Gene-level variability, pathway-level convergence: A systems view of vitamin D signaling

Vitamin D signaling produces context-dependent transcriptional responses, but how gene-level variability relates to recurrent pathway-level programs across perturbational models remains incompletely defined. To systematically characterize these responses, we analyzed publicly available LINCS L1000 perturbational transcriptomic data comprising 258 replicate-supported 24-h signatures across five LINCS cell-line models and seven vitamin D-related compounds. Global transcriptomic analysis indicated that cellular context contributes slightly more to transcriptional variability than compound identity and dose. At the gene level, we defined a direction-specific consensus transcriptional core composed of 42 upregulated and 35 downregulated genes, which was used to derive an operational transcriptional activity metric (core_score). Despite strong context-dependent variability at the gene level, pathway-level analysis revealed recurrent functional themes involving metabolic regulation, stress response, proteostatic control, and proliferative programs. Dose-related analyses showed aggregate dose-ordered core_score trends in several cellular contexts, but these associations should be interpreted as dataset-level patterns rather than compound-specific pharmacodynamic curves. Transcript-level assessment of selected VDR/RXR-axis genes showed small or context-dependent changes in VDR, CYP24A1, CYP27B1, and RXR isoform transcripts, indicating that transcript abundance of these selected components alone does not explain downstream response heterogeneity. Overall, this study provides a reproducible, hypothesis-generating framework for distinguishing shared and context-dependent vitamin D-related transcriptional programs in the analyzed LINCS subset.