TY - JOUR
T1 - Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits
AU - Stolze, Lindsey K.
AU - Conklin, Austin C.
AU - Whalen, Michael B.
AU - López Rodríguez, Maykel
AU - Õunap, Kadri
AU - Selvarajan, Ilakya
AU - Toropainen, Anu
AU - Örd, Tiit
AU - Li, Jin
AU - Eshghi, Anna
AU - Solomon, Alice E.
AU - Fang, Yun
AU - Kaikkonen, Minna U.
AU - Romanoski, Casey E.
N1 - Funding Information:
This research was supported by National Institutes of Health ( NIH ) grants to C.E.R. ( R00HL123485 and R01HL147187 ), as well as by the following training fellowships: T32ES007091-36A1 (L.K.S and A.C.C.), American Heart Association 20PRE35200195 (L.K.S.), T32ES007091-36A1 (A.E.S.), and the Achievement Rewards for College Scientists ( ARCS ) Foundation in Phoenix (A.C.C.). Additional support was provided to Y.F. by R01HL138223 and R01HL136765 . M.U.K. and group members AT, KÕ, TÖ, and M.L.R. were supported by grants from the Academy of Finland ( 287478 , 319324 , and 314554 to M.U.K.), the European Research Council ( ERC ) research and innovation program ( 802825 ), the Finnish Foundation for Cardiovascular Research , the Sigrid Jusélius Foundation , and the Jane and Aatos Erkko Foundation . M.L.R. was also supported by personal grants from the Finnish Foundation for Cardiovascular Research , the Finnish Cultural Foundation , and the Finnish Diabetes Research Foundation . I.S. and A.T. were supported by the University of Eastern Finland Doctoral Program in Molecular Medicine .
Funding Information:
This research was supported by National Institutes of Health (NIH) grants to C.E.R. (R00HL123485 and R01HL147187), as well as by the following training fellowships: T32ES007091-36A1 (L.K.S and A.C.C.), American Heart Association 20PRE35200195 (L.K.S.), T32ES007091-36A1 (A.E.S.), and the Achievement Rewards for College Scientists (ARCS) Foundation in Phoenix (A.C.C.). Additional support was provided to Y.F. by R01HL138223 and R01HL136765. M.U.K. and group members AT, K?, T?, and M.L.R. were supported by grants from the Academy of Finland (287478, 319324, and 314554 to M.U.K.), the European Research Council (ERC) research and innovation program (802825), the Finnish Foundation for Cardiovascular Research, the Sigrid Jus?lius Foundation, and the Jane and Aatos Erkko Foundation. M.L.R. was also supported by personal grants from the Finnish Foundation for Cardiovascular Research, the Finnish Cultural Foundation, and the Finnish Diabetes Research Foundation. I.S. and A.T. were supported by the University of Eastern Finland Doctoral Program in Molecular Medicine.
Publisher Copyright:
© 2020 American Society of Human Genetics
PY - 2020/6/4
Y1 - 2020/6/4
N2 - The identification of causal variants and mechanisms underlying complex disease traits in humans is important for the progress of human disease genetics; this requires finding strategies to detect functional regulatory variants in disease-relevant cell types. To achieve this, we collected genetic and transcriptomic data from the aortic endothelial cells of up to 157 donors and four epigenomic phenotypes in up to 44 human donors representing individuals of both sexes and three major ancestries. We found thousands of expression quantitative trait loci (eQTLs) at all ranges of effect sizes not detected by the Gene-Tissue Expression Project (GTEx) in human tissues, showing that novel biological relationships unique to endothelial cells (ECs) are enriched in this dataset. Epigenetic profiling enabled discovery of over 3,000 regulatory elements whose activity is modulated by genetic variants that most frequently mutated ETS, AP-1, and NF-kB binding motifs, implicating these motifs as governors of EC regulation. Using CRISPR interference (CRISPRi), allele-specific reporter assays, and chromatin conformation capture, we validated candidate enhancer variants located up to 750 kb from their target genes, VEGFC, FGD6, and KIF26B. Regulatory SNPs identified were enriched in coronary artery disease (CAD) loci, and this result has specific implications for PECAM-1, FES, and AXL. We also found significant roles for EC regulatory variants in modifying the traits pulse pressure, blood protein levels, and monocyte count. Lastly, we present two unlinked SNPs in the promoter of MFAP2 that exhibit pleiotropic effects on human disease traits. Together, this supports the possibility that genetic predisposition for complex disease is manifested through the endothelium.
AB - The identification of causal variants and mechanisms underlying complex disease traits in humans is important for the progress of human disease genetics; this requires finding strategies to detect functional regulatory variants in disease-relevant cell types. To achieve this, we collected genetic and transcriptomic data from the aortic endothelial cells of up to 157 donors and four epigenomic phenotypes in up to 44 human donors representing individuals of both sexes and three major ancestries. We found thousands of expression quantitative trait loci (eQTLs) at all ranges of effect sizes not detected by the Gene-Tissue Expression Project (GTEx) in human tissues, showing that novel biological relationships unique to endothelial cells (ECs) are enriched in this dataset. Epigenetic profiling enabled discovery of over 3,000 regulatory elements whose activity is modulated by genetic variants that most frequently mutated ETS, AP-1, and NF-kB binding motifs, implicating these motifs as governors of EC regulation. Using CRISPR interference (CRISPRi), allele-specific reporter assays, and chromatin conformation capture, we validated candidate enhancer variants located up to 750 kb from their target genes, VEGFC, FGD6, and KIF26B. Regulatory SNPs identified were enriched in coronary artery disease (CAD) loci, and this result has specific implications for PECAM-1, FES, and AXL. We also found significant roles for EC regulatory variants in modifying the traits pulse pressure, blood protein levels, and monocyte count. Lastly, we present two unlinked SNPs in the promoter of MFAP2 that exhibit pleiotropic effects on human disease traits. Together, this supports the possibility that genetic predisposition for complex disease is manifested through the endothelium.
KW - association mapping
KW - complex disease
KW - endothelial cells
KW - epigenetics
KW - genomics
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U2 - 10.1016/j.ajhg.2020.04.008
DO - 10.1016/j.ajhg.2020.04.008
M3 - Article
C2 - 32442411
AN - SCOPUS:85085611847
VL - 106
SP - 748
EP - 763
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
SN - 0002-9297
IS - 6
ER -