Fig. 4

Mechanisms of resistance and toxicities. (A) Genes encoding immune checkpoints, such as lymphocyte activation 3 (LAG3) and T cell immunoglobulin and ITIM domain (TIGIT), as well as exhaustion-associated transcription factors, including basic leucine zipper ATF-like transcription factor (BATF) and inhibitor of DNA binding 2 (ID2), were highly expressed in infusion products. Among them, TIGIT has been used as a potential target with suggested beneficial efficacy in both in vitro and in vivo experiments. In addition, the number of CAR Treg cells also increased significantly in infusion products. (B) The T_H2 pathway was absent, and early memory-like T cell subsets (T_SCM and T_CM) were decreased in infusion products. (C) scRNAseq profiling revealed that CD19-negative leukemic cells were present before CAR T-cell therapy. CD34⁺CD22⁺CD19⁻ progenitor cells are B-ALL cells with negative CD19 expression that carry oncogenic lesions and lead to leukemia. In addition, regulatory programs of B-cell activation and germinal center reaction occurring in B-ALL cells can reduce CD19 expression. (D) IL-6, recognized as pivotal for CRS pathogenesis, is specifically and highly expressed by monocytes. (E) Targeting CD19⁺ mural cells, critical for BBB integrity, may lead to ICANS of CAR T-cell therapy. Reactivation of HHV-6⁺ CAR T-cells in the infusion product may cause ICANS. IACs, more IL-17 A polyfunctional T cells, and fewer CD4⁺CD57^–Helios⁺ CAR T-cells in the infusion product are associated with high-grade ICANS. (F) Integrative analyses of single-cell sequencing datasets promote a deeper understanding of CAR antigen expression and identification of safer and more effective targets