CCTP-Atlas: Compartment-Resolved Ciliary Transcriptional Dysregulation in Tetralogy of Fallot, A Six-Dataset Integrative Meta-Analysis

Abstract

Background. Primary cilia coordinate Hedgehog-dependent outflow tract morphogenesis. Concurrent human genetics implicates ciliary loss-of-function in nonsyndromic tetralogy of Fallot (TOF) risk, yet compartment-resolved ciliary transcriptional programmes in public TOF snRNA-seq remain unmapped at module resolution. Methods. We curated a Cardiac Ciliary Transcriptomic Panel (CCTP; 1,611 genes; four modules) and executed a ten-phase integrative pipeline on six public sc/snRNA-seq resources. Differentially expressed gene tables were harmonised (adjusted p < 0.05; |log2FC| [≥] 0.5 where available), mapped to CCTP modules, and tiered by evidence strength. Patient-level pseudobulk (three TOF versus five donors), permutation-validated Compartment Dysregulation Index (CMDI), Cross-Species Concordance Score (CSCS), STRING protein-protein interaction analysis, and diffusion pseudotime on 17,290 Ho organoid cells were performed. Results. Among 1,263 unique CCTP-associated hits, 396 genes recurred in at least two dataset tables (exploratory tier; Tier A endothelial anchor n = 24 from Zulibiya et al.). Only Zulibiya endothelial M1 structural-assembly CMDI exceeded a module-size-matched permutation null (p = 0.015). Patient-level pseudobulk returned zero false-discovery-rate-significant CCTP genes. CCTP-conditioned overlap with recent ciliary genetics was non-significant (Fisher p {approx} 0.13). Ho organoid pseudotime showed highest M1/M2 activity at day 8, declining toward day 21. Genome-wide CSCS classified 11 genes as fully conserved and 136 as partially conserved among scoreable orthologs. Conclusions. Ciliary transcriptional correlates in TOF are compartment-specific and module-structured, with the strongest inferential signal in TOF endothelium (M1). CCTP-Atlas provides a reproducible, tiered prioritisation resource linking public TOF snRNA-seq, organoid maturation proxies, and partial cross-species patterns. Findings are hypothesis-generating and complement but do not replicate recent ciliary genetics evidence until expanded cohorts and functional validation are performed. Data availability. Processed gene lists, manifests, and scripts. Source datasets: GSE203274, GSE168464, GSE166462, GSE126128; Li et al. (2025) supplementary tables. This is a preprint and has not been peer-reviewed.