High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

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  • Author: Åkerborg, Örjan

    Royal Institute of Technology, Sweden

  • Author: Spalinskas, Rapolas

    Royal Institute of Technology, Sweden

  • Author: Pradhananga, Sailendra

    Royal Institute of Technology, Sweden

  • Author: Anil, Anandashankar

    Royal Institute of Technology, Sweden

  • Author: Höjer, Pontus

    Royal Institute of Technology, Sweden

  • Author: Poujade, Flore Anne

    Karolinska Institutet, Sweden

  • Author: Folkersen, Lasse

    Department of Health Technology, Technical University of Denmark

  • Author: Eriksson, Per

    Karolinska Institutet, Sweden

  • Author: Sahlén, Pelin

    Karolinska Institutet, Sweden

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BACKGROUND: Genetic variant landscape of coronary artery disease is dominated by noncoding variants among which many occur within putative enhancers regulating the expression levels of relevant genes. It is crucial to assign the genetic variants to their correct genes both to gain insights into perturbed functions and better assess the risk of disease. 

METHODS: In this study, we generated high-resolution genomic interaction maps (≈750 bases) in aortic endothelial, smooth muscle cells and THP-1 (human leukemia monocytic cell line) macrophages stimulated with lipopolysaccharide using Hi-C coupled with sequence capture targeting 25 429 features, including variants associated with coronary artery disease. We also sequenced their transcriptomes and mapped putative enhancers using chromatin immunoprecipitation with an antibody against H3K27Ac. 

RESULTS: The regions interacting with promoters showed strong enrichment for enhancer elements and validated several previously known interactions and enhancers. We detected interactions for 727 risk variants obtained by genome-wide association studies and identified novel, as well as established genes and functions associated with cardiovascular diseases. We were able to assign potential target genes for additional 398 genome-wide association studies variants using haplotype information, thereby identifying additional relevant genes and functions. Importantly, we discovered that a subset of risk variants interact with multiple promoters and their expression levels were strongly correlated. 

CONCLUSIONS: In summary, we present a catalog of candidate genes regulated by coronary artery disease-related variants and think that it will be an invaluable resource to further the investigation of cardiovascular pathologies and disease.

Original languageEnglish
Article numbere002353
JournalCirculation: Genomic and precision medicine
Volume12
Issue number3
Pages (from-to)101-112
Number of pages12
ISSN2574-8300
DOIs
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • Coronary artery disease, Gene, Genomics, Haplotype, Inflammation

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