Genetically distinct pathogenesis of epstein‐barr virus (ebv)‐positive versus ebv‐negative classical hodgkin (chl) lymphoma

Introduction: Latent EBV infection of the cHL clone is more frequent in the mixed-cellularity (MC) histological subtype, in early childhood and older adulthood, and in developing countries. Based on these and other epidemiologic features, EBV+ cHL has been hypothesized to have distinct etiology and pathogenesis compared to EBV− cHL. However, the landscape of genetic lesions in the EBV+ cHL genome is incompletely defined. Methods: We studied 57 cHL cases (10–83 year-old; 41 EBV−, 16 EBV+) by whole-exome sequencing/WES (n = 56 cases; 34 from Tiacci et al. Blood 2018; 18 from Wienand et al. Blood Adv 2019; and 4 cases newly added) and/or whole-genome sequencing/WGS (32 cases newly processed, including 31 also subjected to WES). Tumor and normal cells were purified from frozen samples by microdissection (n = 39; 9 EBV+, 30 EBV−) or flow cytometry (n = 18; 7 EBV+, 11 EBV−). EBV+ and EBV- cases were sequenced at identical median depths (WGS 44X; WES 146X) and subjected to the same bioinformatics pipelines. Results: Clonal nonsynonymous somatic mutations were much fewer in EBV+ versus EBV− cHL (median 4.5 vs. 57; p = 0.0013), and the same was observed for total mutations genome-wide (median 112 vs. 6826; p < 0.0001). In contrast, within EBV− cHL, MC (n = 6) and non-MC (n = 33) cases had similar mutation load (p = 0.56), indicating a link with viral status rather than histological subtype. AID-associated mutational signatures were stronger in EBV− versus EBV+ cHL, both genome-wide (SBS9, q = 0.069; SBS85, q = 0.023) and in the target region of 126 genes known to undergo AID-driven aberrant somatic hypermutation (median of 4 vs. 0 mutations/Mb; p = 0.045). Compared to EBV− cHL, EBV+ cHL had fewer mutations or copy number alterations in ≥1 genes of multiple pathways that drive cHL pathogenesis and can be activated by EBV latent proteins (possibly surrogating cellular genetic lesions). In particular (Figure A): (i) JAK-STAT signaling genes STAT6, SOCS1, CSF2RB and JAK2 were mutated in 85% EBV− versus 47% EBV+ cases (p = 0.0057); (ii) PI3K-AKT signaling genes GNA13 and ITPKB were mutated in 34% EBV− versus 7% EBV+ cases (p = 0.047); and (iii) NF-κB signaling genes TNFAIP3, NFKBIE and REL were mutated in 85% EBV− versus 47% EBV+ cases (p = 0.0057). EBV− cHL had also more frequent mutations of the MHC-I genes B2M and HLA-A/B/C (56% vs. 20% in EBV+ cHL, p = 0.0032; Figure A), possibly to prevent presentation of tumor neo-antigens generated by the much higher mutation burden. In contrast (Figure B), EBV+ cases showed germline homozygosity of ≥1 HLA-I genes more often than EBV− cases (53% vs. 19%; p < 0.05), particularly for HLA-C (33% vs. 2%; p = 0.0039), which may predispose to development of EBV+ cHL through a reduced diversity of HLA-I alleles available for viral antigen presentation. Encore Abstract - previously submitted to EHA 2023 Keywords: genomics, epigenomics, and other-omics, Hodgkin lymphoma, tumor biology and heterogeneity No conflicts of interests pertinent to the abstract. * K. Gomez and G. Schiavoni are co-first authors. ^ R. Rabadan and Tiacci are co-last authors.