Supplementary Figure S3. Flow cytometry gating strategy and additional patient characteristics.

Tissue-resident memory T (TRM) cells stably occupy tissues and contribute to immunosurveillance, where they are associated with favorable survival outcomes in solid tumors. Although TRM cells have been observed in lymph nodes, their phenotype and prognostic significance in diffuse large B-cell lymphoma (DLBCL) remains uncharacterized. In this study, CD103+ T cells were quantified in DLBCL samples by immunofluorescence staining of tissue biopsies and flow cytometry of cell disaggregates and linked with clinical outcomes. Across two patient cohorts, CD103+ T cells were identified in both nodal and extranodal DLBCL, and higher CD103+ T-cell levels correlated with superior clinical outcomes. Single-cell RNA sequencing revealed ITGAE-expressing T cells in both malignant and reactive lymph node samples. However, transcriptional profiles differed as a canonical TRM population was exclusively observed in the malignant setting. This TRM cluster was enriched for genes associated with cytotoxicity and activation and was validated in an external cellular indexing of transcriptomes and epitopes by sequencing (CITEseq) dataset. Flow cytometry additionally confirmed protein expression of TRM markers (CXCR6, CD39, and PD-1) on CD69+CD103+ T cells. We assessed functional activity in coculture experiments of CD103+ versus CD103- T cells with autologous CD20+ B cells, in which CD103+ T cells displayed enhanced killing. CD103+ TRM cells in DLBCL represent a prognostically favorable population with an activated/cytotoxic T-cell phenotype.

Supplementary Figure S6. Representative gating strategy used to identify T cells and CD103+ T cells.

Supplementary Table S4: Previously published gene signatures defining TRM cells used in GSEA

Supplementary Figure S5. Identification of ITGAE expressing cells and factors affecting CD103 expression.

ABSTRACT:High-grade B-cell lymphoma with "double-hit" MYC and BCL2 rearrangements (HGBCL-DH-BCL2) is associated with poor outcomes following standard chemoimmunotherapy, prompting dose-intensive regimen use. However, the benefit of intensification is unclear due to rarity precluding randomized trials, and selection bias in retrospective comparisons. In 2015, BC Cancer introduced a provincial guideline recommending dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab (DA-EPOCH-R) for fit patients aged ≤75 years with HGBCL-DH-BCL2 identified by routine cytogenetic testing. To assess this guideline's impact, we compared the outcomes of patients with de novo HGBCL-DH-BCL2 tumors of diffuse large B-cell lymphoma (DLBCL) morphology across 2 eras. The DA-EPOCH-R era (2015-2020) included patients diagnosed after guideline implementation. The historic era (2005-2010) included patients identified from a historic province-wide cohort of patients with DLBCL morphology tumors that underwent universal cytogenetic testing in a research setting, predominantly treated with standard chemoimmunotherapy. Two-year overall survival (OS) was significantly improved in the DA-EPOCH-R vs historic era (75% vs 47%, P = .008) in HGBCL-DH-BCL2, whereas OS remained unchanged in DLBCL, not otherwise specified (78% vs 76%, P = .17). Within HGBCL-DH-BCL2, tumors harboring immunoglobulin MYC partner loci (43%) and those expressing the dark-zone signature (77%) were associated with the most substantial survival improvements. In a contemporary cohort of HGBCL-DH-BCL2 histologically transformed from follicular lymphoma (FL) in the DA-EPOCH-R era, outcomes of patients who were chemoimmunotherapy-naïve were comparable to those with de novo disease, whereas patients treated with chemoimmunotherapy for FL prior to transformation had poor outcomes. These data support using DA-EPOCH-R in select patients with HGBCL-DH-BCL2 of DLBCL morphology.

High-grade B-cell lymphoma, not otherwise specified (HGBCL, NOS), is defined by morphologic features intermediate between Burkitt lymphoma and diffuse large B-cell lymphoma (DLBCL). Lymphomas with a complex 11q aberration or concurrent MYC- and BCL2- or BCL6- rearrangements are excluded from this category. However, the reproducibility of the diagnosis of HGBCL, NOS is unknown to date. Expert hematopathologists of the Lymphoma/Leukemia Molecular Profiling Project reviewed 92 cases submitted as HGBCL, NOS. At least 3/4 hematopathologists reviewing cases independently confirmed the diagnosis in 30/92 (33%) cases, while 13 cases (14%) were reclassified as DLBCL. The remaining 49 cases were jointly reviewed by the consensus panel of 10 to 15 pathologists, confirming an additional 9 HGBCL, NOS. The remaining cases were reclassified as DLBCL or other aggressive B-cell lymphomas or were excluded due to insufficient material. In aggregate, only 39/92 (42%) of initially submitted cases were confirmed as HGBCL, NOS, demonstrating poor interobserver agreement. Interestingly, however, there were no significant differences between the initially submitted cohort and those ultimately confirmed by the pathology review panel concerning dark zone signature (DZsig) expression, frequency of MYC -rearrangements and cell of origin, among others. Despite the finding that pathologists can identify cytomorphological features associated with adverse biological characteristics, the poor reproducibility of high-grade morphology and molecular heterogeneity suggests that HGBCL, NOS does not represent a distinct clinicopathologic entity and that more objective markers of distinct biologic features, such as the DZsig, may better separate cases into relevant diagnostic categories than morphology alone.

ABSTRACT:Heterogeneous nuclear ribonucleoprotein U (hnRNPU) is a ubiquitously expressed, pleiotropic DNA and RNA binding protein involved in RNA metabolism. Heterozygous HNRNPU nonsense mutations have been observed in a variety of B-cell lymphomas, but the functional consequence of these mutations remains largely unknown. Through a large meta-analysis of genome- and exome-wide sequencing data, we find that these mutations are more common among tumors with MYC rearrangements, including high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (12.1%), and Burkitt lymphoma (5.2%). Using isogenic cell line models, we demonstrate that HNRNPU is a haploinsufficient tumor suppressor, with inactivation of a single allele promoting cell cycle entry through widespread alteration of the gene expression and splicing landscape. We show that reduced hnRNPU expression consistently lowers MYC levels while simultaneously enhancing E2F-driven signaling. This creates a cellular state in which MYC-induced stress may be buffered while cell cycle progression is maintained. Finally, we show that owing to this increased dependence on E2Fs for proliferative signaling, HNRNPU-mutated lymphomas are more sensitive to E2F inhibitors. These results highlight hnRNPU-mediated regulation of MYC and its downstream effects as possible new avenues for therapeutic intervention in MYC-driven lymphomas.

Supplementary Figure S1. TMA with CD69 staining and additional patient characteristics.

Abstract Diffuse large B-cell lymphoma (DLBCL) is a biologically heterogeneous disease. Two genomic classification systems, LymphGen and DLBclass, are capable of reproducibly classifying single tumors into subtypes with prognostic relevance in the context of standard-of-care R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) chemoimmunotherapy. Preliminary data from subgroup analyses of clinical trials suggest that the distinct biological features are targetable with drugs that exploit subtype-specific vulnerabilities, and large clinical trials are being designed to test this hypothesis. Although whole-exome sequencing (WES) remains the gold standard for each of these classification systems, smaller targeted sequencing panels reduce costs associated with sequencing, data storage, and processing. Here, we describe the design and validation of a targeted sequencing panel (LySeqST) that captures the genomic features required specifically for LymphGen classification. We perform in silico theoretical and real-world validation vs WES data and demonstrate that LySeqST can be used to accurately classify DLBCL tumors using both LymphGen and DLBclass. In an unselected population-based cohort, we determine the real-world proportions and validate the prognostic relevance of LymphGen subtypes, confirming that only tumors expressing the dark zone gene expression signature are consistently associated with inferior outcomes. Our results support the use of LySeqST for accurate genomic classification of DLBCL.

High-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBCL-DH-BCL2), or "double-hit lymphoma," has been associated with a high risk of central nervous system (CNS) relapse. However, historic estimates are impacted by selection bias. We report CNS relapse rates associated with HGBCL-DH-BCL2 from a population-based cohort with complete fluorescence in situ hybridization testing, as well as diffuse large B-cell lymphoma morphology (DLBCL) tumors expressing the dark-zone gene expression signature (DZsig), which was originally derived from HGBCL-DH-BCL2. The 2-year CNS relapse risk in HGBCL-DH-BCL2 was 6.8%. CNS relapses were early, predominantly leptomeningeal (73%), and co-occurred with systemic relapse (64%). High-risk CNS International Prognostic Index (CNS-IPI) and concordant bone marrow involvement were associated with an elevated CNS relapse risk in HGBCL-DH-BCL2. The "refined cell-of-origin" classification assigned 20% of DLBCL morphology tumors with germinal center B-cell-like phenotype (GCB-DLBCL) into a distinct subgroup based on DZsig expression (DZsig+). CNS relapse risk in DZsig+ (2 year: 6.4%) was independent of HGBCL-DH-BCL2 status and was further stratified by the CNS-IPI. CNS relapse in DZsig-negative GCB-DLBCL was rare (2-year risk, 1.4%; P = .04 vs DZsig+) and exclusively parenchymal. Altogether, the CNS relapse risk in HGBCL-DH-BCL2 is lower than previously reported, and DZsig refines risk stratification in GCB-DLBCL.

Abstract: Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. Leveraging comparison cohorts of diffuse large B-cell lymphoma, NOS (DLBCL-NOS) and Burkitt lymphoma (BL), and molecular frameworks described in these entities, our analysis revealed a heterogenous molecular landscape, reminiscent of DLBCL-NOS but with an enrichment of BL features. By cell-of-origin classification, 59% were germinal center B-cell–like (GCB), and 25% were activated B-cell–like (ABC). LymphGen, a genetic classifier for DLBCL-NOS, assigned a genetic subtype to 34% of HGBCL-NOS. Although classification rate was lower than in DLBCL-NOS (66%), assigned subtypes spanned the spectrum of LymphGen classes, including 31% of ABCs classified as MCD. Features differentiating HGBCL-NOS from DLBCL-NOS included MYC rearrangement (47% vs 6%); dark zone signature (DZsig) expression (45% vs 7%); and more frequent mutation of ID3, MYC, CCND3, and TP53, all common to BL. A genetic classifier that differentiates DLBCL-NOS from BL classified 53% of DZsig+ tumors as BL-like, and those classified as DLBCL-like were frequently BCL2-rearranged. Among DZsig− GCB tumors, 95% were DLBCL-like. Centralized pathology review reclassified almost half of tumors as DLBCL-NOS but did not identify a more homogenous HGBCL-NOS population, with no difference in features between confirmed and reclassified tumors. In conclusion, molecular testing enables a subset of HGBCL-NOS to be assigned to established categories. Based on rarity and diagnostic challenges, broader inclusion of HGBCL-NOS should be considered in biomarker-driven DLBCL trials.

Genetic subtyping of diffuse large B-cell lymphoma (DLBCL) has been slow to gain clinical adoption. Available classifiers either leave many tumours unclassified or depend on exome-wide features and copy-number profiles, which are not always available in routine practice. We introduce DLBCLone, a neighbourhood-based framework that enables panel-aware genetic subtyping compatible with existing taxonomies. DLBCLone learns a 2-D reference map of mutation profiles (UMAP) from a labeled training cohort, freezes this map, and deterministically projects new cases into the same latent space. Class labels are then inferred by weighted K-nearest neighbours, limiting over-assignment by considering the local density of unclassified neighbours. By default, classification thresholds optimize per-class balanced accuracy, but can be adjusted to suit study needs. The framework is intended to emulate (or "clone") existing schemas such as LymphGen or DLBClass. Trained on a harmonized cohort of 2,130 DLBCLs, DLBCLone classifiers for different gene panels achieved consistently improve classification rates relative to fixed-threshold baselines while maintaining a reasonable per-class performance. On an in-house cohort of 323 patients, it assigned an additional 98 samples without compromising accuracy relative to LymphGen. On an external exome-sequenced subset from a 1,001-patient cohort, DLBCLone achieved a 51% classification rate (vs 36% for LymphGen) at an overall accuracy of 0.70. Compared with another LymphGen approximator (LymphPlex), DLBCLone reached a 74% classification rate (vs 55%). In general, the DLBCLone-reclassified tumours had molecular features consistent with their new labels. DLBCLone provides a deterministic, reproducible, and extensible approach to genetic subtyping under real-world constraints, facilitating prospective studies that rely on either targeted panels or more comprehensive sequencing strategies. DLBCLone is open source and available in the GAMBLR.predict package (https://github.com/morinlab/gamblr.predict). ### Competing Interest Statement RDM is an inventor on a patent relating to genetic subtyping of DLBCL ### Clinical Protocols ### Funding Statement This study was funded by the Canadian Institutes for Health Research and the Terry Fox Research Institute. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The BC Cancer Research Ethics Board gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes No new data was produced in this study. All data used in this study is available through the repositories and study accessions detailed in the text.

Aggressive B-cell lymphomas are a heterogeneous group of neoplasms, organized in the current classifications into more than 20 categories on the basis of morphology, immunophenotype, clinical presentation, and limited molecular features. Over the past 25 years, there has been an exponential accumulation of detailed genomic characterizations of these lymphomas. Many defined categories have been confirmed as relatively homogeneous, fulfilling the classification ideal of sharing core biological hallmarks. However, the largest group, diffuse large B-cell lymphoma, not otherwise specified, which makes up 70-74% of the patients, has been revealed to be remarkably heterogeneous at a genomic and biological level. In this review, we summarize the current state of knowledge and then propose an evolution of the classification of aggressive B-cell lymphomas to a genomics-informed taxonomy built around normal B-cell development and the different modes by which lymphomas achieve key hallmarks of cancer-hallmarks that can inform on patient management.

Fluorescence in situ hybridization (FISH) using break-apart probes is recommended for identifying high-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBCL-DH-BCL2). Unbalanced MYC break-apart patterns, where the red or green signal is lost, are commonly reported as an equivocal result by clinical laboratories. In a cohort of 297 HGBCL-DH-BCL2, 13% of tumors had unbalanced MYC break-apart patterns with loss of red (LR: 2%) or green (LG: 11%) signal. To determine the significance of these patterns, MYC rearrangements were characterized by sequencing in 130 HGBCL-DH-BCL2, including 3 LR and 14 LG tumors. A MYC rearrangement was identified for 71% of tumors with LR or LG patterns, with the majority involving immunoglobulin loci or other recurrent MYC rearrangement partners. The architecture of these rearrangements consistently preserved the rearranged MYC allele, with the MYC gene predicted to be on the derivative chromosome containing the signal that is still present in nearly all cases. MYC protein expression, MYC mRNA expression, and the proportion of tumors expressing the dark zone signature was not significantly different between balanced and unbalanced groups. These results support a recommendation that unbalanced MYC break-apart FISH patterns be reported as positive for MYC rearrangement in the context of diagnosing HGBCL-DH-BCL2.

Introduction Plasmablastic lymphoma (PBL) is a rare aggressive subtype of lymphoma. It is more common in HIV positive patients, and is often associated with Epstein-Barr virus (EBV) and MYC rearrangements. PBL is characterized by markers of plasmacytic differentiation including CD138 and MUM1/IRF4, and loss of B-cell markers such as CD20, which suggests a cell of origin similar to that of multiple myeloma (MM) or activated B-cell-like (ABC) diffuse large B-cell lymphoma (DLBCL). The standard of care for PBL is CHOP-based chemotherapy but this is frequently not curative. Other than EBV-negative status, which defines a high-risk group, no other biological features have been discovered that are associated with outcomes. Methods Here, we provide a comprehensive analysis of the genomic and transcriptomic landscape of PBL using a collection of 176 exomes and genomes (n=55 new, contributed by Lymphoma/Leukemia Molecular Profiling Project [LLMPP] sites and centrally reviewed by the LLMPP pathology panel [WHO 2016]; n=121 previously published [PMID: 33225311, 33951889, 34465776, 34714908]), 65 transcriptomes (n=44 new; n=21 published) and 37 in situ single cell transcriptomic profiles (CosMx Spatial Molecular Imager) from archival diagnostic tissue biopsies. Somatic mutations (SNVs/Indels) were identified using an ensemble of four variant callers (Strelka2, Lofreq, Mutect2, SAGE). Salmon and DESeq2 were used to identify differentially expressed genes. This multi-omics dataset was compared to other known B-cell malignancies including 92 MM, 238 Burkitt lymphomas (BL), and 208 DLBCLs. Cell segmentation of the CosMx data was performed using Baysor and downstream analyses were conducted using the Seurat workflow. For functional validation, cell viability assays (CellTiter-Glo Luminescent Assay) were conducted in the PBL cell line, PBL-1, and 4 control DLBCL cell lines. Results Within the cohort, 63% (106/169) of primary PBL cases were EBV-positive (EBV+) and 57% (82/144) harbored MYC rearrangements (MYC+). When stratifying patients by EBV and MYC rearrangement status, mutations in different genes were enriched in each group: STAT3 occurred in 55% (29/53) of EBV+/MYC+ PBLs; NOTCH1 in 19% (7/36) of EBV+/MYC-; MYC in 24% (6/25) and TP53 in 40% (10/25) of EBV-/MYC+ tumors; TET2 was mutated in 38% (9/24) and KRAS in 25% (6/24) of EBV-/MYC- PBLs. EBV-/MYC+ tumors represented a subgroup of patients with dismal outcomes. The 2-year overall survival (OS) of these patients was 22% compared to 61%, 78%, and 54% of EBV+/MYC+, EBV+/MYC-, and EBV-/MYC- PBL patients, respectively (log-rank test p-adj. < 0.05). Consistent with previous studies, we observed recurrent mutations affecting JAK-STAT (STAT3, SOCS1, SOCS3, DUSP2) in 41% of cases and RAS-RAF (NRAS, KRAS, BRAF) signaling in 38% of all PBLs. In contrast to ABC-DLBCL, very few mutations occurred in the NF-κB signalling pathway. Accordingly, PBL showed marked downregulation of genes involved in B-cell receptor and NF-κB signaling. Consistent with the lack of reliance on these pathways, functional analyses in PBL-1 showed resistance to treatment to ibrutinib as well as PI3K- and MALT1-inhibitors. Moreover, constitutive expression of the IκBα super-repressor did not affect viability of PBL-1 cells. In situ single cell transcriptomic data analyses showed a sparse tumor microenvironment (TME) in PBL, with the primary non-malignant cell types being, on average, 10% macrophages, 7% NK/T cells, and 4% stromal cells of all represented cell types. EBV+/MYC+ tumors displayed a more abundant immune cell population with higher levels of macrophages (median 12%) and NK/T cells (median 9%), whereas EBV-/MYC- tumors were composed of the lowest levels of immune cells (median 4% macrophages and 1% NK/T cells). With respect to malignant cell phenotypes, we noted a novel population of SPP1-expressing cells that were enriched in EBV+/MYC+ tumors and a population of CD44-expressing cells that were enriched in EBV+/MYC- tumors. Conclusion Here we present novel subgroups of PBL with unique biology and clinical outcomes. We show that PBL does not rely on B-cell receptor signaling, instead relying on potentially targetable vulnerabilities in JAK-STAT, NOTCH, and RAS-RAF signaling according to EBV positivity and MYC rearrangement status. Lastly, we provide insight into the TME of PBL and demonstrate a novel population of SPP1 and CD44 expressing malignant cells in EBV+ tumors.

ABSTRACT:Rearrangements that place the oncogenes MYC, BCL2, or BCL6 adjacent to superenhancers are common in mature B-cell lymphomas. Lymphomas with diffuse large B-cell lymphoma (DLBCL) or high-grade morphology with both MYC and BCL2 rearrangements are classified as high-grade B-cell lymphoma with MYC and BCL2 rearrangements ("double hit"; HGBCL-DH-BCL2) and are associated with aggressive disease and poor outcomes. Although it is established that MYC rearrangements involving immunoglobulin (IG) loci are associated with inferior outcomes relative to those involving other non-IG superenhancers, the frequency of and mechanisms driving IG vs non-IG MYC rearrangements have not been elucidated. Here, we used custom targeted capture and/or whole-genome sequencing to characterize oncogene rearrangements across 883 mature B-cell lymphomas including Burkitt lymphoma, follicular lymphoma, DLBCL, and HGBCL-DH-BCL2 tumors. We demonstrate that, although BCL2 rearrangement topology is consistent across entities, HGBCL-DH-BCL2 have distinct MYC rearrangement architecture relative to tumors with single MYC rearrangements or with both MYC and BCL6 rearrangements (HGBCL-DH-BCL6), including both a higher frequency of non-IG rearrangements and different architecture of MYC::IGH rearrangements. The distinct MYC rearrangement patterns in HGBCL-DH-BCL2 occur on the background of high levels of somatic hypermutation across MYC partner loci in HGBCL-DH-BCL2, creating more opportunity to form these rearrangements. Furthermore, because 1 IGH allele is already disrupted by the existing BCL2 rearrangement, the MYC rearrangement architecture in HGBCL-DH-BCL2 likely reflects selective pressure to preserve both BCL2 and B-cell receptor expression. These data provide new mechanistic explanations for the distinct patterns of MYC rearrangements observed across different lymphoma entities.