Clinical Evidence That Deficiency of the Methylcytosine Dioxygenase TET2 Gene Promotes the Clonal Expansion and Therapeutic Efficacy of CD19-Directed T Cells

Adoptive transfer of autologous chimeric antigen receptor (CAR) T cells that target tumor antigens can induce remissions in patients with hematologic malignancies. A major obstacle to successful clinical responses in some patient populations has been infusion with ineffective cell populations that are terminally differentiated, exhausted, poorly proliferative and short-lived. Understanding and manipulating the mechanistic pathways that sustain T cell potency will potentially unlock durable responses to tumors. Here we present an unusual case that helps clarify determinants of CAR T cell persistence. A 78-year-old individual with advanced chronic lymphocytic leukemia (CLL) was infused with CAR T cells that target CD19 (CTL019). CAR T cell expansion was delayed and not evident until 50 days following infusion and anti-tumor activity was observed in the peripheral blood, lymph nodes as well as bone marrow, accompanied by complete remission that has been sustained for over 4.5 years. Retrospective analyses revealed that at the peak of in vivo CAR T cell activity, over 94% percent of CD8+ CTL019 cells originated from a single clone in which lentiviral vector-mediated insertion of the CAR transgene led to monoallelic loss of TET2 . Accordingly, examination of polyadenylated TET2 RNA populations showed the appearance of new chimeric RNAs that spliced from TET2 exon 9 into the vector and terminated, truncating the encoded protein. Further analysis revealed that this patient had a germline polymorphism in the other allele of TET2 . This was a missense variant at amino acid 1879 (exon 11), converting the wildtype residue, glutamic acid, to glutamine (protein change: pE1879Q; cDNA change: c.5635G>C; allele frequency of approximately 50%). TET2 deficient CTL019 cells exhibited reduced cytosine hydroxymethylation and a chromatin accessibility profile measured by ATAC-Seq consistent with altered T cell differentiation. Furthermore, at the peak of in vivo engraftment, CAR T cells from this subject showed an early (central) memory phenotype which differs from CTL019 cells of other complete responding patients that are instead characterized by late (effector) memory differentiation at the height of their response. Experimental knock-down of TET2 in healthy donor CAR T cells altered their differentiation and augmented CTL019 effector function in a manner that was consistent with the effects of TET2 deficiency observed in this subject. Our findings suggest that the profound clonal expansion of a single TET2 deficient CAR T cell resulted in a complete and durable remission of CLL, highlighting the potential for epigenetic modulation of ineffective patient T cells to generate curative T cell products.