Single-cell RNA and V(D)J sequencing of ide-cel and cilta-cel infusion product and PBMCs

Chimeric antigen receptor autologous T-cells (CAR-T) targeting B-cell maturation antigen (BCMA) have revolutionized the treatment of relapsed and refractory multiple myeloma (RRMM). Idecabtagene vicleucel (ide-cel) and ciltacabtagene autoleucel (cilta-cel) have demonstrated superior outcomes over standard of care. We sought to examine the biological differences between agents by analyzing infusion products (IP) and CAR-enriched peripheral blood mononuclear cells (PBMCs) using single-cell RNA sequencing (scRNAseq). Libraries (scRNAseq/VDJ) were generated from 52 samples; 40 unique ide-cel IP and CAR-enriched PBMCs from 6 matched ide-cel and 6 unique cilta-cel patients at expansion. Reads were aligned to a modified GRCh38 reference to identify ide-cel/cilta-cel constructs, CD4 and CD8 cells were analyzed separately. Differential gene expression and pathway analysis were conducted (Seurat v5), generating sample-level pathway signatures through single-sample gene set enrichment analysis (ssgsea). Following quality control, 247,500 cells were analyzed (117,530 CD4 cells/80,939 CD8 cells). Ide-cel IP from patients with durable responses (DR) had higher ide-cel construct expression, enhanced NFKB signaling and anti-apoptotic gene signatures, which were linked to improved progression free survival. CAR+ ide-cel PBMCs in DRs exhibited upregulated ribosomal genes and higher expression of CD27, KLF2, TCF7, and the ide-cel construct. Relative to ide-cel, cilta-cel CAR+ cells showed higher expression of CD27, GZMK, TCF7, and a 4-fold increase in CAR expression. Cilta-cel's TCR repertoire was less clonal and more diverse. This study elucidates the distinct characteristics of ide-cel and cilta-cel, offering insights into their differing clinical efficacy in the treatment of patients with RRMM.