Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

English version

Autoři: Sylvia T. Nurnberg ^aff001; Marie A. Guerraty ^aff001; Robert C. Wirka ^aff002; H. Shanker Rao ^aff001; Milos Pjanic ^aff002; Scott Norton ^aff003; Felipe Serrano ^aff004; Ljubica Perisic ^aff005; Susannah Elwyn ^aff001; John Pluta ^aff001; Wei Zhao ^aff001; Stephanie Testa ^aff001; YoSon Park ^aff003; Trieu Nguyen ^aff002; Yi-An Ko ^aff003; Ting Wang ^aff002; Ulf Hedin ^aff005; Sanjay Sinha ^aff004; Yoseph Barash ^aff003; Christopher D. Brown ^aff003; Thomas Quertermous ^aff002; Daniel J. Rader ^aff001
Působiště autorů: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America ^aff001; Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America ^aff002; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America ^aff003; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom ^aff004; Department of Molecular Medicine and Surgery, Karolinska Institute, Solna, Sweden ^aff005
Vyšlo v časopise: Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases. PLoS Genet 16(1): e1008538. doi:10.1371/journal.pgen.1008538
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1008538

Souhrn

Genome-wide association studies have identified multiple novel genomic loci associated with vascular diseases. Many of these loci are common non-coding variants that affect the expression of disease-relevant genes within coronary vascular cells. To identify such genes on a genome-wide level, we performed deep transcriptomic analysis of genotyped primary human coronary artery smooth muscle cells (HCASMCs) and coronary endothelial cells (HCAECs) from the same subjects, including splicing Quantitative Trait Loci (sQTL), allele-specific expression (ASE), and colocalization analyses. We identified sQTLs for TARS2, YAP1, CFDP1, and STAT6 in HCASMCs and HCAECs, and 233 ASE genes, a subset of which are also GTEx eGenes in arterial tissues. Colocalization of GWAS association signals for coronary artery disease (CAD), migraine, stroke and abdominal aortic aneurysm with GTEx eGenes in aorta, coronary artery and tibial artery discovered novel candidate risk genes for these diseases. At the CAD and stroke locus tagged by rs2107595 we demonstrate colocalization with expression of the proximal gene TWIST1. We show that disrupting the rs2107595 locus alters TWIST1 expression and that the risk allele has increased binding of the NOTCH signaling protein RBPJ. Finally, we provide data that TWIST1 expression influences vascular SMC phenotypes, including proliferation and calcification, as a potential mechanism supporting a role for TWIST1 in CAD.

Klíčová slova:

Gene expression – Genetic loci – Genome-wide association studies – Coronary heart disease – Arteries – Coronary arteries – Vascular diseases – Smooth muscle cells

Zdroje

1. McPherson R, Tybjaerg-Hansen A. Genetics of Coronary Artery Disease. Circ Res. 2016;118(4):564–78. doi: 10.1161/CIRCRESAHA.115.306566 26892958.

2. Nikpay M, Goel A, Won HH, Hall LM, Willenborg C, Kanoni S, et al. A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease. Nat Genet. 2015;47(10):1121–30. doi: 10.1038/ng.3396 26343387

3. Nelson CP, Goel A, Butterworth AS, Kanoni S, Webb TR, Marouli E, et al. Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nat Genet. 2017;49(9):1385–91. doi: 10.1038/ng.3913 28714975.

4. Klarin D, Zhu QM, Emdin CA, Chaffin M, Horner S, McMillan BJ, et al. Genetic analysis in UK Biobank links insulin resistance and transendothelial migration pathways to coronary artery disease. Nat Genet. 2017;49(9):1392–7. doi: 10.1038/ng.3914 28714974

5. van der Harst P, Verweij N. The Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease. Circ Res. 2017. doi: 10.1161/CIRCRESAHA.117.312086 29212778.

6. Tada H, Won HH, Melander O, Yang J, Peloso GM, Kathiresan S. Multiple associated variants increase the heritability explained for plasma lipids and coronary artery disease. Circ Cardiovasc Genet. 2014;7(5):583–7. doi: 10.1161/CIRCGENETICS.113.000420 25170055

7. Dichgans M, Malik R, Konig IR, Rosand J, Clarke R, Gretarsdottir S, et al. Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. Stroke. 2014;45(1):24–36. doi: 10.1161/STROKEAHA.113.002707 24262325

8. Pickrell JK, Berisa T, Liu JZ, Segurel L, Tung JY, Hinds DA. Detection and interpretation of shared genetic influences on 42 human traits. Nat Genet. 2016;48(7):709–17. doi: 10.1038/ng.3570 27182965.

9. Chasman DI, Lawler PR. Understanding AAA Pathobiology: A GWAS Leads the Way. Circ Res. 2017;120(2):259–61. doi: 10.1161/CIRCRESAHA.116.310395 28104763

10. Braenne I, Civelek M, Vilne B, Di Narzo A, Johnson AD, Zhao Y, et al. Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. Arterioscler Thromb Vasc Biol. 2015;35(10):2207–17. doi: 10.1161/ATVBAHA.115.306108 26293461

11. Zhao Y, Chen J, Freudenberg JM, Meng Q, Rajpal DK, Yang X. Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci. Arterioscler Thromb Vasc Biol. 2016;36(5):928–41. doi: 10.1161/ATVBAHA.115.306725 26966275.

12. Franzen O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, et al. Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. Science. 2016;353(6301):827–30. doi: 10.1126/science.aad6970 27540175

13. Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015;13(5):311–9. doi: 10.1089/bio.2015.0032 26484571

14. Consortium GT. Genetic effects on gene expression across human tissues. Nature. 2017;550:204. https://www.nature.com/articles/nature24277#supplementary-information. 29022597

15. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. Epub 2016/06/09. doi: 10.1186/s13059-016-0974-4 27268795

16. Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, et al. A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. Bioinformatics. 2019;35(13):2315–7. Epub 2018/11/27. doi: 10.1093/bioinformatics/bty960 30475984

17. Dai W, Li Y, Lv YN, Wei CD, Zheng HY. The roles of a novel anti-inflammatory factor, milk fat globule-epidermal growth factor 8, in patients with coronary atherosclerotic heart disease. Atherosclerosis. 2014;233(2):661–5. doi: 10.1016/j.atherosclerosis.2014.01.013 24561551.

18. Wang M, Wang HH, Lakatta EG. Milk fat globule epidermal growth factor VIII signaling in arterial wall remodeling. Curr Vasc Pharmacol. 2013;11(5):768–76. doi: 10.2174/1570161111311050014 22272902

19. Yi YS. Functional Role of Milk Fat Globule-Epidermal Growth Factor VIII in Macrophage-Mediated Inflammatory Responses and Inflammatory/Autoimmune Diseases. Mediators Inflamm. 2016;2016:5628486. doi: 10.1155/2016/5628486 27429513

20. Su M, Yue Z, Wang H, Jia M, Bai C, Qiu W, et al. Ufmylation is Activated in Vascular Remodeling and Lipopolysaccharide-Induced Endothelial Cell Injury. DNA and cell biology. 2018. doi: 10.1089/dna.2017.4073 29461087.

21. Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nurnberg ST, Diaz R, et al. Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus. PLoS Genet. 2013;9(7):e1003652. doi: 10.1371/journal.pgen.1003652 23874238

22. Nurnberg ST, Cheng KR, Raiesdana A, Kundu R, Miller CL, Kim JB, et al. Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap. Plos Genetics. 2015;11(5). UNSP e1005155 doi: 10.1371/journal.pgen.1005155 26020946

23. Kim JB, Pjanic M, Nguyen T, Miller CL, Iyer D, Liu B, et al. TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells. PLoS Genet. 2017;13(5):e1006750. doi: 10.1371/journal.pgen.1006750 28481916

24. Strickland DK, Au DT, Cunfer P, Muratoglu SC. Low-density lipoprotein receptor-related protein-1: role in the regulation of vascular integrity. Arteriosclerosis, thrombosis, and vascular biology. 2014;34(3):487–98. doi: 10.1161/ATVBAHA.113.301924 24504736

25. Collaboration IRGCERF, Sarwar N, Butterworth AS, Freitag DF, Gregson J, Willeit P, et al. Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies. Lancet. 2012;379(9822):1205–13. doi: 10.1016/S0140-6736(11)61931-4 22421339

26. Sun X, Sun J, Zhao D, Song Y, Yu L. Phosphatase and actin regulator 1 rs9349379 polymorphism is associated with an elevated susceptibility to coronary artery disease: a meta-analysis. J Gene Med. 2019:e3110. Epub 2019/07/07. doi: 10.1002/jgm.3110 31278837.

27. Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, et al. A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell. 2017;170(3):522–33 e15. Epub 2017/07/29. doi: 10.1016/j.cell.2017.06.049 28753427

28. Wang X, Musunuru K. Confirmation of Causal rs9349379- PHACTR1 Expression Quantitative Trait Locus in Human-Induced Pluripotent Stem Cell Endothelial Cells. Circ Genom Precis Med. 2018;11(10):e002327. Epub 2018/10/26. doi: 10.1161/CIRCGEN.118.002327 30354304

29. Hixson JE, Jun G, Shimmin LC, Wang Y, Yu G, Mao C, et al. Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons. Sci Rep. 2017;7(1):4091. doi: 10.1038/s41598-017-04433-x 28642624

30. Canela-Xandri O, Rawlik K, Tenesa A. An atlas of genetic associations in UK Biobank. Nat Genet. 2018;50(11):1593–9. Epub 2018/10/24. doi: 10.1038/s41588-018-0248-z 30349118.

31. Bellenguez C, Strange A, Freeman C, Wellcome Trust Case Control C, Donnelly P, Spencer CC. A robust clustering algorithm for identifying problematic samples in genome-wide association studies. Bioinformatics. 2012;28(1):134–5. doi: 10.1093/bioinformatics/btr599 22057162

32. Duan L, Wei L, Tian Y, Zhang Z, Hu P, Wei Q, et al. Novel Susceptibility Loci for Moyamoya Disease Revealed by a Genome-Wide Association Study. Stroke. 2018;49(1):11–8. doi: 10.1161/STROKEAHA.117.017430 29273593.

33. Matsukura M, Ozaki K, Takahashi A, Onouchi Y, Morizono T, Komai H, et al. Genome-Wide Association Study of Peripheral Arterial Disease in a Japanese Population. PLoS One. 2015;10(10):e0139262. doi: 10.1371/journal.pone.0139262 26488411.

34. Iso T, Hamamori Y, Kedes L. Notch signaling in vascular development. Arterioscler Thromb Vasc Biol. 2003;23(4):543–53. doi: 10.1161/01.ATV.0000060892.81529.8F 12615665.

35. Fouillade C, Monet-Lepretre M, Baron-Menguy C, Joutel A. Notch signalling in smooth muscle cells during development and disease. Cardiovasc Res. 2012;95(2):138–46. doi: 10.1093/cvr/cvs019 22266753.

36. Tian Y, Xu Y, Fu Q, Chang M, Wang Y, Shang X, et al. Notch inhibits chondrogenic differentiation of mesenchymal progenitor cells by targeting Twist1. Mol Cell Endocrinol. 2015;403:30–8. doi: 10.1016/j.mce.2015.01.015 25596548

37. Wang Z, Li Y, Kong D, Sarkar FH. The role of Notch signaling pathway in epithelial-mesenchymal transition (EMT) during development and tumor aggressiveness. Curr Drug Targets. 2010;11(6):745–51. doi: 10.2174/138945010791170860 20041844

38. Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014;55(1):5–14. Epub 2014/07/06. doi: 10.1016/j.molcel.2014.06.015 24996062.

39. Serrano F, Bernard WG, Granata A, Iyer D, Steventon B, Kim M, et al. A Novel Human Pluripotent Stem Cell-Derived Neural Crest Model of Treacher Collins Syndrome Shows Defects in Cell Death and Migration. Stem Cells Dev. 2019;28(2):81–100. Epub 2018/10/31. doi: 10.1089/scd.2017.0234 30375284

40. Gomez D, Owens GK. Smooth muscle cell phenotypic switching in atherosclerosis. Cardiovasc Res. 2012;95(2):156–64. Epub 2012/03/13. doi: 10.1093/cvr/cvs115 22406749

41. Shanahan CM, Crouthamel MH, Kapustin A, Giachelli CM. Arterial calcification in chronic kidney disease: key roles for calcium and phosphate. Circ Res. 2011;109(6):697–711. Epub 2011/09/03. doi: 10.1161/CIRCRESAHA.110.234914 21885837

42. Pai A, Leaf EM, El-Abbadi M, Giachelli CM. Elastin degradation and vascular smooth muscle cell phenotype change precede cell loss and arterial medial calcification in a uremic mouse model of chronic kidney disease. Am J Pathol. 2011;178(2):764–73. Epub 2011/02/02. doi: 10.1016/j.ajpath.2010.10.006 21281809

43. Folkersen L, Persson J, Ekstrand J, Agardh HE, Hansson GK, Gabrielsen A, et al. Prediction of ischemic events on the basis of transcriptomic and genomic profiling in patients undergoing carotid endarterectomy. Mol Med. 2012;18:669–75. doi: 10.2119/molmed.2011.00479 22371308

44. Azghandi S, Prell C, van der Laan SW, Schneider M, Malik R, Berer K, et al. Deficiency of the stroke relevant HDAC9 gene attenuates atherosclerosis in accord with allele-specific effects at 7p21.1. Stroke. 2015;46(1):197–202. doi: 10.1161/STROKEAHA.114.007213 25388417.

45. Jung HY, Yang J. Unraveling the TWIST between EMT and cancer stemness. Cell Stem Cell. 2015;16(1):1–2. doi: 10.1016/j.stem.2014.12.005 25575073.

46. Qin Q, Xu Y, He T, Qin C, Xu J. Normal and disease-related biological functions of Twist1 and underlying molecular mechanisms. Cell Res. 2012;22(1):90–106. doi: 10.1038/cr.2011.144 21876555

47. Vincentz JW, Firulli BA, Lin A, Spicer DB, Howard MJ, Firulli AB. Twist1 controls a cell-specification switch governing cell fate decisions within the cardiac neural crest. PLoS Genet. 2013;9(3):e1003405. doi: 10.1371/journal.pgen.1003405 23555309

48. Schlueter J, Brand T. Subpopulation of proepicardial cells is derived from the somatic mesoderm in the chick embryo. Circ Res. 2013;113(10):1128–37. doi: 10.1161/CIRCRESAHA.113.301347 24019406.

49. Wirka RC, Wagh D, Paik DT, Pjanic M, Nguyen T, Miller CL, et al. Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis. Nat Med. 2019;25(8):1280–9. Epub 2019/07/31. doi: 10.1038/s41591-019-0512-5 31359001.

50. Chen PY, Qin L, Baeyens N, Li G, Afolabi T, Budatha M, et al. Endothelial-to-mesenchymal transition drives atherosclerosis progression. J Clin Invest. 2015;125(12):4514–28. doi: 10.1172/JCI82719 26517696

51. Mahmoud MM, Kim HR, Xing R, Hsiao S, Mammoto A, Chen J, et al. TWIST1 Integrates Endothelial Responses to Flow in Vascular Dysfunction and Atherosclerosis. Circ Res. 2016;119(3):450–62. doi: 10.1161/CIRCRESAHA.116.308870 27245171

52. Boucher J, Gridley T, Liaw L. Molecular pathways of notch signaling in vascular smooth muscle cells. Front Physiol. 2012;3:81. doi: 10.3389/fphys.2012.00081 22509166

53. Domenga V, Fardoux P, Lacombe P, Monet M, Maciazek J, Krebs LT, et al. Notch3 is required for arterial identity and maturation of vascular smooth muscle cells. Genes Dev. 2004;18(22):2730–5. doi: 10.1101/gad.308904 15545631

54. Joutel A, Corpechot C, Ducros A, Vahedi K, Chabriat H, Mouton P, et al. Notch3 mutations in CADASIL, a hereditary adult-onset condition causing stroke and dementia. Nature. 1996;383(6602):707–10. doi: 10.1038/383707a0 8878478.

55. Lee MP, Yutzey KE. Twist1 directly regulates genes that promote cell proliferation and migration in developing heart valves. PLoS One. 2011;6(12):e29758. doi: 10.1371/journal.pone.0029758 22242143

56. Bildsoe H, Fan X, Wilkie EE, Ashoti A, Jones VJ, Power M, et al. Transcriptional targets of TWIST1 in the cranial mesoderm regulate cell-matrix interactions and mesenchyme maintenance. Dev Biol. 2016;418(1):189–203. doi: 10.1016/j.ydbio.2016.08.016 27546376.

57. Otsuka F, Sakakura K, Yahagi K, Joner M, Virmani R. Has our understanding of calcification in human coronary atherosclerosis progressed? Arterioscler Thromb Vasc Biol. 2014;34(4):724–36. Epub 2014/02/22. doi: 10.1161/ATVBAHA.113.302642 24558104

58. Zhao Q, Wirka R, Nguyen T, Nagao M, Cheng P, Miller CL, et al. TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression. Genome Med. 2019;11(1):23. doi: 10.1186/s13073-019-0635-9 31014396

59. Thakore PI, D’Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015;12(12):1143–9. Epub 2015/10/27. doi: 10.1038/nmeth.3630 26501517

60. Zhao Q, Wirka R, Nguyen T, Nagao M, Cheng P, Miller CL, et al. TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression. Genome Med. 2019;11(1):23. Epub 2019/04/25. doi: 10.1186/s13073-019-0635-9 31014396