Longitudinal single-cell immunoprofiling links durable CAR T response to sustained activation and clonotypic expansion of the native cytotoxic T cell repertoire

CD19-directed chimeric antigen receptor (CAR) T-cell therapy has transformed outcomes for patients with relapsed/refractory large B-cell lymphoma (LBCL), yet the mechanisms underlying durable remission remain incompletely understood. While CAR T-cell persistence is associated with response, long-term remission can occur despite rapid CAR T clearance, suggesting the involvement of additional immune mechanisms. To investigate the role of the native T-cell repertoire in shaping response durability, we performed single-cell RNA and TCR sequencing (scRNA-seq/scTCR-seq) on longitudinal peripheral blood samples from LBCL patients treated with axicabtagene ciloleucel (axi-cel) in the ZUMA-1 trial. We compared immune landscapes and clonotypic dynamics among patients achieving durable remission (>1 year), those experiencing early relapse (<6 months), and those with refractory disease. Patients with long-term remission exhibited increased cytotoxic, proinflammatory, and proliferative native T-cell subsets, while early relapse was associated with immunoregulatory populations that may suppress T-cell activation. TCR profiling revealed robust clonotypic expansion of native cytotoxic T cells post-infusion in durable responders, with expansion patterns strongly predicting clinical outcomes. Notably, TCR screens did not identify known viral targets, suggesting tumor-specific immunity may mediate ongoing remission. These findings propose native T-cell clonotypic expansion as a key determinant of durable response to CAR T therapy and highlight its predictive potential for long-term clinical outcomes. PBMC samples were collected from 32 LBCL patients at leukapheresis, as well as at 4 weeks, 6 months, and 12 months post-CAR T infusion. These samples were analyzed using scRNA-seq and scTCR-seq. ***Submitters state that this submission includes only processed data files due to patient privacy restrictions. Raw sequencing data can be provided following a request for a Data Use Agreement with Kite Pharma, Inc., in accordance with participating patient consent. Kite is committed to sharing clinical trial data with external medical experts and scientific researchers in the interest of advancing public health. Anonymized individual patient data can be provided for studies of Kite or Gilead compounds approved in the US and the EU with a marketing authorization date on or after 1 January 2014 to qualified researchers based on submitted curriculum vitae and reflecting no conflicts of interest. Approval of such requests is at Kite’s discretion and is dependent on the nature of the request, the merit of the research proposed, the availability of the data, and the intended use of the data. Data requests should be sent to [e-mail] and will be addressed within 60 days.