Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma

CD19-directed chimeric antigen receptor (CAR-19)-T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. While host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients who relapse retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 CAR-19-treated large B-cell lymphoma patients. We find that pre-treatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients failed by CAR-T therapy. Pretreatment reduced expression or mono-allelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are due to multiple mechanisms. Our study shows tumor-intrinsic genomic alterations are key among the complex interplay of factors that underly CAR-19 efficacy and resistance for large B-cell lymphomas.