CD22-Directed CAR T Cell Single Cell Multiomic Features Associated with Immune Effector Cell-Associated Hemophagocytic Lymphohistiocytosis-like Syndrome (IEC-HS)

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.911-911
• Main Authors: Kramer, Anne Marijn, Murty, Tara, Chen, Yiyun, Srinagesh, Hrishikesh, Hamilton, Mark P., Mo, Kelvin C., Prabhu, Snehit, Desai, Moksha, Kuo, Adam, Ehlinger, Zachary, Reynolds, Warren D., Baird, John H., Su, Yi-Jiun, Agarwal, Neha, Sahaf, Bita, Muffly, Lori, Mackall, Crystal L., Miklos, David B., Frank, Matthew J., Good, Zinaida
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-198688

Introduction In a Phase 1 trial we studied CD22-directed CAR T cell therapy (CAR22) for the treatment of patients with relapsed/refractory large B cell lymphoma (LBCL) who had progressed after CD19-directed CAR T cell therapy (CAR19). In this study of 38 patients, CAR22 demonstrated an overall objective response rate (ORR) of 68% and a complete response (CR) rate of 53% (Frank MJ, et al., Lancet 2024). Despite overall favorable toxicity, high CAR22 expansion was linked to the development IEC-HS (n=5) versus no IEC-HS (n=33) (median 2378 vs. 189 CAR22-positive cells/μL; p=0.0016). IEC-HS is associated with delayed recovery, a severe immunocompromised state, and increased risk of non-relapse morbidity and mortality. CAR22-associated IEC-HS typically occurs 1-2 weeks after cytokine release syndrome (CRS) resolves, suggesting it has unique pathophysiology. Here, we report on multiomic single-cell analyses identifying features in both CAR22 products and expanding in vivo CAR22 cells associated with IEC-HS. Methods Single-cell RNA transcriptome (scRNA-seq) and αßTCR sequence were assessed via single cell sequencing on the 10x Genomics platform. We tracked individual T cell clonotypes from pre-manufacture apheresis material, final CAR22 products, at day 14 (peak expansion), and at day 28 post-infusion. We also performed bulk assay for transposase-accessible chromatin using sequencing (ATAC-seq) analyses on CAR22 products. Results Our computational pipeline was applied to a cohort of 19 patients, representative of the study population in terms of age, sex, CAR22 cell dose, adverse events, and clinical outcomes. A total of 70 samples, including 781,747 cells and 280,449 unique TCR clonotypes, were analyzed by scRNA-seq. Pairwise differential accessibility analyses of bulk ATAC-seq of CAR+ cells from products associated with the development of IEC-HS (n=4) versus not (n=15), identified enrichment of open chromatin regions in genes associated with NF-κB signaling (RELA, NFKB1, RELB); NFAT family members crucial for T cell activation, differentiation, and cytokine production (NFATC1, NFATC2, NFATC3); and the RFX family involved in regulating MHC class II expression (RFX3, RFX4, RFX8). Covarying neighborhood analysis (CNA) identified a region of clonally expanded CD8 T cells from product to peak expansion, 14 days after infusion, associated with IEC-HS. Differential gene expression analyses of these expanded cells revealed significant upregulation of interferon-stimula