Genotoxicity associated with retroviral CAR transduction of ATM-deficient T cells

Abstract Somatic variants in DNA damage-response genes such as ATM are widespread in hematologic malignancies. ATM protein is essential for double-strand DNA break repair. Germline ATM-deficiencies underlie ataxia-telangiectasia (A-T), a disease manifested by radio-sensitivity, immunodeficiency and predisposition to lymphoid malignancies. A-T patients diagnosed with malignancies have poor tolerance to chemotherapy or radiation. We investigated chimeric-antigen receptor (CAR) T cells using primary T-cells from patients with A-T (ATM-/-), heterozygote donors (ATM+/-) and healthy donors. ATM-/- T-cells proliferate and can be successfully transduced with CARs, though functional impairment of ATM-/- CAR-T cells was observed. Retroviral transduction of the CAR in ATM-/- T-cells resulted in high rates of chromosomal lesions at CAR insertion sites, as confirmed by next-generation long-read sequencing. This work suggests that ATM is essential to preserve genome integrity of CAR-T cells during retroviral manufacturing, and its lack poses a risk of chromosomal translocations and potential leukemogenicity.