Bone marrow immune cell state analysis and selective APC alterations in prolonged cytopenia following CAR T-cell therapy.

Abstract

e19018 Background: Prolonged cytopenia (PSC) following chimeric antigen receptor (CAR) T-cell therapy is common and associated with infectious morbidity. Early post–CAR T infections are predominantly bacterial, with later viral complications and less frequent invasive fungal infections. We evaluated whether PSC is associated with transcriptional impairment of innate antimicrobial programs or with selective differences in immune cell states within the bone marrow. Methods: We analyzed publicly available bone marrow scRNA-seq data from 22 CAR T recipients (Strati et al., GSE216005), sampled beyond day 30 post-infusion and classified as PSC or non-PSC per original clinical annotation. Antigen-presenting cells (APCs; monocytes and dendritic cells) and myeloid populations were evaluated using predefined transcriptional modules capturing HLA class II antigen presentation, interferon-associated HSPC injury, innate bacterial and antifungal sensing, neutrophil antimicrobial effector function, and neutrophil immaturity. To avoid cell-count–driven inference, primary analyses were performed at the patient level using median module scores and per-patient fractions of transcriptionally defined cell states, with Wilcoxon rank-sum testing. Results: Patient-level median immune signatures showed substantial overlap between PSC and non-PSC patients across interferon-associated HSPC injury programs, APC interferon signaling, neutrophil antimicrobial effectors, innate bacterial sensing, antifungal pathways, and neutrophil immaturity states. In contrast, cell-state–aware analyses revealed a significant difference in APC composition: non-PSC patients exhibited a higher fraction of APCs in an HLA class II–low transcriptional state, whereas PSC patients demonstrated relative depletion of this state (Wilcoxon p = 0.007). Neutrophil antimicrobial, bacterial, and antifungal transcriptional programs were preserved across groups. Conclusions: In this CAR T bone marrow scRNA-seq cohort, PSC was not associated with global transcriptional impairment of innate antimicrobial programs but was associated with a selective shift in APC state composition. These findings suggest that PSC-associated infection risk may be driven more by the severity and duration of cytopenia and altered immune regulation than by intrinsic dysfunction of remaining innate immune cells. Despite clear mechanistic immune differences at the cell-state level, patient-level comparisons of several immune programs were underpowered, underscoring the need for larger, multicenter immune-phenotyping cohorts to inform infection-risk stratification and supportive care strategies following CAR T therapy.