Cell-cycle phase synchrony (κ) as a quantitative readout of tumor microenvironment immune reprogramming: Integration of R-loop dynamics, iron metabolism, and therapeutic resistance in melanoma

Background: Cell-cycle dysregulation is a hallmark of cancer, yet existing approaches quantify proliferative activity rather than the coordination of cycle progression across cells within a population. Whether tumor cells are more synchronized than surrounding microenvironment cells, and whether such synchrony reflects biology of therapeutic relevance, remains unexplored. Results: We present cellcycleSync, a framework that maps single-cell expression onto continuous phase angles via PCA and estimates population-level synchrony using the von Mises concentration parameter kappa. In two independent melanoma cohorts (GSE72056, n = 19; GSE115978, n = 29), actively cycling tumor cells exhibited significantly higher kappa than all microenvironment cell types (T.CD8, n = 8, p = 0.008, BH-adjusted p = 0.039). Multi-gene-set testing (seven markers, 35/37 consistent) and independent algorithm cross-validation confirmed robustness. Macrophages uniquely exhibited reversed kappa in R-loop/SASP gene sets, consistent with SASP responder status. Iron metabolism inversely correlated with kappa in CD8 T cells (rho = -0.72, p = 0.001). Post-treatment tumors showed elevated kappa, suggesting therapeutic selection for synchronized subclones. Conclusions: Phase synchrony differs systematically between tumor and microenvironment cells. The convergence of kappa, R-loop dynamics, and iron metabolism points to a SASP-driven three-cell positive feedback loop with implications for treatment sequencing and multi-target intervention strategies.