Xie, Linzhi

Abstract Background Despite CD19-directed chimeric antigen receptor T (CAR-T) therapy achieving remarkable remission rates in relapsed/refractory B-cell acute lymphoblastic leukemia (R/R B-ALL), long-term survival remains constrained by T-cell exhaustion and immunosuppressive microenvironments. Dasatinib, a tyrosine kinase inhibitor (TKI), has been shown to alleviate T cell exhaustion and enhance CAR-T cell persistence, demonstrating therapeutic synergy in newly diagnosed ALL. However, it may also suppress CAR-T cytotoxicity and is ineffective against BCR-ABLT315I mutations. Third-generation TKIs, including ponatinib and olverembatinib, effectively overcome T315I-mediated resistance, yet their impact on CAR-T cell function and immune modulation remains insufficiently defined. Methods and Results: We first established in vitro co-culture models of CD19 CAR-T cells with the B-ALL cell line NALM6 to evaluate the effects of dasatinib, ponatinib and olverembatinib on resting and tumor antigen-activated CAR-T cells. At clinically relevant concentrations, none of the TKIs affected resting CAR-T viability. In contrast, upon activation, all three TKIs significantly inhibited CAR-T activation, cytotoxicity, and cytokine secretion (IL-2, TNF-α, IFN-γ), while reducing activation-induced CAR-T cell apoptosis. TKIs treatment also downregulated exhaustion markers (eg. PD-1, TIM3, LAG3) and promoted differentiation toward naïve (TN) and central memory (TCM) subsets, while reducing terminal effector T cells. After the drug elution, CAR-T cells regained their cytolytic function in response to tumor targets. Notably, ponatinib-treated CAR-T cells exhibited higher levels of IFN-γ, TNF-α and IL-2 post-washout compared to other groups. Importantly, the TN/TCM phenotype and low exhaustion marker expression were preserved after washout in all TKI-treated groups. Transcriptomic profiling of CAR-T cells in vitro revealed that all three TKIs downregulated key exhaustion-associated genes, including PDCD1, HAVCR2, CTLA4 and NR4A1, along with upregulation of stemness- and memory-associated genes (eg. CCR7, TCF7, LEF1, IL7R). Gene set enrichment analysis showed inhibition of T-cell activation, apoptosis, glycolysis, and TGF-β signaling by all TKIs. Remarkably, ponatinib uniquely activated the IFN-γ pathway, suggesting superior immunostimulatory effects. Mechanistically, all three TKIs suppressed the phosphorylation of AKT, p38 MAPK, and NF-κB p65, indicating shared inhibition of downstream TCR signaling. Based on these findings, we evaluated ponatinib in a clinical setting. A prospective study (No. ChiCTR2000036350) enrolled three R/R B-ALL patients with the BCR-ABLT315I mutation. All the patients received CD19 CAR-T cell therapy followed by ponatinib maintenance, initiated two months post-infusion. All three patients remained progression-free during ponatinib maintenance. Notably, the DNA copies of CAR-T cells remained detectable at months 5 and 9 after ponatinib treatment in two patients, respectively. To further explore the in vivo effects of ponatinib on T cells and other immune cells,peripheral blood mononuclear cells were collected from these patients before and one month after ponatinib initiation for single-cell RNA sequencing. Ponatinib exposure led to an increased proportion of CD8+T cells and a decreased abundance of myeloid cells subsets. Within T cells, effector cells expanded while Tregs and exhausted T cells decreased. Differential gene analysis showed suppression of activation, adhesion, apoptosis, and PD-1/PD-L1 signaling, aligning with in vitro results. Functional scoring revealed enhanced cytotoxicity, IFN-γ responses, and reduced glycolysis, exhaustion, TGF-β, and Treg signatures. Furthermore, analysis of NK cell subsets showed enhanced cytolytic scores and enrichment of proliferation and immune activation pathways, suggesting that ponatinib preserves innate immune responses in vivo. Conclusions: This study provides preclinical and preliminary clinical evidence that third-generation TKIs, particularly ponatinib, can effectively alleviate CAR-T cell exhaustion, promote memory phenotypes, and remodel the immune microenvironment. Compared to dasatinib and olverembatinib, ponatinib uniquely enhances effector cytokine production and activates the IFN-γ pathway. These findings support ponatinib as a promising combinatorial agent with CAR-T therapy, offering a rational strategy for improving outcomes in patients with T315I-mutated R/R B-ALL.

Multiple myeloma (MM), an incurable hematologic malignancy, presents significant challenges in managing its recurrence. The bone marrow tumor microenvironment (BM-TME) is critical to MM progression. However, classical immune checkpoint blockade (ICB) therapies, like anti-PD1, have shown limited efficacy in MM. Therefore, elucidating the compositional features and regulatory mechanisms of the TIME in MM is crucial for developing novel immunotherapeutic targets. Tissue-resident memory CD8+ T cells (CD8+ TRMs) reside indefinitely at multiple anatomical locations like the skin, intestine, and bone marrow, functioning as frontline responders against reencountered pathogens and tumors. Whether CD8+ TRMs within BM-TME are involved in the MM cell immune escape and pathogenesis has not been systematically elucidated. Firstly, we leverage single-cell RNA sequencing (scRNA-seq) to dissect the BM CD8+ T cells across patients at different stages of MM, and identify that CD69+CD8+ T subsets were BM residents, and the proportion of BM CD8+ TRMs between health donors and MM patients was comparable. Moreover, our findings indicated that BM CD8+ TRMs exhibit exhausted features and enrichment of NK genes with MM progresses. Importantly, we observed a considerable elevation of the NK gene KLRB1 and its encoded protein CD161 in BM CD8+ TRMs in MM patients. Immunofluorescence labeling of BM biopsy samples from MM patients confirmed the infiltration of the BM-TME with CD3+CD8+CD69+CD161+ cells. Then, we found that KLRB1 expression in BM CD8+ TRMs was higher than that of other classical inhibitory receptor genes (e.g., PDCD1, CTLA4, LAG3), and CLEC2D (encodes the ligand of CD161) was also markedly expressed in patients' MM cells, exhibiting considerably higher than classical immunosuppressive receptor ligand genes (e.g., PDL1, CD80, CD86). Moreover, patients with higher CLEC2D expression had unfavorable overall survival. We further found that the CD161 expression was higher in CD69+CD8+ TRMs compared to circulating CD69-CD8+ T cells, and the percentage of BM CD161+CD8+ TRMs in MM patients was significantly higher than in healthy donors, while there was no difference for PD-1, LAG3, and TIM3 expression. Notably, only a small fraction of BM CD8+ TRMs have mucosal-associated invariant T cell phenotypes (identified by CD161+TCR-Vα7.2+). Additionally, the CLEC2D expression of BM cells was analyzed, and the highest level of CLEC2D expression was observed in B cells from MM patients, followed by plasma cells. Importantly, CLEC2D expression in MM patients was significantly higher than in plasma cells from healthy donors. Next, to investigate whether the blockade of CD161 could restore the function of CD8+ TRMs, the primary BM cells from MM patients were isolated and stimulated ex vivo. Compared to the anti-PD-1 and isotype group, CD161 blocking presents enhanced CD8+ TRMs proliferation and cytokine secretion levels (TNF-α, IFN-γ, IL2), increasing MM cells apoptosis. Chimeric antigen receptor T (CAR-T) cell therapy has achieved impressive success in treating relapsed/refractory MM. How to prevent CAR-T cell exhaustion and enhance function remains a significant challenge. Therefore, we next set out to investigate the impact of CD161 on CAR-T cells. Our results demonstrated that CD161 was highly expressed in early peripheral blood (PB) CAR-T cells after infusion in MM patients but decreased with time. Moreover, the CD161 expression of CAR-T cells was considerably higher than endogenous T cells. Notably, BM-derived CAR-T cells have higher CD161 expression than PB counterparts for the same patient, suggesting CD161 may have BM-specific expression enrichment. After co-culturing MM and CAR-T cells in vitro for 24 hours, we found that blocking CD161 led to an augmented proportion of CAR-T cells, increased IFN-γ secretion, and a notable elevation in tumor cell apoptosis compared to the anti-PD-1 and isotype groups. Taken together, we demonstrated that CD8+ TRMs constitute a vital anti-tumor cell subset in the MM BM-TME, which exhibits a high expression of the inhibitory CD161 receptor, binding to the CLEC2D expressed by MM cells, thereby mediating the dysfunction of CD8+ TRMs. Blocking the CD161-CLEC2D pathway is expected to become a novel target for MM immunotherapy. The combination of CD161 inhibitors and CAR-T cell therapy can potentially enhance the anti-myeloma function of CAR-T cells.