Integrated transcriptomic and cistromic analyses reveal associations between mechanotransduction-associated transcription and clock-gene expression in pulmonary arterial hypertension and TEAD-sensitive CRY1/CLOCK responses

Pulmonary arterial hypertension (PAH) involves vascular remodeling in an abnormal mechanical environment, but the relationship between mechanotransduction-associated transcription and clock-gene expression remains unclear. We integrated three PAH lung transcriptomic cohorts, donor-level endothelial analyses, vascular cell-state and spatial transcriptomic data, endothelial perturbation transcriptomics, and chromatin-binding data, with validation in human pulmonary artery endothelial cells (HPAECs). In 83 PAH lung samples, restricted maximum likelihood (REML) random-effects pooling showed a positive association between mechanotransduction and clock-related scores (Spearman ρ = 0.393, 95% confidence interval 0.185–0.567; Hartung–Knapp sensitivity P = 0.0279), which weakened when restricted to genes detectable across cohorts. Endothelial pseudobulk data from GSE169471 supported a positive donor-level association ( n = 8, ρ = 0.738); the six-donor GSE210248 analysis used different score pairs. Associations varied in direction across vascular cell states, while molecular programs in 217 spatial regions differed by donor and lesion context. In HUVECs, activated YAP/TAZ increased CRY1 and CLOCK expression, with partial attenuation by TEAD-binding-deficient mutants. ChIP-seq identified candidate binding sites near both genes. In HPAECs, a stiffer substrate was associated with higher nuclear YAP/TAZ and CRY1/CLOCK protein levels; construct comparisons and independent TEAD1 knockdown supported TEAD-sensitive expression induction. Beyond prior CRY1 findings, this study provides evidence for CLOCK responses in pulmonary artery endothelium and cell-state heterogeneity. The findings support a candidate regulatory link, not altered circadian function or a causal mechanism of PAH vascular remodeling.