Universal base-edited CAR7 T cells for T-cell acute lymphoblastic leukemia

Abstract

Abstract Background Base editing (BE) by cytidine deamination offers advantages over canonical clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene knockout in mediating efficient and multiplexed gene disruption without causing chromosomal breaks. In combination with lentiviral transduction, BE was used to manufacture universal donor, ‘off-the-shelf’ chimeric antigen receptor (CAR) T cells with specificity for CD7 (CAR7) for use in relapsed/refractory T-cell acute lymphoblastic leukaemia (r/r T-ALL). Inactivation of three genes encoding the T cell receptor β chain, CD7 and CD52 was incorporated to prevent graft-versus-host disease (GVHD), avoid fratricide and enable evasion of Alemtuzumab, respectively. Methods An open label, single arm, non-randomised Phase 1 clinical trial (ISRCTN15323014) supported by MRC and Wellcome Trust was sponsored by Great Ormond Street Hospital NHS Trust. Between 1 April 2022 and 31 May 2025, nine children <16-years with r/r T-ALL were dosed. Two additional adults aged 28 and 38 were treated under specials licence access arrangements. BE-CAR7 T cells were infused after lymphodepletion (LD) with fludarabine (150 mg per square meter), cyclophosphamide (120 mg/kg) and alemtuzumab (1 mg/kg). All subjects had quantifiable disease loads with leukemia associated immunophenotypes all exhibiting CD7 > 99%. Patients received 0.2-2.0 x 106 CAR T cells/kg and those achieving remission by D28 proceeded to allogeneic hematopoietic stem cell transplantation (allo-SCT). Primary objectives related to safety and secondary objectives to duration of remission, disease-free and overall survival. Results All subjects had received multiple lines of therapy, including previous allo-SCT in 3 cases. Pre-LD blast counts in the BM after debulking ranged between 0.18-86%. Two patients had evidence of extra-medullary disease (central nervous system and ocular). Cytokine release syndrome (CRS) developed between 1-5 days after BE-CAR7 infusion, with 9/11 (81%) patients experiencing grade 1-2 and two patients (19%) experienced grade 3-4 CRS. Ten patients developed erythematous maculo-papular skin rashes between 6-10 days after BE-CAR7 infusion, which were self limiting or managed with topical or systemic steroids until resolution by D21. Where skin biopsy was undertaken, histological changes were reported as non-specific, with no evidence of GVHD. Grade 1 immune effector cell-associated neurotoxicity syndrome (ICANS) was documented in 3/11 (27%) patients. BE-CAR7 T-cells were detected in blood within 7-14 days by flow cytometry and/or by molecular chimerism and vector copy quantification. All subjects were found to have complete morphological remission with incomplete count recovery (CRi) at D28. Nine subjects (82%) achieved MRD remissions (by flow and/or PCR) that allowed them to proceed to allo-SCT, while two patients with elevated MRD in bone marrow received palliation. Transplant conditioning ahead of allo-SCT removed residual BE-CAR7 T cells and enabled donor-derived, multilineage immune reconstitution. As anticipated, viral reactivations were frequent, and three patients experienced significant virus-related morbidity post-transplant. Overall, 7/11 (63%) subjects dosed were in ongoing remission 3-36 months after transplant, and suspected CD7 negative leukemic escape has been documented in 2 patients. Conclusions Universal BE-CAR7 T cells offer the prospect of leukemic remission for patients with CD7+ r/r T-ALL ahead of allo-SCT and will be further assessed in children and adults in extended cohorts.