Tumor-derived microRNA-125a impairs CART cell function and predicts treatment failure in B cell malignancies

Abstract Background Chimeric antigen receptor T cell (CART) therapy has revolutionized treatment for hematologic malignancies. However, durable remission following anti-CD19 CART therapy (CART19) remains limited to 40–50% of patients, often due to tumor relapse and CART dysfunction (PMID:31501612). We previously demonstrated that tumor-derived extracellular vesicles (EVs) from patients with chronic lymphocytic leukemia (CLL) can directly impair CART function (PMID:33388419). In this study, we aimed to identify tumor-derived EV microRNA (miRNA) cargo associated with clinical CART failure in B cell malignancies and define how they mechanistically drive CART cell dysfunction. Methods To achieve these aims, we profiled tumor-derived EV miRNA cargo using small RNA sequencing (RNAseq) in two independent patient cohorts. Cohort 1 compared plasma-derived EVs from untreated CLL patients to those from healthy donor EVs to identify miRNAs enriched in CLL (n=23). Cohort 2 included patients with diffuse large B cell lymphoma (DLBCL) treated with axicabtagene ciloleucel (CART19, n=12). Here, plasma EV miRNAs were analyzed at baseline (pre-CART treatment) and 1-month post-CART treatment and compared between CART responders (complete remission at 6 months) and nonresponders (no response at 1 month). Enriched miRNAs from both cohorts were identified following miRNA count normalization and differential expression analysis using adjusted p values of ≤0.05. Functional studies were conducted by transfecting CART19-28ζ cells with synthetic miRNA mimics or scrambled controls. CART cells were also generated with stable overexpression of miRNA via lentiviral shRNA delivery. CART function was assessed via in vitro killing, proliferation, apoptosis assays, RNAseq, and in vivo tumor xenograft models. Results In Cohort 1, we identified several miRNAs including miR-125a to be significantly enriched in CLL-derived EVs relative to healthy controls. Similarly, in Cohort 2, miRNA-125a was also identified among the miRNAs enriched in nonresponders vs. responders to CART treatment; Notably, miR-125a was significantly enriched in nonresponders at baseline (pre-CART treatment) and 1-month post-CART treatment (p=0.0177, p=0.0196). To define the functional effects of miR-125a, we delivered synthetic mimics or stable shRNA constructs encoding miR-125a into CART cells. Delivery of miR-125a was confirmed by RT-qPCR (p<0.0001 for mimic vs. scramble, p=0.0069 for shRNA vs. scramble). Here, miR-125a delivery and overexpression impaired CART cytotoxicity/killing of target tumor cells (~25% reduction, p= 0.0039), decreased antigen-specific proliferation (~47% reduction, p=0.0002), and increased apoptosis following antigen stimulation (1.8-fold increase, p=0.0002) as compared to scramble controls in vitro. We next studied how miR-125a impacts CART functions in vivo. Here, tumor-bearing mice treated with miR-125a–overexpressing CART cells (CART sh125a) exhibited accelerated tumor progression (4.1-fold increase, p=0.0019) and significantly reduced survival as compared to mice treated with scramble control CART treatment (CART shScr) (20% vs 80% survival at day 35, p=0.0064), underscoring the dramatic detrimental impact of miR-125a on therapeutic efficacy. To uncover changes in CART gene expression induced by miR-125a delivery, RNAseq was also performed across stimulated CART sh125a vs. CART shScr cells. CART sh125a cells demonstrated broad transcriptional changes, with gene set enrichment of E2F targets, G2/M checkpoint, and apoptosis pathways (FDR p<0.0001, p<0.0001, and p=0.006) further validating the role of miR-125a in disrupting CART cell cycle control, proliferation, and survival. Conclusion In summary, our study identifies miR-125a as a tumor-derived EV cargo that drives CART dysfunction in two separate B cell malignancies (CLL and DLBCL). miR-125a was enriched in both CLL EVs and nonresponders to CART19 therapy at baseline prior and post CART treatment. Functional studies demonstrate that miR-125a delivery and overexpression directly impair CART cytotoxicity and proliferation, increase CART apoptosis, reduce therapeutic efficacy in tumor xenograft models, and disrupt key pathways related to CART cell cycle regulation and survival. These findings position miR-125a as both a key mechanistic driver of CART failure and a potential predictive biomarker for treatment response, while highlighting it as a possible therapeutic target to improve CART outcomes in the clinic.