Journal Article

281 T cell metabolic pathway enrichment profiles associated with clinical response in CD19 CAR-T therapy for aggressive B-cell non-Hodgkin’s lymphoma

Wang Panwen, Tan, Melinda, Bennani, Nabila N, Dong Haidong, Khurana Arushi, Shao Zuoyi, Wang, Yucai, Durani Urshila, Villasboas Jose, Li, Ying, Silva Corraes Andre de Menezes, Ma, Audrey, Hu, Zeng, Hampel, Paul, Johnston, Patrick, Wu, Chen, Regan, Kevin, Paludo Jonas, Mondello Patrizia, Lin, Yi, Ansell, Stephen

2025

Overview

BackgroundCAR T-cell therapy has achieved remarkable responses in patients with relapsed/refractory aggressive B-cell non-Hodgkin’s lymphoma (NHL). However, 20-30% of patients present with primary refractory disease, and 30-40% relapse, often within 6 months. We examined the metabolic profiles of T-cell subsets in patients who received CD19 CAR T-cell therapy to identify correlations to clinical response and uncover potential targets for therapy.MethodsSingle-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing (scTCR-seq) were performed on peripheral blood mononuclear cells at three timepoints: before lymphodepletion (BL), peak CAR-T expansion (PK), and one-month post-infusion (M1). scRNA-seq/scTCR-seq data were processed with CellRanger v7.0.1, followed by downstream analysis using the immunopipe pipeline.1 Metabolic landscape analysis was conducted on T cell clusters, and pathway enrichment was compared across clinical response groups: CR (complete remission for at least 6 months), PD1 (primary refractory), and PD2 (relapsed after partial or complete response).ResultsWe analyzed 107,035 T cells from 77 serial samples among 32 subjects (16 CR, 12 PD2, 4 PD1). Patients in CR showed an expansion of Th2 cell cluster with enrichment of steroid hormone biosynthesis pathway at BL and PK compared to PD1 patients. Additionally, Tregs were enriched for inositol phosphate metabolism at PK in CR, but not in PD1 and PD2.By contrast, patients in PD1, displayed Treg and Th2 cell clusters enriched for the citric acid cycle (TCA) pathway at BL and PK compared to CR and PD2. Furthermore, these patients presented CD8 effector memory (Tem) and CD8 naïve cell clusters enriched for oxidative phosphorylation (OxPhos), and Th2 clusters with increased glycolysis/gluconeogenesis (GLY) activity at CART peak. GLY pathway was also enriched in tumor recirculating CD8 effector memory (Tem) at PK in PD1 compared to PD2.Finally, patients in PD2 had enrichment for inositol phosphate metabolism in CD8 naïve population at BL and in Tregs and Th1 cells at month 1 compared to CR.ConclusionsWe identified dynamic metabolic profile changes in different T cell populations early in the course of CAR-T therapy that are associated with clinical response. The enrichment of TCA and GLY pathways may reflect altered metabolic function in exhausted T cells. OxPhos has been implicated in mitochondrial functions, whereas inositol phosphate metabolism may play a role in modulating therapeutic response. Further studies of T cell metabolic functions could inform therapeutic strategies to improve clinical response in CAR-T therapy.ReferenceWang P, Yu Y, Dong H, et al. Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline. NAR Genomics and Bioinformatics. 2025;7(2).Ethics ApprovalIRB ID: 16-008261 Mayo clinic RochesterConsentWritten informed consent was obtained from the patient for publication of this abstract. A copy of the written consent is available for review by the Editor of this journal

• Publisher: BMJ Publishing Group LTD
• Subject: Consent / Lymphocytes / Lymphoma / Metabolism