Genetic Mutation and Epigenetic Silencing Drive Antigen-Negative Relapse in CD7 CAR-T Treated T-cell Lymphoid Malignancies

CD7 is a promising target for chimeric antigen receptor (CAR) T-cell therapy in T-cell lymphoid malignancies; however, antigen loss-mediated relapse emerged as a major challenge. Herein, we systematically analyzed the genetic and epigenetic alterations of paired specimens (pre-treatment and relapsed) from 10 patients with T-cell lymphoma/leukemia receiving CD7 CAR-T cells. Overall, we identified three distinct mechanisms underlying CD7 loss: Firstly, frameshift insertion (Pt4; c.164dupG:p.R55fs) or deletion (Pt7; c.122delG:p.G41Efs*19) resulting in truncation of the CD7 transmembrane domain in two of ten patients; Secondly, hypermethylation of the CD7 promoter in seven of ten patients without CD7 mutation; Thirdly, simultaneous occurrence of promoter region hypermethylation and multiple in-frame mutations with predicted functional interference in one of ten patients (Pt2). Collectively, these findings demonstrated that both clonal heterogeneity and epigenetic plasticity drive antigen-negative relapse in T-cell lymphoid malignancies under the selective pressure of CD7 CAR-T therapy.