Single-nucleus Chromatin Accessibility Profiling Highlights Regulatory Mechanisms of Coronary Artery Disease Risk

Overview

Journal Nat Genet

Specialty Genetics

Date 2022 May 19

PMID 35590109

Authors

Adam W Turner

Shengen Shawn Hu

Jose Verdezoto Mosquera

Wei Feng Ma

Chani J Hodonsky

Doris Wong

Gaelle Auguste

Yipei Song

Katia Sol-Church

Emily Farber

Soumya Kundu

Anshul Kundaje

Nicolas G Lopez

Lijiang Ma

Saikat Kumar B Ghosh

Suna Onengut-Gumuscu

Euan A Ashley

Thomas Quertermous

Aloke V Finn

Nicholas J Leeper

Jason C Kovacic

Johan L M Bjorkegren

Chongzhi Zang

Clint L Miller

Affiliations

Soon will be listed here.

Abstract

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.

Citing Articles

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References

Calderon D, Nguyen M, Mezger A, Kathiria A, Muller F, Nguyen V . Landscape of stimulation-responsive chromatin across diverse human immune cells. Nat Genet. 2019; 51(10):1494-1505. PMC: 6858557. DOI: 10.1038/s41588-019-0505-9. View

Corces M, Trevino A, Hamilton E, Greenside P, Sinnott-Armstrong N, Vesuna S . An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017; 14(10):959-962. PMC: 5623106. DOI: 10.1038/nmeth.4396. View

Nott A, Holtman I, Coufal N, Schlachetzki J, Yu M, Hu R . Brain cell type-specific enhancer-promoter interactome maps and diseaserisk association. Science. 2019; 366(6469):1134-1139. PMC: 7028213. DOI: 10.1126/science.aay0793. View

Lin M, Chen T, Leaf E, Speer M, Giachelli C . Runx2 Expression in Smooth Muscle Cells Is Required for Arterial Medial Calcification in Mice. Am J Pathol. 2015; 185(7):1958-69. PMC: 4484217. DOI: 10.1016/j.ajpath.2015.03.020. View

Virmani R, Kolodgie F, Burke A, Finn A, Gold H, Tulenko T . Atherosclerotic plaque progression and vulnerability to rupture: angiogenesis as a source of intraplaque hemorrhage. Arterioscler Thromb Vasc Biol. 2005; 25(10):2054-61. DOI: 10.1161/01.ATV.0000178991.71605.18. View

Chiou J, Zeng C, Cheng Z, Han J, Schlichting M, Miller M . Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Nat Genet. 2021; 53(4):455-466. PMC: 9037575. DOI: 10.1038/s41588-021-00823-0. View

Alencar G, Owsiany K, Karnewar S, Sukhavasi K, Mocci G, Nguyen A . Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis. Circulation. 2020; 142(21):2045-2059. PMC: 7682794. DOI: 10.1161/CIRCULATIONAHA.120.046672. View

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

Granja J, Corces M, Pierce S, Bagdatli S, Choudhry H, Chang H . ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet. 2021; 53(3):403-411. PMC: 8012210. DOI: 10.1038/s41588-021-00790-6. View

10.

Gate R, Cheng C, Aiden A, Siba A, Tabaka M, Lituiev D . Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet. 2018; 50(8):1140-1150. PMC: 6097927. DOI: 10.1038/s41588-018-0156-2. View

11.

Muto Y, Wilson P, Ledru N, Wu H, Dimke H, Waikar S . Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Nat Commun. 2021; 12(1):2190. PMC: 8044133. DOI: 10.1038/s41467-021-22368-w. View

12.

Browning S, Browning B . Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81(5):1084-97. PMC: 2265661. DOI: 10.1086/521987. View

13.

Phanstiel D, Boyle A, Araya C, Snyder M . Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics. 2014; 30(19):2808-10. PMC: 4173017. DOI: 10.1093/bioinformatics/btu379. View

14.

Shirai M, Imanaka-Yoshida K, Schneider M, Schwartz R, Morisaki T . T-box 2, a mediator of Bmp-Smad signaling, induced hyaluronan synthase 2 and Tgfbeta2 expression and endocardial cushion formation. Proc Natl Acad Sci U S A. 2009; 106(44):18604-9. PMC: 2773962. DOI: 10.1073/pnas.0900635106. View

15.

Bryois J, Garrett M, Song L, Safi A, Giusti-Rodriguez P, Johnson G . Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nat Commun. 2018; 9(1):3121. PMC: 6081462. DOI: 10.1038/s41467-018-05379-y. View

16.

Erdmann J, Kessler T, Venegas L, Schunkert H . A decade of genome-wide association studies for coronary artery disease: the challenges ahead. Cardiovasc Res. 2018; 114(9):1241-1257. DOI: 10.1093/cvr/cvy084. View

17.

Nyati K, Agarwal R, Sharma P, Kishimoto T . Arid5a Regulation and the Roles of Arid5a in the Inflammatory Response and Disease. Front Immunol. 2019; 10:2790. PMC: 6906145. DOI: 10.3389/fimmu.2019.02790. View

18.

Stolze L, Conklin A, Whalen M, Lopez Rodriguez M, Ounap K, Selvarajan I . Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits. Am J Hum Genet. 2020; 106(6):748-763. PMC: 7273528. DOI: 10.1016/j.ajhg.2020.04.008. View

19.

Wirka R, Wagh D, Paik D, Pjanic M, Nguyen T, Miller C . Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis. Nat Med. 2019; 25(8):1280-1289. PMC: 7274198. DOI: 10.1038/s41591-019-0512-5. View

20.

Nagao M, Lyu Q, Zhao Q, Wirka R, Bagga J, Nguyen T . Coronary Disease-Associated Gene Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway. Circ Res. 2019; 126(4):517-529. PMC: 7274203. DOI: 10.1161/CIRCRESAHA.119.315968. View