regeneron: Consultancy; Gilead Sciences: Research Funding; Astra Zeneca: Honoraria. Reinhardt: CDL Therapeutics: Current holder of individual stocks in a privately-held company; Gilead: Research Funding; Merck: Consultancy; Vertex: Consultancy; AstraZeneca: Consultancy; Abbvie: Consultancy. OffLabel Disclosure: Treatment of DLBCL patients with ibrutinib and venetoclax.

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<p>BCR sequencing</p>

<p>Table S2 contains a summary of the B cell receptor sequencing data of lymphoma samples. It includes 1) an overview of the investigated samples, 2) a list of characteristics of the dominant clone of each lymphoma sample, 3) a list comparing the frequencies of V family usage in WT samples to the lymphoma frequency, 4) the frequencies of FR and CDR mutations in samples analyzed by full-length BCR sequencing.</p>