B Cell Receptor Silencing Reveals Origin and Impacts Treatment of High-Grade B Cell Lymphomas with MYC and BCL2 Rearrangements

High-grade B cell lymphomas with MYC and BCL2 rearrangements, also referred as MYC/BCL2 double-hit lymphomas (HGBCL-DH-BCL2), represent highly aggressive B cell malignancies with dismal prognosis and limited therapeutic options. Beside the suggested origin from germinal center (GC) B cells, pathogenesis of HGBCL-DH-BCL2 remains largely unknown.

The B cell receptor (BCR) represents a major signaling hub and preferred therapeutic target for several mature B cell lymphoma/leukemias. We investigated expression of BCR complex components, including immunoglobulin (IG) heavy (H) and light (L) chains, and CD79A and CD79B signaling subunits in 93 HGBCL-DH-BCL2 cases. In 66% of the tumors, undetectable IGM/D/G/A IGH (IGH^UND) protein assessed by immunohistochemistry, flow cytometry and proximity ligation assays was linked to CD79B downregulation and intracellular retention. Remaining 34% predominantly expressed surface (s) IGM/CD79B/CD79A⁺ BCR complexes. Bulk and spatial transcriptomics identify IGH^UND and IGH⁺ HGBCL-DH-BCL2 lymphomas as distinct biological entities, with the former resembling GC DZ B cells limiting T cell recall. Instead, IG⁺ HGBCL-DH-BCL2 established an immune/stromal cell-rich microenvironment permetated by immunosuppressive cell types and soluble signals, with transcriptional similarities to GC light zone-resident B cells. IGH^UND HGBCL-DH-BCL2 selected significantly higher c-MYC expression than their IGH⁺ counterparts and boosted mitochondrial respiration. IGH^UND and IGH⁺ tumors shared non-synonymous single-nucleotide variants in several genes recurrently mutated in classical Follicular Lymphoma (FL), while selecting subset-specific gene mutations indicative of distinct evolutionary trajectories. IGH^UND HGBCL-DH-BCL2 preserved potentially productive, hypermutated IGH variable (V) gene rearrangements, counterselecting structure-damaging aminoacid replacements, while bypassing antigen-driven selection. IGH^UND HGBCL-DH-BCL2 originated from IGG/IGA class switched GC B cells, while IGH-expressing tumors were selected for continuous IGM expression. IGH analyses in 13 metachronous tumor pairs reveal that IGH shutdown and class choice are pre-determined in the FL preceding HGBCL-DH-BCL2. Mutational analyses on metachronous cases indicate that HGBCL-DH-BCL2 can either evolve from FL, or arise from a FL/HGBCL-DH-BCL2 common precursor cell (CPC) through branched evolution. IGH^UND HGBCL-DH-BCL2 showed recurrent (43%) bi-allelic disruption of the IGH locus, which only occasionally intercepted the MYC locus. Sequencing of the t(8;22) translocation breakpoint in an IGH^UND HGBCL-DH-BCL2 case, revealed juxtaposition of MYC to the IG lambda (L) J2 gene segment, replacing recombination signal sequences, consistent with illegitimate RAG1/2-dependent VJ recombination. In support of this, lymphoma cells showed widespread RAG1/2 expression, with similar results confirmed in 26 % of additional HGBCL-DH-BCL2 cases, and in corresponding t(8;22)⁺ cell lines, which commonly lacked sIG expression. We show that in HGBCL-DH-BCL2, RAG1/2 (re-)expression is facilitated by BCR downregulation, recalling mechanisms of BCR revision/editing promoting secondary IG light chain V gene rearrangements. In line with this, IGH^UND HGBCL-DH-BCL2 showed a striking bias for IG lambda light chain usage, at the expense of IG kappa chains, which were predominant among the IGH⁺ counterparts. Importantly, patient-derived IGH^UND HGBCL-DH-BCL2 lymphoma cell lines showed in vitro resistance to the sCD79B-targeting antibody-drug conjugate Polatuzumab-Vedotin (PV). In conclusion, we report, for the first time, the predominant shutdown of sBCR expression in HGBCL-DH-BCL2. BCR silencing, starting in the t(14;18)⁺ FL/CPC cell triggers RAG1/2-dependent BCR editing, which favors t(8;22), IGL::MYC rearrangements, and, possibly non IG-MYC translocations, ultimately driving transformation into IGH^UND HGBCL-DH-BCL2. Our results reconcile with the reduced efficacy of PV in the treatment of HGBCL-DH-BCL2, urging for routine surface CD79B assessment to guide treatment indication.