Transcriptomic and phenotypic analyses reveal time-qualified patterns featuring Chimeric Antigen Receptor-T cells (CAR-T) dynamics

To investigate the transcriptional and phenotypic basis of this phenomenon, CD7-CAR T cells and empty vector (EV) controls were synchronized by serum shock and profiled by RNA sequencing across a 24-hour time-course (0, 6, 12, 18, 24 h), alongside cosinor analysis of cytotoxicity, cytokine secretion, exhaustion markers, and immunophenotyping.

CD7-CAR T cells showed a more coordinated core clock gene network than EV controls, with hallmark immune/proliferative pathways peaking in a late window (16–20 h) and greater-amplitude oscillations in cytotoxicity and cytokine secretion. Circadian phase inferred in an independent T-ALL cohort (n = 1,334) using CYCLOPS was concordant with the in vitro model, and event-free survival was significantly worse in the fourth phase quartile (p = 0.011).