Gould, Clare

Abstract Background Primary CNS lymphoma (PCNSL) is a rare, aggressive diffuse large B-cell lymphoma confined to the CNS, with poor outcomes. Virally associated PCNSL, including AIDS-related PCNSL (AR-PCNSL) and CNS post-transplant lymphoproliferative disorder (CNS-PTLD) accounts for ~10% of cases and is strongly linked to EBV infection and poor prognosis. In our prior Blood (Gandhi et al. 2021) study, targeted sequencing showed that EBV⁺ PCNSL lacks canonical MYD88, CD79B, and PIM1 mutations and retains intact HLA class I/II, suggesting distinct immunobiology. However, questions remain regarding the immune microenvironment, broad mutational landscape, and intratumoral heterogeneity. Here, we present the first large-scale comprehensive integrated analysis of virally associated PCNSL to define subtype-specific vulnerabilities and therapeutic implications. Methods FFPE brain biopsies from 72 PCNSL patients (40 EBV- de novo PCNSL, 32 EBV+ PCNSL including 18 AR-PCNSL and 14 CNS-PTLD) were analyzed. Immune gene expression was profiled using the NanoString PanCancer Immune Panel. Whole exome sequencing (WES) defined recurrent driver mutations, tumor mutational burden (TMB), and LymphGen classification (excluding A53 subtype). Single nuclei RNA sequencing (snRNA-seq) using the 10x Genomics Chromium Flex platform characterized cellular heterogeneity. Results WES demonstrated a marked reduction in canonical mutations (MYD88L265P, CD79B, PIM1, CARD11) in CNS-PTLD (0%) and AR-PCNSL (29%) vs. de novo PCNSL (87.5%; p<0.0001). AR-PCNSL had a distinct mutational signature when compared with CNS-PTLD and de novo PCNSL. NOTCH1/2 mutations were significantly enriched in AR-PCNSL (71%) vs. CNS-PTLD (9%) and de novo PCNSL (33%) (p<0.01). NLRC5 mutations were present in 64% of AR-PCNSL cases, higher than the 25% observed in de novo PCNSL and were absent in CNS-PTLD. TMB was significantly elevated in AR-PCNSL (mean 26.27 mutations/Mb) vs. de novo PCNSL (17.22) and CNS-PTLD (11.01; p=0.0018) underscoring pronounced genomic instability and suggesting HIV may exert a mutagenic influence beyond immunosuppression. EBV driven subtypes lacked MCD features and were more often classified as ST2 or unassigned. Despite NOTCH2 mutations, AR-PCNSL cases were not classified under the BN2 subtype, further highlighting limitations in current molecular classification systems to accurately stratify virally associated PCNSL. Immune transcriptomic profiling revealed further distinctions within EBV+ PCNSL. CNS-PTLD showed increased expression of genes related to antigen presentation (p<0.0001), cytotoxicity (p=0.0019), and T cell function (p<0.0001), suggesting retained immune responsiveness. AR-PCNSL exhibited significant suppression of HLA class I/II genes (p=0.0027 and p<0.0001 respectively), despite intact genomic loci, implicating post-transcriptional or epigenetic silencing. Immune cell composition revealed reduced macrophage infiltration and suppressed CD4 expression in AR-PCNSL. CNS-PTLD showed higher expression of checkpoint molecules LAG3, TIM3, and CTLA4, consistent with T cell exhaustion. snRNA-seq profiling of AR-PCNSL identified distinct malignant and non-malignant cell populations, including a reduced CD4⁺ compartment and altered microglial/macrophage populations and cell states compared to de novo PCNSL, corroborating bulk transcriptomic data, amongst other ongoing analysis. Conclusion This study represents the largest and most comprehensive immunogenomic investigation of virally associated PCNSL. AR-PCNSL and CNS-PTLD lack canonical PCNSL driver mutations and instead harbor distinct mutational signatures, including NOTCH pathway alterations in AR-PCNSL. These findings underscore divergent pathogenic mechanisms and support tailored therapies. AR-PCNSL is marked by high TMB, suppressed antigen presentation, and reduced CD4⁺ infiltration, indicating profound immune dysfunction. CNS-PTLD retains immune functionality but shows checkpoint upregulation and T cell exhaustion. Despite both being EBV-driven and CNS-restricted, they display distinct molecular and immunological programs, suggesting context specific EBV mechanisms. These findings challenge existing classification systems and support CNS-specific molecular frameworks to guide therapeutic interventions including BTK inhibition for NOTCH-mutated lymphoma. They lay the foundation for precision approaches in EBV⁺ PCNSL, including immune restoration, antigen-specific T cell therapy, and epigenetic modulation.

PURPOSE Peripheral T-cell lymphoma (PTCL) includes heterogeneous clinicopathologic entities with numerous diagnostic and treatment challenges. We previously defined robust transcriptomic signatures that distinguish common PTCL entities and identified two novel biologic and prognostic PTCL-not otherwise specified subtypes (PTCL-TBX21 and PTCL-GATA3). We aimed to consolidate a gene expression–based subclassification using formalin-fixed, paraffin-embedded (FFPE) tissues to improve the accuracy and precision in PTCL diagnosis. MATERIALS AND METHODS We assembled a well-characterized PTCL training cohort (n = 105) with gene expression profiling data to derive a diagnostic signature using fresh-frozen tissue on the HG-U133plus2.0 platform (Affymetrix, Inc, Santa Clara, CA) subsequently validated using matched FFPE tissues in a digital gene expression profiling platform (nCounter, NanoString Technologies, Inc, Seattle, WA). Statistical filtering approaches were applied to refine the transcriptomic signatures and then validated in another PTCL cohort (n = 140) with rigorous pathology review and ancillary assays. RESULTS In the training cohort, the refined transcriptomic classifier in FFPE tissues showed high sensitivity (> 80%), specificity (> 95%), and accuracy (> 94%) for PTCL subclassification compared with the fresh-frozen–derived diagnostic model and showed high reproducibility between three independent laboratories. In the validation cohort, the transcriptional classifier matched the pathology diagnosis rendered by three expert hematopathologists in 85% (n = 119) of the cases, showed borderline association with the molecular signatures in 6% (n = 8), and disagreed in 8% (n = 11). The classifier improved the pathology diagnosis in two cases, validated by clinical findings. Of the 11 cases with disagreements, four had a molecular classification that may provide an improvement over pathology diagnosis on the basis of overall transcriptomic and morphological features. The molecular subclassification provided a comprehensive molecular characterization of PTCL subtypes, including viral etiologic factors and translocation partners. CONCLUSION We developed a novel transcriptomic approach for PTCL subclassification that facilitates translation into clinical practice with higher precision and uniformity than conventional pathology diagnosis.

Abstract Primary central nervous system lymphoma (PCNSL) is confined to the brain, eyes, and cerebrospinal fluid without evidence of systemic spread. Rarely, PCNSL occurs in the context of immunosuppression (eg, posttransplant lymphoproliferative disorders or HIV [AIDS-related PCNSL]). These cases are poorly characterized, have dismal outcome, and are typically Epstein-Barr virus (EBV)-associated (ie, tissue-positive). We used targeted sequencing and digital multiplex gene expression to compare the genetic landscape and tumor microenvironment (TME) of 91 PCNSL tissues all with diffuse large B-cell lymphoma histology. Forty-seven were EBV tissue-negative: 45 EBV− HIV− PCNSL and 2 EBV− HIV+ PCNSL; and 44 were EBV tissue-positive: 23 EBV+ HIV+ PCNSL and 21 EBV+ HIV− PCNSL. As with prior studies, EBV− HIV− PCNSL had frequent MYD88, CD79B, and PIM1 mutations, and enrichment for the activated B-cell (ABC) cell-of-origin subtype. In contrast, these mutations were absent in all EBV tissue-positive cases and ABC frequency was low. Furthermore, copy number loss in HLA class I/II and antigen-presenting/processing genes were rarely observed, indicating retained antigen presentation. To counter this, EBV+ HIV− PCNSL had a tolerogenic TME with elevated macrophage and immune-checkpoint gene expression, whereas AIDS-related PCNSL had low CD4 gene counts. EBV-associated PCNSL in the immunosuppressed is immunobiologically distinct from EBV− HIV− PCNSL, and, despite expressing an immunogenic virus, retains the ability to present EBV antigens. Results provide a framework for targeted treatment.