Circadian Clock-Gene Structure Couples with PD-L1 Across Six Cancer Types and Defines Survival-Associated Subtypes in Melanoma

Background. Circadian disruption is classified by IARC as a probable human carcinogen (Group 2A). The relationship between clock-gene expression structure and immune checkpoint engagement across cancer types is poorly characterized. We hypothesized that circadian program state and PD-L1 engagement are coupled, reflecting distinct modes of immune evasion. Methods. We analyzed bulk RNA-seq and clinical data from six TCGA cohorts ( tumors; SKCM, LUAD, BRCA, COAD, HNSC, LUSC). Per-sample circadian coefficient of variation (CV) across six clock genes (ARNTL, CLOCK, PER1, PER2, CRY1, CRY2) served as a transcriptional clock-structure proxy. Tumors were classified as Active Masking (high PD-L1 + high BMAL1 + low PER1) or Temporal Decoherence (low PD-L1 + low B2M). Survival used Kaplan-Meier, log-rank, and RMST on a deduplicated cohort (). Sensitivity analyses included threshold sweeps, immune-fraction residualization, purity stratification, and an independent observability index. Results. Circadian CV was negatively correlated with PD-L1 in all six cohorts ( to, all FDR ). Tumors showed lower CV than matched normals in 4/5 types (“locked, not broken”). Active Masking showed better survival than Decoherence in melanoma (log-rank, BH ; RMST months at 10 years, 95% CI ). The signal was robust to threshold choice (9/11 percentiles significant), survived immune residualization (4/4 cohorts), and was captured by an independent observability index (). A continuous PD-L1 clock interaction term was FDR-significant in melanoma (Cox HR, ), indicating non-additive coupling. The negative direction was consistent in 3/3 external immunotherapy cohorts (GSE91061 melanoma, ; GSE78220 melanoma ; GSE115821 melanoma ; individually underpowered, directionally consistent across 9/9 datasets). Conclusions. Circadian clock-gene structure and checkpoint engagement are coupled across six cancer types. Active Masking and Decoherence define two immune-evasion endpoints with a melanoma-dominant survival association and a significant checkpoint-clock interaction effect that motivates prospective testing as a complement to existing immunotherapy biomarkers.