Germinal center (GC)-derived lymphomas arise within a specialized immune ecosystem, yet whether malignant cells direct its remodeling remains unclear. Integrating genomic, transcriptomic, spatial, and functional analyses across follicular lymphoma and diffuse large B-cell lymphoma, we define a developmental framework linking malignant B-cell differentiation state to tumor microenvironment (TME) organization. Rather than segregating by histology, lymphomas align along a shared differentiation continuum in which proliferative dark zone (DZ) states associate with immune-depleted TMEs, whereas post-GC/memory B-cell (MBC) states drive inflamed but immunosuppressed TMEs. Spatial profiling reveals collapse of GC architecture and emergence of suppressive myeloid niches along this trajectory. Single-cell lineage reconstruction uncovers a DZ-to-MBC developmental axis underlying lymphoma evolution. Genetic reprogramming in vivo demonstrates that malignant differentiation state is sufficient to instruct TME remodeling. Collectively, these findings establish malignant differentiation state as a causal determinant of immune architecture across GC-derived lymphomas and identify lineage-directed immune reprogramming as a potential therapeutic strategy.

BackgroundTP53 mutational status (TP53ms) is prognostically important in myeloid neoplasms. Immunohistochemistry (IHC) of p53 has been used as a surrogate for TP53 mutations, with faster results than next-generation sequencing (NGS) and cytogenetic analysis. Given the challenges posed by heterogeneous p53 IHC expression, this study aims to evaluate the interobserver interpretation of p53 stain as a surrogate marker for TP53m.MethodsFifty-three bone marrow (BM) specimens previously diagnosed as myeloid neoplasms or nonneoplastic BM specimens with available concurrent TP53ms were evaluated. p53 IHC staining was performed on all 53 core biopsy or clot sections. TP53 mutation was found in 24 cases (TP53m). Twenty-nine specimens were TP53 wild-type and served as the control group. Six hematopathologists (HPs) blinded to the diagnosis and TP53m independently scored the p53 staining pattern of the biopsies/clot sections for overall staining percentage (OSP) and staining intensity (dark staining percentage as a percentage of total cells (DCP)).ResultsThe intraclass correlation was excellent for OSP (0.927) and good for DCP (0.848). For OSP, a cutoff of 30% resulted in sensitivity of 83.3%, specificity of 89.7%, PPV of 87.0%, and NPV of 86.7%. For DCP, a cutoff of 10% achieved sensitivity of 87.5%, specificity of 96.6%, PPV of 95.4%, and NPV of 90.3%. Additionally, DCP significantly correlated with the VAF of TP53m (R = 0.469, p = 0.028).ConclusionHigh inter-rater reliability for OSP and DCP supports integrating p53 IHC into bone marrow evaluations for rapid TP53m assessment. With superior specificity and predictive values, DCP proves to be a more reliable diagnostic marker for TP53 mutations. While this approach shows promise for myeloid neoplasms, further validation is needed to overcome challenges and expand its clinical utility for tailored treatment strategies.

Pyroptosis is a form of programmed cell death characterized by the cleavage of gasdermin (GSDM) family proteins that form pores in the plasma membrane, cell rupture, and the release of pro-inflammatory cytokines. In this study, we performed immunohistochemistry for cleaved GSDMD, GSDME-N-terminal, and GSDMC in two different cohorts of diffuse large B-cell lymphoma (DLBCL), and analyzed their prognostic and immune impact. The results showed frequent cleaved GSDMD (GSDMD-N-terminal) expression. Only cytoplasmic GSDMD-N-terminal expression correlated with significantly better patient survival in two cohorts. In contrast, GSDME was mainly expressed in the vascular endothelium, correlated with significantly adverse prognostic effect. Correlating with the multiplex fluorescent immunohistochemistry (mfIHC) results, we found that cytoplasmic GSDMD-N-terminal expression was associated with increased CD38+ (activated) M1 macrophages in both cohorts, cognate interactions between live DLBCL cells and activated M1 macrophages (and T cells), and lower PD-1/PD-L1 expression in the analyzed cases. In contrast, T cell pyroptosis, lymphoma cell resistance to cell death, and phagocytosis by M2 macrophages were observed in cells with nuclear GSDMD-N-terminal expression. Bulk gene expression profiling and deconvolution analysis for patients with cytoplasmic GSDMD-N-terminal expression revealed downregulation of “Don’t eat me” signaling genes, upregulation of many RNA genes, decreased frequency of “Inflammatory” lymphoma microenvironment subtype, increased abundance of prognostically favorable cell states and ecotypes, and decreased abundance of T cell exhaustion state. In summary, this study showed distinct cellular and subcellular patterns of three gasdermin proteins and their associated immune response phenotypes and prognostic effects, with implications for novel therapeutic strategies for B-cell lymphoma.

Large B-cell lymphoma with IRF4 rearrangement (LBCL-IRF4) predominantly affects children and young adults (CAYA) and presents as localized disease with excellent prognosis. Although most tumors harbor IRF4 rearrangements (IRF4-R), the existence of cryptic rearrangements has been suggested. Whether IRF4-R LBCL in adults represents the same biological entity remains unclear. To address this question, 35 CAYA patients diagnosed with LBCL-IRF4 and 7 adult (>40-year-old) LBCL with IRF4-R were investigated by an integrative molecular approach. Targeted sequencing structural variant analysis (SV-NGS) confirmed the IRF4-R in 84% of investigated cases. In CAYA, an enrichment (55% vs 29% in adults) of translocations involving IGH, with a breakpoint cluster 3' to IRF4 (EXOC2) was observed, including a cryptic insertion of IGHM-IGHJ5 into IRF4 locus. Novel translocations, IRF4::MIR142 in two CAYA (7%) and IRF4::BATF in one adult, were discovered. Whole-exome sequencing analysis identified unreported mutations in LBCL-IRF4 as YY1 and ZC3H12A (11% each). The high incidence of mutations affecting the B-cell receptor/NF-KB pathways in LBCL-IRF4 was confirmed in cases with diffuse component only. None of the CAYA tumors were classified by LymphGen tool. Adult IRF4-R LBCL showed higher levels of genetic complexity and a distinct mutational profile with mutations on KMT2D and DTX1 (43% each), and MYD88-L265P (29%), and were predicted as EZB or MCD (29% each). These differential genetic features were in line with different clinical presentations (extranodal involvement and advanced stage). In conclusion, IRF4-R architecture and mutational profile differ according to age, supporting that not all cases should be classified as LBCL-IRF4.

This chapter covers the diffuse and aggressive B-cell lymphomas that arise in immunocompetent patients with a focus on the recent advances in our understanding of the clinical and biologic features that define these disease entities as reflected in the 2016 revision of the World Health Organization classification of lymphoid neoplasm. Diseases discussed include: diffuse large B-cell lymphoma (DLBCL), NOS; T-cell/histiocyte-rich large B-cell lymphoma; primary DLBCL of the central nervous system; primary cutaneous DLBCL, leg type; EBV-positive DLBCL, NOS; EBV-positive mucocutaneous ulcer; DLBCL associated with chronic inflammation; primary mediastinal large B-cell lymphoma; intravascular large B-cell lymphoma; ALK-positive large B-cell lymphoma; lymphomatoid granulomatosis; plasmablastic lymphoma; Burkitt lymphoma and Burkitt-like lymphoma with 11q aberration; high-grade B-cell lymphomas, NOS; and high-grade B-cell lymphomas with MYC and BCL2 and/or BCL6 gene rearrangement (double and triple hit lymphomas).

Anaplastic large cell lymphoma (ALCL) cases were discussed at the 2023 Society of Hematopathology/European Association for Haematopathology workshop held on November 9-11, 2023, in Houston, Texas. This session focused on the clinical and pathologic spectrum of 3 types of ALCL: anaplastic lymphoma kinase (ALK)-positive, ALK-negative, and breast implant associated (BIA). Cases of primary cutaneous ALCL were excluded because they were included in another session. Although the diagnosis of ALCL is often straightforward, the 42 submitted cases encompassed unusual clinical presentations, morphologic variants, and atypical immunophenotypes, exemplifying potential difficulties and challenges in establishing the diagnosis of ALCL. Distinguishing ALCL from CD30-positive peripheral T-cell lymphoma, not otherwise specified, or classic Hodgkin lymphoma was discussed. In patients with a previous history of mycosis fungoides and other T-cell lymphoma/leukemia, the differential diagnosis of a CD30-positive T-cell lymphoma mimicking ALCL (mycosis fungoides transformation vs de novo ALCL) was also discussed. In patients with suspected BIA-ALCL, it is critical to properly handle the periprosthetic fluid when the disease first presents and the capsule at the time of initial capsulectomy to make a correct diagnosis and pathologic staging because a missed diagnosis may lead to disease progression. Comprehensive immunohistochemical analysis; fluorescence in situ hybridization for DUSP22, TP63, or JAK2 rearrangement; assessment of clonality of the T-cell receptor and immunoglobulin genes; and sequencing for mutations were performed as part of the workup of the submitted cases, particularly on ALK-negative ALCL cases, emphasizing the importance of ancillary testing in establishing the diagnosis.

We hypothesized that a set of immunohistochemistry (IHC) stains could be used to distinguish Burkitt lymphoma (BL), the quintessential B-cell lymphoma with a germinal center B-cell (GCB) dark zone (DZ) expression signature, from diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS). This might also be applicable to high-grade B-cell lymphomas (HGBCLs) with MYC and BCL2 rearrangements (double-hit lymphomas [DHLs]) and triple-hit lymphomas (THLs). A 5-marker IHC algorithm was designed from gene lists that distinguish physiologic DZ from light zone GCBs. In training and validation cohorts, we distinguished BL from DLBCL, NOS with high sensitivity and specificity. Because DHLs/THLs are enriched for the gene expression DZ signature (DZsig), we evaluated 19 DHLs/THLs and 4 HGBCLs, NOS. Most (83%) cases were IHC DZ. The NanoString DLBCL90 assay was performed on 34 cases to correlate IHC DZ results with the molecular DZsig. The IHC DZ call was significantly associated with the DZsig (P = .0011). The sensitivity and specificity of IHC to recognize DZsig+ cases among DLBCL, NOS and DHLs with BCL2 rearrangements/THLs were 91% and 100%, respectively. The IHC DZ algorithm can support a diagnosis of BL and identifies MYC-BCL2 DHLs/THLs with a molecular DZsig.

Primary testicular (PT) diffuse large B-cell lymphoma (DLBCL) is a rare and aggressive lymphoma with distinct clinical and molecular characteristics. To identify prognostic biomarkers in PT-DLBCL, in this study we analyzed DNA and RNA samples of PT-DLBCL tumors from 206 patients using next-generation sequencing platforms and assays. Genetic alteration analysis found that multiple chromosomal copy number variations (CNVs), TP53 transcript mutations with high variant allele frequency, and MCD subtype had significantly adverse prognostic effects, whereas elevated microsatellite instability had a significantly favorable prognostic effect in PT-DLBCL. Targeted RNA-seq analysis identified a PTL gene expression signature by comparing PT-DLBCL with systemic DLBCL and revealed the heterogeneity within PT-DLBCL by unsupervised clustering, which classified PT-DLBCLs into a testicular lymphoma tumor (TLT) subtype and a microenvironment (ME) subtype. The TLT subtype featured upregulation of genes functioning in DNA damage response, DNA repair, chromatin remodeling, the cell cycle, and the nucleus, and was associated with significantly poorer patient survival and higher frequencies of MYD88 mutations, multiple CNVs, MCD subtype, bulk tumors, and elderly patients in the PT-DLBCL cohort. In contrast, the ME subtype distinctively featured upregulation of various signaling pathway genes involving the tumor microenvironment and downregulation of BTK and B-cell receptor signaling genes, and was associated with significantly better clinical outcome than the TLT subtype of PT-DLBCL independently of CNVs, MCD and MYD88 mutation and than systemic DLBCL. Moreover, genomic microRNA profiling analysis identified a PTL microRNA signature significantly differentially expressed between PT-DLBCL and systemic DLBCL patients and within the PT-DLBCL cohort, and PT-DLBCL patients with higher expression of 16 PTL microRNAs (14 are testicular tissue-specific) had significantly better survival. In summary, this study revealed the molecular heterogeneity in genetic abnormalities and expression profiles of coding genes and microRNAs within the PT-DLBCL entity, and identified significant prognostic biomarkers and PTL signatures.

OBJECTIVE:The successful diagnosis and classification of lymphoid neoplasms in blood and bone marrow is the responsibility of the practicing pathologist. This guide provides a general "roadmap" for this process, from initial case recognition to final classification. METHODS:The integration of hematologic, morphologic, immunophenotypic, and genetic features for the full spectrum of precursor and mature B-cell, T-cell, and natural killer-cell neoplasms that typically manifest in blood and bone marrow is included. RESULTS:Classification systems for lymphoid neoplasms provide criteria for pathologists to render a diagnosis that is optimal for patient care, treatment, and outcome prediction. CONCLUSIONS:This guide provides diagnostic strategies for lymphoid neoplasms encountered in blood and bone marrow specimens using both the International Consensus Classification and the World Health Organization fifth edition classification systems. Key tips are provided for each entity along with testing requirements, differential diagnosis, nonneoplastic mimics, and other unique features based on the experience of the Bone Marrow Pathology Group members.

Pyroptosis has emerged as a novel form of programmed cell death implicated in tumorigenesis and antitumor immunity. To gain knowledge on the role of pyroptosis in diffuse large B-cell lymphoma (DLBCL), we assessed expression of cleaved gasdermin D (GSDMD), GSDME, and GSDMC by immunohistochemistry (IHC) in a large number of DLBCL specimens, and correlated the expression to patient survival and immune biomarkers quantified by multiplex fluorescent IHC, separately in two subcohorts treated by R-CHOP or CHOP chemotherapy. We found that cleaved GSDMD cytoplasmic expression was significantly associated with better survival of patients with DLBCL, increased CD38+ M1-like macrophages (CD68+CD163- or CD11c+), and higher CD38+ percentages in both two subcohorts, as well as lower PD-L1 expression in macrophages and PD-1 expression in T cells in the R-CHOP cohort (PD-1 and PD-L1 were not evaluated in the CHOP cohort). In contrast, GSDME was mainly expressed in endothelial cells, and showed significantly unfavorable prognostic effects and associations with higher CD31+ and CD3+ cell densities in both two subcohorts. In addition, GSDME+ and high GSDMC expression were associated with higher CD38+ cell densities (including CD38+ M1-like macrophages) and percentages in the R-CHOP cohort, whereas GSDME+ was associated with increased M2-like macrophages in the CHOP cohort. Together, these prognostic and correlative results indicate that gasdermins and pyroptosis have important roles in DLBCL. R01CA233490, Duke University startup fund Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Despite a characteristic indolent course, a substantial subset of follicular lymphoma (FL) patients has an early relapse with a poor outcome. Thus far, efforts to identify factors that predict survival have been unsuccessful. However, we and others have demonstrated the prognostic relevance of CD4+ T cells in the tumor microenvironment (TME) of FL and developed a bio-clinical risk model (called BioFLIPI) that offers improved risk stratification (Mondello et al, BCJ 2021). However, the mechanisms defining different BioFLIPI scores remain to be fully understood. To identify the programs associated with the BioFLIPI scores, we first interrogated the RNA-seq of purified B cells from 67 newly diagnosed FL1-3A (BioFLIPI 1 n=21; BioFLIPI 2-3 n=36; BioFLIPI 4 n=10). We found 1,156 upregulated genes and downregulation of 930 genes in BioFLIPI 4 vs 1, including well-known immune molecules such as CD70, IL10RA, CD69, and CCR6 (FDR<0.05). Gene set enrichment analysis (GSEA) using the MSigDB confirmed a negative enrichment in multiple immune response and interferon gamma signatures and revealed striking positive enrichment for cell proliferation and antigen presentation pathways in BioFLIPI 4 compared to BioFLIPI 1 tumors. The same pathways were dysregulated in BioFLIPI 2-3 but a lower magnitude. To investigate the somatic mutations associated with different BioFLIPI scores, we performed WES of the same 67 FLs and further expanded this cohort for a total of 90 patients (BioFLIPI 1 n=26; BioFLIPI 2-3 n=51; BioFLIPI 4 n=13). We found enrichment for mutations in several regulators of the germinal center in BioFLIPI 4 and 2-3, such as MEF2B (p=0.029), FOXO1 (p=0.038) and IRF8 (p=0.035), suggesting the cooperation of multiple oncogenic events promoting lymphomagenesis. In contrast, BioFLIPI 1 tumors harbored a higher rate of mutations in TNFRSF14 gene, known to enhance anti-lymphoma immune response. To investigate whether BioFLIPI modulates immune signatures of the microenvironment, we performed TME deconvolution by applying CIBERSORTx to bulk RNA-seq of these 67 FLs. We found that FLs with BioFLIPI 4 and 2-3 were enriched for CD4+ Tcm exh (p=0.02), Tem exh (p=0.04), Tfhexh (p=0.07) and NK cells (p=0.01) compared to BioFLIPI 1. In line with this data, CyTOF performed on a subset of these patients (BioFLIPI 1 n=12; BioFLIPI 2-3 n=25; BioFLIPI 4 n=6) confirmed progressive increase of CD4+ Tcm exh (p=0.006), Tem exh (p=0.009) and Tfh exh (p=0.025) cells from BioFLIPI 1 to BioFLIPI 4. Single cell RNA/BCR-seq of 21 FLs (BioFLIPI 1 n=6; BioFLIPI 2-3 n=12; BioFLIPI 4 n=3) corroborated a higher abundance of Tem exh, cytotoxic (CTL) Tem exh, Tfhexh and NK cells in BioFLIPI 4 and 2-3. Conversely, CD8+ naïve T cells were prevalent in BioFLIPI 1 tumors. Differential gene expression in T cell clusters from BioFLIPI 4 vs BioFLIPI 1 FL revealed a marked upregulation of multiple immune genes involved in antigen presentation (e.g., HLA-DRB, HLA-DQA, HLA-DPA/B) and immune response (e.g., ETS1, TNFSF8, IL7R). GSEA showed a positive enrichment for antigen presentation signatures and negative enrichment for TNFα signaling and Oxphos metabolism. Similar findings were observed in BioFLIPI 2-3 FLs. Using CellChat analysis, we found a stronger interaction between malignant B cells and Tem exh and CTL Tem exh cells in BioFLIPI 4 and 2-3 vs BioFLIPI 1 tumors. This was linked to an increased strenght of MHCI-CD8 interaction and concordant decrease of MHCII-CD4. Notably, the suppressive BTLA-TNFRSF14 signaling axis was present in BioFLIPI 4 and 2-3 but not in BioFLIPI 1 FLs. This was accompanied by a decreased signaling through TNF/LTA-TNFRSF1B, CD80/CD86-CD28/CTLA4. Linking the BioFLIPI-specific immunogenicity to lymphomagenesis, we found that FL patients with BioFLIPI 4 had two-three folds higher risk of transformation to an aggressive lymphoma (12% vs 7%) or death (21% vs 3%) than those with BioFLIPI 1, suggesting that this immune dysfunction favors the expansion of a dominant tumor clone and promotes a more aggressive form of FL. Collectively, our findings demonstrate that BioFLIPI scores in FL reflect distinct patterns of tumor immunogenicity that shape the TME. Notably, high BioFLIPI scores are paradoxically associated with enhanced antigen presentation alongside a suppressed immune response. This suggests a sustained antigen-specific T cell response that may drive immune exhaustion, promote tumor progression, and ultimately lead to histologic transformation

Background: Pyroptosis is a form of programmed cell death characterized by cleavage of gasdermin (GSDM) family proteins that form pores in the plasma membrane, cell rupture, and release of pro-inflammatory cytokines. Its pro-inflammatory potential has garnered significant research attention in recent years but has not been studied in lymphoma. Patients and Methods: We performed immunohistochemistry for cleaved GSDMD (n-terminal) in two large cohorts of diffuse large B-cell lymphoma (DLBCL) with multiplex fluorescent IHC (mfIHC) data, and analyzed for prognostic and immune impact. Results: Cleaved GSDMD was frequently expressed in DLBCL, and only the cytoplasmic (versus nuclear) form of expression correlated with significantly better patient survival in two DLBCL cohorts. To understand the expression at the single-cell level, we examined mfIHC results, which revealed that GSDMD+cells were tumor or immune cells, and varied in Ki-67, BCL2, and MYC expression. Cases with cytoplasmic cleaved GSDMD expression had higher mean and median levels of CD38+ (activated) M1 macrophages in two cohorts and lower PD-1/PD-L1 expression, as well as phenotypes of cognate interactions between live activated M1 macrophages, DLBCL cells, and T cells in spatially resolved immune landscape by mfIHC. In contrast, phagocytosis of pyroptotic lymphoma cells by M2 macrophages and cell death of T cells were observed in cases with predominantly nuclear form of cleaved GSDMD expression. Bulk gene expression profiling analysis identified a large proportion of RNA genes upregulated in DLBCLs with cytoplasmic cleaved GSDMD expression, and deconvolution analysis found decreased frequency of the “Inflammatory” lymphoma microenvironment (LME) subtype, increased frequency of cell states and ecotypes with favorable prognostic associations, and decreased frequency of T cell exhaustion states. Summary: Analysis of pyroptosis-inducing cleaved GSDMD (n-terminal) expression in a large number of DLBCL patients revealed dinstinctive cytoplasmic and nuclear expression patterns in live and pyroptotic cells associated with different prognostic and immune effects. Cytoplasmic cleaved GSDMD expression is a marker of cognate interactions between live cells (e.g., activated M1 macrophages) associated with adaptive responses and favorable prognostic effects, whereas nuclear cleaved GSDMD expression is associated with immunosuppressive mechanisms, including T cell death and phagocytosis by M2 macrophages.

Over the past decade, classification systems using high-throughput genetic data have been developed to identify molecular subtypes of DLBCL. Although not a primary goal, these classifiers were also proposed as prognostic factors in their respective publications. To date, however, no study has directly compared these classifiers' ability to predict overall (OS) and event-free survival (EFS) in the same cohort. Herein, we sought to systematically compare predictive performance, benchmarked against the IPI, of several current established molecular classifiers and evaluate if any add significant independent prognostic information beyond the IPI. WES (including paired germline filter) and RNAseq data from newly diagnosed DLBCL patients (N=432; 2018 WHO criteria) in the Mayo Clinic/University of Iowa Lymphoma Molecular Epidemiology Resource (MER) were available for analysis (WES n=112, RNAseq n=40, or both n=280). The number of cases able to be classified (including as unclassified) for each classifier was as follows: IPI (432, 100%), cell-of-origin (COO, by Hans algorithm; 346, 80.1%), refined COO (by gene expression with Dark Zone Signature; 320, 100%), Haematological Malignancy Research Network (HMRN; 349, 89.0%), B-cell state (320, 100%), Lymphoma Ecotype (320, 100%), Lymphoma Microenvironment (LME; 320, 100%), Tumor microenvironment (TME26; 320, 100%), SubLymE (312, 97.5%), LymphGen (358, 91.3%), and DLBclass (223, 58.2%). OS was defined as time from diagnosis to all-cause death while EFS was defined as time from diagnosis to disease progression, initiation of second-line treatment, or all-cause death. We calculated Harrell's c-statistics for each Cox proportional hazards model evaluating the discriminative performance of each classifier in predicting OS/EFS. Using bootstrap validation, we obtained optimism-corrected c-statistics, which we report in the results. We performed likelihood ratio tests (LRT) comparing a univariable Cox model with IPI alone and models including both IPI and a given classifier to assess if a classifier provided independent prognostic information beyond the IPI. All patients were treated with immunochemotherapy (IC) with curative intent, 247 (57%) were male, median age at diagnosis was 65 years (IQR 55-72 years), 390 (96%) were White, 209 (60%) had GCB subtype by Hans, 22 (5.1%) had MYC double-hit by FISH (MYC and BCL2 or BCL6), and 162 (37.9%) had an IPI ≥ 3. The median follow-up was 7.0 years, 167 (39%) experienced an event, and 137 (32%) died. In a univariable Cox model, the c-statistic for IPI predicting OS was 0.66 (95% confidence interval [CI] 0.61-0.70). All other classifiers had c-statistics of ≤0.56. The c-statistic for IPI predicting EFS was 0.64 (95% CI 0.60-0.69), and all other classifiers had c-statistics of ≤0.58. The univariate DLBclass results for OS and EFS were not significantly impacted when restricted to cases with confidence >0.7 (n=136). In Cox models of IPI alone versus IPI plus an individual classifier, the only classifier that provided statistically significant, independent information for OS was TME26 (LRT p=0.02). Adjusting for IPI, patients who were TME26-negative had significantly inferior OS compared to TME26-positive cases (HR 1.63, 95% CI 1.07-2.47; p=0.02). For EFS, DLBclass (restricted to confidence >0.7) added significant prognostic information beyond IPI (LRT p=0.02). This finding was largely driven by C5 subtype; relative to C1 subtype and adjusting for IPI, C5 subtype had significantly inferior EFS (HR 5.53, 95% CI 1.81-17.0; p=0.003). In summary, we compared prognostic performance of multiple DLBCL molecular classifiers with respect to OS and EFS in a single real-world, prospective cohort of newly diagnosed, IC-treated DLBCL. Our data supports two key findings: all classifiers had modest performance for prognosis, and none individually outperformed the IPI in predicting OS nor EFS. Second, only TME26 and DLBclass (confidence >0.7) provided additional prognostic information beyond that captured by the IPI for OS and EFS, respectively. This finding suggests that the tumor immune microenvironment and characteristics of C5 DLBCLs (ABC-subtype, CD79B mutations) can potentially offer significant independent information for predicting survival and response to front-line immunochemotherapy. If replicated, these findings could inform risk-adapted treatment approaches and aid in identifying high-risk patients for enrollment in genomically-informed clinical trials.

Marginal zone lymphoma (MZL) is an uncommon non-Hodgkin B-cell lymphoma accounting for 7-10% of lymphoma diagnoses. Extranodal MZL (EMZL) of mucosa-associated lymphoid tissue (MALT) is the most common subtype (61%) of MZL. While the mutational landscape, chromosomal aberrations and transcriptome of nodal and splenic MZL have been extensively evaluated, the mutational landscape of EMZL has only been evaluated in a small number of patients and mainly by targeted sequencing. Consequently, the comprehensive genomic landscape of EMZL remains largely uncharacterized. Herein, we performed whole exome sequencing followed by targeted sequencing of potential tumor driver genes, copy number and/or RNA transcriptome analyses in 165 patients with pretreatment EMZL tumors involving 16 anatomic locations. All samples were collected and underwent expert review as part of the Atlas of Blood Cancer Genomes consortium. The most common anatomic locations were ocular adnexa (OAMZL) (n=35), gastric (n=25, including 6 positive for Helicobacter pylori), salivary glands (n=25), and lungs (n=24). Using common criteria for variant mutation calling and significant focal copy number (CN), we identified 1218 variants (1030 missense and 188 truncation mutations) across 174 genes and 2837 CN focal alterations (1614 copy gains and 1223 copy number losses). Of these genes, 44 and 11 were mutated in >5% and >10% of specimens, respectively. We detected variants identified previously by targeted sequencing in EMZL from different locations (e.g. TNFAIP3 (A20) (12%), TBL1XR1 (13%), SPEN (10%), CARD11 (7%), TET2 (7%) and CREBBP (6%)). We detected mutations in KLF2 (10 mutations in 8 EMZL patients) and PTPRD (7 mutations in 7 EMZL patients) that were previously suggested to be specific for splenic and nodal MZL, respectively. We also detected variants not previously reported in EMZL, including a transcriptional factor ZEB2, LRP1B,and others. The most frequently mutated gene in our study (25% of tumors) was IGLL5. Some mutations were limited to specific locations (e.g. ZEB2 mutations seen exclusively in gastric and salivary gland EMZL), while most were observed across all anatomic locations. There was no association between specific mutations and clonal IGHV, in contrast to previous reports. Using Enrichr tool, we observed enrichment of mutations in genes belonging to the B cell receptor activation, NOTCH signaling, Wnt-beta catenin signaling, NF-kB signaling , PI3K AKT signaling, DNA repair and other pathways. Chromosomal and copy number changes were also commonly observed including previously reported trisomy of chromosomes 3 and 18. Combining DNA mutations and CN alterations, the number of genetic lesions per tumor sample in the 174 mutated genes ranged from 0 to 95, with an average load of 17 lesions per case. RNA sequencing was successful in 159 EMZL tumors from 16 distinct anatomic locations. Unsupervised clustering using all genes with a median log2-normalized gene expression value greater than 5 and a standard deviation greater than 1 (1323 genes) demonstrated that the majority of gastric EMZL with and without H. pylori infections clustered together on 2 dendrograms as did most of the samples of OAMZL. Since the clustering could be forced by organ-specific and not tumor-specific gene expression, we next focused on the expression of the 345 genes from the LM22 matrix that passed our transcriptomic row filtering. Unsupervised clustering resulted in clustering of most gastric EMZL irrespective of H. pylori positivity together in the same dendrogram branch, accompanied by few additional EMZL from other anatomic locations. Most of the EMZL samples from other locations did not show preferential co-clustering together. On comparison of gene expression between gastric and OAMZL, there was enrichment of the B-cell receptor signaling pathway, B-cell activation, B-cell naïve and B-cell memory cells, B-cell proliferation and NF-kB signaling in the latter. Immune microenvironment analysis showed a statistically significant increase in resting mast cells and decrease in M1 macrophages in gastric EMZL and increase in regulatory T cells in salivary EMZL. The broad genomic studies reported here underscore the biological similarity of EMZL across anatomical sites with the potential exceptions of gastric EMZL (regardless of H. Pylori status). These data provide valuable genomic and transcriptomic resources to inform future diagnostic and therapeutic strategies.