Abstract Body (Do not enter title and authors here): Introduction: Hypoxia and ischemia drive pathogenic vascular remodeling and endothelial cell (EC) dysfunction, leading to the progression of vascular diseases, such as coronary artery disease (CAD). Emerging evidence highlights the importance of long-range genomic interactions between non-coding intergenic single nucleotide polymorphisms (SNPs) and gene promoters in EC reprogramming. However, their functional relevance to CAD remains unclear.

Hypothesis: Hypoxia triggers chromatin remodeling in ECs, altering genomic interactions and gene expression and thereby promoting EC dysfunction in CAD.

Methods and Results: We employed Micro-C analysis of cultured human ECs to assess chromatin architecture changes under hypoxic compared with normoxic conditions and integrated these results with RNA sequencing data to correlate genomic interactions with gene expression changes. Among 162477 interactions identified, the interaction between SNP rs115561468 and promoter region of Metastasis Lung Cancer Associated Transcript 1 (MALAT1) was significantly enriched in hypoxia (p=8.38x10^-25). A prior genome-wide association study (GWAS, N=2466) linked the T allele of this SNP to higher plasma trimethyllysine (TML) levels (p=3x10^-32), a metabolite linked to higher atherosclerosis risk. Our analysis of the All of Us database identified this allele as a risk factor for developing CAD (p=0.00356). Ex-vivo proteomic analysis and in-vitro chromatin immunoprecipitation followed by quantitative PCR revealed allele-specific protein binding patterns at the SNP, suggesting the presence of potential allele-specific transcriptional regulators of MALAT1, including SFPQ and HNRNPA3. Correspondingly, SFPQ and HNRNPA3 knockdown in cultured ECs increased MALAT1 expression in normoxic and hypoxic conditions. In CRISPR-edited isogenic, induced pluripotent stem cell-derived endothelial cells, MALAT1 was found upregulated under hypoxia in all genotypes, but the magnitude of induction was significantly greater in cells carrying the T allele. Functionally, exogenous TML drove endothelial pathophenotypes, including increased apoptosis and decreased proliferation.

Conclusion: Our work reveals a hypoxia-sensitive, SNP-driven regulatory mechanism linking MALAT1 activity, TML metabolism to endothelial dysfunction, carrying broad implications for understanding the genetic predisposition to CAD pathogenesis, providing new insights into how genetic and metabolic factors converge to promote the disease.