Abstract Background Pulmonary arterial hypertension (PAH) is a complex and highly morbid vascular disease with a strong genetic component. While rare coding mutations such as BMPR2 contribute to familial PAH, most cases are sporadic and genetically heterogeneous. A recent genome-wide association study (GWAS) identified chromosome 8q11.23 as the most significant susceptibility locus (OR = 1.8). However, because GWAS primarily captures statistical associations, the biological mechanisms by which this non-coding locus contributes to PAH pathogenesis remain unknown. Methods We established an integrative post-GWAS functional genomics pipeline to identify pathogenic effector genes and regulatory mechanisms at the 8q11.23 locus. This approach combined experimental SNP-nuclear protein binding assays, high-resolution Micro-C chromatin conformation mapping, computational JASPAR transcription-factor motif prediction, AlphaFold3 structural modeling of SNP-DNA and protein-DNA interactions, and functional validation in human pulmonary artery endothelial cells (PAECs). Results Haplotype SNPs in the linkage disequilibrium of the 8q11.23 locus were analyzed. Experimental screening prioritized rs4738801 as a functional SNP (fSNP), which exhibited allele-specific nuclear protein binding and robust long-range chromatin interactions, with the strongest loop anchored at the SOX17 promoter demonstrated by micro-C analysis. JASPAR motif prediction identified FUBP1 as the top-ranked transcription factor predicted to bind the fSNP. DNA pulldown mass spectrometry and Western blotting confirmed FUBP1’s allele-specific binding. AlphaFold3 modeling demonstrated that the KH2 domain of FUBP1 preferentially binds the G allele by recognizing a TGT core motif at rs4738801, whereas the C allele induces a conformational shift that increases the KH2-DNA distance from 4.3 Å to 8.8 Å, consistent with reduced binding affinity. AlphaFold3 spatial modeling further revealed close contacts between FUBP1 KH2 domain and DNA sequences 60 bp upstream of the SOX17 transcription start site, supporting an FUBP1-mediated chromatin loop bridging rs4738801 to the SOX17 promoter. Functional studies in PAECs and rodent PAH models demonstrated that FUBP1 regulates SOX17 expression and endothelial function and modulates experimental PAH pathogenesis. Conclusion Our integrative functional genomics analysis identifies FUBP1 as a key pathogenic mediator linking the non-coding fSNP rs4738801 to SOX17 regulation through a long-range chromatin interaction. These findings provide a mechanistic explanation for the GWAS association at 8q11.23 and reveal a novel regulatory pathway contributing to PAH susceptibility. This abstract is funded by: NIH
W Sun (Fri,) studied this question.