Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma

Fifty percent of diffuse large B cell lymphoma (DLBCL) cases lack cellsurface expression of the class I major histocompatibility complex (MHC-I), thus escaping recognition by cytotoxic T cells. Here we show that, across B cell lymphomas, loss of MHC-I, but not MHC-II, is preferentially restricted to DLBCL. To identify the involved mechanisms, we performed whole exome and targeted HLA deepsequencing in 74 DLBCL samples, and found somatic inactivation of B2M and the HLA-I loci in 80% (34 of 42) of MHC-I-NEG tumors. Furthermore, 70% (22 of 32) of MHC-I-POS DLBCLs harbored monoallelic HLA-I genetic alterations (MHC-I-POS/mono), indicating allelespecific inactivation. MHC-INEG and MHC-I-POS/mono cases harbored significantly higher mutational burden and inferred neoantigen load, suggesting potential coselection of HLA-I loss and sustained neoantigen production. Notably, the analysis of >500,000 individuals across different cancer types revealed common germline HLA-I homozygosity, preferentially in DLBCL. In mice, germinal-center B cells lacking HLA-I expression did not progress to lymphoma and were counterselected in the context of oncogene-driven lymphomagenesis, suggesting that additional events are needed to license immune evasion. These results suggest a multistep process of HLA-I loss in DLBCL development including both germline and somatic events, and have direct implications for the pathogenesis and immunotherapeutic targeting of this disease.

Automated summary

The loss of MHC-I in DLBCL is associated with somatic inactivation of HLA-I loci and has a significant impact on neoantigen and mutational burden. There is a multistep process of HLA-I loss in DLBCL development involving both germline and somatic events.