The impact of clonal hematopoiesis on CAR-T cell therapy outcomes: A single-center analysis

Abstract Background: Clonal hematopoiesis (CH), including both clonal hematopoiesis of indeterminate potential (CHIP, VAF ≥2%) and micro-clonal hematopoiesis (micro-CH, VAF 0.5-2%), affects most CAR-T recipients. However, the impact of CH burden on CAR-T efficacy and toxicity remains incompletely understood. Methods: We retrospectively analyzed 65 patients who received CAR-T therapy (axicabtagene ciloleucel n=41, brexucabtagene autoleucel n=15, tisagenlecleucel n=3, others n=6) for relapsed or refractory lymphomas and myelomas at Vanderbilt University Medical Center. Next-generation sequencing was conducted on apheresis samples to identify CH mutations. We assessed complete response (CR) rates, cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), overall survival (OS), and progression-free survival (PFS). Outcomes were stratified by CH burden (no CH, micro-CH only, CHIP) and age (<60 vs ≥60 years). Inflammatory biomarker signatures were assessed using the InflaMix model (Raj et al. Nature Medicine 2025). Results: Among 65 patients (median age 61 years) with a median follow-up of 25.8 months, 58.5% had some form of CH: 24.6% micro-CH only, 20.0% CHIP only, and 13.8% both. The most common mutations in CHIP patients were PPM1D (54.5%), DNMT3A (45.5%), TP53 (27.3%), and ASXL1 (9.1%). Patients with any CH were significantly older (mean age 63.8 vs 54.0 years, p<0.001). A complex relationship emerged between CH burden and outcomes. Day 30 CR rates were: micro-CH 75.0%, no CH 55.6%, and CHIP 59.1%. At 1-year follow-up, OS showed a trend favoring micro-CH patients (81.8%) compared to no CH (69.1%) and CHIP (63.0%), although this did not reach statistical significance (log-rank p=0.07). In patients <60 years, micro-CH showed 100% 1-year OS (n=4) versus 73.7% for no CH and 75.0% for CHIP. In patients ≥60 years, micro-CH maintained superiority with 75.0% 1-year OS versus 62.5% for no CH and 57.1% for CHIP. CRS occurred in 82.5% of patients overall, with similar rates across CH categories (no CH 85.2%, micro-CH only 81.3%, CHIP 81.8%, p=0.93). ICANS rates showed a non-significant trend toward lower incidence in micro-CH patients (43.8% vs 59.3% no CH vs 54.5% CHIP, p=0.58). No grade 4-5 CRS or ICANS events occurred regardless of CH status. Cox proportional hazards models, adjusted for age, gender, and prior lines of therapy, showed no significant association between CH status and survival outcomes (p=0.2 for OS). When combined with InflaMix inflammatory signatures, patients with CHIP and high inflammation had the poorest OS (HR 1.60, 95% CI 0.67-3.84 for CHIP vs no CH), though not statistically significant. Conclusion: This analysis indicates a potential protective role of micro-CH in CAR-T therapy, with these patients achieving the highest CR and 1-year OS rates despite older age. The link between clone size and outcomes suggests different biological effects depending on dosage. A pro-inflammatory, dysregulated immune environment is usually associated with clonal hematopoiesis. However, “inflammation” varies widely, and in our cohort, micro-CH clones may be protective. While the absence of any CH might lack this protective inflammatory signaling, small clones could provide necessary immune priming without the dysfunction seen in larger clones. Our results question the traditional VAF ≥2% threshold for clinical importance and imply that comprehensive CH assessment, including micro-CH detection, could enhance risk stratification for immunotherapy patients. Limitations in statistical analysis due to small sample size highlight the need for larger multicenter studies to understand the mechanisms behind the protective effect of micro-CH.