Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission

Affiliations

• Department of Biomedical Engineering, Yale University, New Haven, CT, USA
• Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
• Institute of Materials Science & Engineering, EPFL, Lausanne, Switzerland
• Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
• Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
• Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
• Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
• Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
• Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
• Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
• Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
• Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
• Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
• Human and Translational Immunology, Yale University School of Medicine, New Haven, CT, USA
• Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA

PMID:  #  DOI: 10.1038/s41586-024-07762-w

Abstract

Despite a high response rate in chimeric antigen receptor (CAR) T cell therapy for acute lymphocytic leukaemia (ALL)1,2,3, approximately 50% of patients relapse within the first year4,5,6, representing an urgent question to address in the next stage of cellular immunotherapy. Here, to investigate the molecular determinants of ultralong CAR T cell persistence, we obtained a single-cell multi-omics atlas from 695,819 pre-infusion CAR T cells at the basal level or after CAR-specific stimulation from 82 paediatric patients with ALL enrolled in the first two CAR T ALL clinical trials and 6 healthy donors. We identified that elevated type 2 functionality in CAR T infusion products is significantly associated with patients maintaining a median B cell aplasia duration of 8.4 years. Analysis of ligand–receptor interactions revealed that type 2 cells regulate a dysfunctional subset to maintain whole-population homeostasis, and the addition of IL-4 during antigen-specific activation alleviates CAR T cell dysfunction while enhancing fitness at both transcriptomic and epigenomic levels. Serial proteomic profiling of sera after treatment revealed a higher level of circulating type 2 cytokines in 5-year or 8-year relapse-free responders. In a leukaemic mouse model, type 2high CAR T cell products demonstrated superior expansion and antitumour activity, particularly after leukaemia rechallenge. Restoring antitumour efficacy in type 2low CAR T cells was attainable by enhancing their type 2 functionality, either through incorporating IL-4 into the manufacturing process or by priming manufactured CAR T products with IL-4 before infusion. Our findings provide insights into the mediators of durable CAR T therapy response and suggest potential therapeutic strategies to sustain long-term remission by boosting type 2 functionality in CAR T cells.

尽管嵌合抗原受体（CAR）T细胞治疗急性淋巴细胞白血病（ALL）具有较高的反应率，约50%的患者在第一年内复发，这在细胞免疫疗法的下一阶段中是一个亟待解决的问题。在这项研究中，我们从82名参与前两次CAR T ALL临床试验的儿童患者和6名健康供体中，获得了695,819个预输注CAR T细胞的单细胞多组学图谱，分析了基础水平或经过CAR特异性刺激后的细胞。我们发现，CAR T输注产品中升高的2型功能性与患者维持中位8.4年的B细胞无白细胞增多症持续时间显著相关。配体-受体相互作用的分析显示，2型细胞通过调节功能失调的亚群来维持整个细胞群体的稳态，而在抗原特异性激活过程中加入IL-4能够缓解CAR T细胞的功能失调，同时在转录组和表观基因组水平上增强其适应性。治疗后血清的连续蛋白质组学分析显示，在5年或8年无复发的应答者中，循环2型细胞因子的水平较高。在白血病小鼠模型中，2型高CAR T细胞产品表现出更优的扩增和抗肿瘤活性，特别是在白血病再次挑战后。通过在制造过程中加入IL-4或在输注前用IL-4对制造的CAR T产品进行预处理，可以增强2型低CAR T细胞的抗肿瘤效能。我们的研究结果提供了对持久性CAR T疗法反应介导因素的见解，并提出了通过增强CAR T细胞的2型功能性来维持长期缓解的潜在治疗策略。