Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

Giuseppe Mocci; Katyayani Sukhavasi; Tiit Örd; Sean Bankier; Prosanta Singha; Uma Thanigai Arasu; Olayinka Oluwasegun Agbabiaje; Petri Mäkinen; Lijiang Ma; Chani J. Hodonsky; Redouane Aherrahrou; Lars Muhl; Jianping Liu; Sonja Gustafsson; Byambajav Byandelger; Ying Wang; Simon Koplev; Urban Lendahl; Gary K. Owens; Nicholas J. Leeper; Gerard Pasterkamp; Michael Vanlandewijck; Tom Michoel; Arno Ruusalepp; Ke Hao; Seppo Ylä-Herttuala; Marika Väli; Heli Järve; Michal Mokry; Mete Civelek; Clint J. Miller; Jason C. Kovacic; Minna U. Kaikkonen; Christer Betsholtz; Johan L.M. Björkegren

doi:10.1161/CIRCRESAHA.123.323184

Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

Giuseppe Mocci, Katyayani Sukhavasi, Tiit Örd, Sean Bankier, Prosanta Singha, Uma Thanigai Arasu, Olayinka Oluwasegun Agbabiaje, Petri Mäkinen, Lijiang Ma, Chani J. Hodonsky, Redouane Aherrahrou, Lars Muhl, Jianping Liu, Sonja Gustafsson, Byambajav Byandelger, Ying Wang, Simon Koplev, Urban Lendahl, Gary K. Owens, Nicholas J. LeeperGerard Pasterkamp, Michael Vanlandewijck, Tom Michoel, Arno Ruusalepp, Ke Hao, Seppo Ylä-Herttuala, Marika Väli, Heli Järve, Michal Mokry, Mete Civelek, Clint J. Miller, Jason C. Kovacic, Minna U. Kaikkonen, Christer Betsholtz, Johan L.M. Björkegren^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.

Original language	English
Pages (from-to)	1405-1423
Number of pages	19
Journal	Circulation research
Volume	134
Issue number	11
Early online date	19 Apr 2024
DOIs	https://doi.org/10.1161/CIRCRESAHA.123.323184
Publication status	Published - 24 May 2024

Keywords

coronary artery disease
gene expression
lipoportein
macrophages
subcutaneous fat

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mocci-et-al-2024-single-cell-gene-regulatory-networks-of-advanced-symptomatic-atherosclerosisFinal published version, 8.3 MBLicence: CC BY-NC-ND

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Mocci, G., Sukhavasi, K., Örd, T., Bankier, S., Singha, P., Arasu, U. T., Agbabiaje, O. O., Mäkinen, P., Ma, L., Hodonsky, C. J., Aherrahrou, R., Muhl, L., Liu, J., Gustafsson, S., Byandelger, B., Wang, Y., Koplev, S., Lendahl, U., Owens, G. K., ... Björkegren, J. L. M. (2024). Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis. Circulation research, 134(11), 1405-1423. https://doi.org/10.1161/CIRCRESAHA.123.323184

@article{84b5b28490174541a0b740c4567776a1,

title = "Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis",

abstract = "BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.",

keywords = "coronary artery disease, gene expression, lipoportein, macrophages, subcutaneous fat",

author = "Giuseppe Mocci and Katyayani Sukhavasi and Tiit {\"O}rd and Sean Bankier and Prosanta Singha and Arasu, {Uma Thanigai} and Agbabiaje, {Olayinka Oluwasegun} and Petri M{\"a}kinen and Lijiang Ma and Hodonsky, {Chani J.} and Redouane Aherrahrou and Lars Muhl and Jianping Liu and Sonja Gustafsson and Byambajav Byandelger and Ying Wang and Simon Koplev and Urban Lendahl and Owens, {Gary K.} and Leeper, {Nicholas J.} and Gerard Pasterkamp and Michael Vanlandewijck and Tom Michoel and Arno Ruusalepp and Ke Hao and Seppo Yl{\"a}-Herttuala and Marika V{\"a}li and Heli J{\"a}rve and Michal Mokry and Mete Civelek and Miller, {Clint J.} and Kovacic, {Jason C.} and Kaikkonen, {Minna U.} and Christer Betsholtz and Bj{\"o}rkegren, {Johan L.M.}",

year = "2024",

month = may,

day = "24",

doi = "10.1161/CIRCRESAHA.123.323184",

language = "English",

volume = "134",

pages = "1405--1423",

journal = "Circulation research",

issn = "0009-7330",

publisher = "Lippincott Williams & Wilkins",

number = "11",

}

Mocci, G, Sukhavasi, K, Örd, T, Bankier, S, Singha, P, Arasu, UT, Agbabiaje, OO, Mäkinen, P, Ma, L, Hodonsky, CJ, Aherrahrou, R, Muhl, L, Liu, J, Gustafsson, S, Byandelger, B, Wang, Y, Koplev, S, Lendahl, U, Owens, GK, Leeper, NJ, Pasterkamp, G, Vanlandewijck, M, Michoel, T, Ruusalepp, A, Hao, K, Ylä-Herttuala, S, Väli, M, Järve, H, Mokry, M, Civelek, M, Miller, CJ, Kovacic, JC, Kaikkonen, MU, Betsholtz, C & Björkegren, JLM 2024, 'Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis', Circulation research, vol. 134, no. 11, pp. 1405-1423. https://doi.org/10.1161/CIRCRESAHA.123.323184

TY - JOUR

T1 - Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

AU - Mocci, Giuseppe

AU - Sukhavasi, Katyayani

AU - Örd, Tiit

AU - Bankier, Sean

AU - Singha, Prosanta

AU - Arasu, Uma Thanigai

AU - Agbabiaje, Olayinka Oluwasegun

AU - Mäkinen, Petri

AU - Ma, Lijiang

AU - Hodonsky, Chani J.

AU - Aherrahrou, Redouane

AU - Muhl, Lars

AU - Liu, Jianping

AU - Gustafsson, Sonja

AU - Byandelger, Byambajav

AU - Wang, Ying

AU - Koplev, Simon

AU - Lendahl, Urban

AU - Owens, Gary K.

AU - Leeper, Nicholas J.

AU - Pasterkamp, Gerard

AU - Vanlandewijck, Michael

AU - Michoel, Tom

AU - Ruusalepp, Arno

AU - Hao, Ke

AU - Ylä-Herttuala, Seppo

AU - Väli, Marika

AU - Järve, Heli

AU - Mokry, Michal

AU - Civelek, Mete

AU - Miller, Clint J.

AU - Kovacic, Jason C.

AU - Kaikkonen, Minna U.

AU - Betsholtz, Christer

AU - Björkegren, Johan L.M.

PY - 2024/5/24

Y1 - 2024/5/24

N2 - BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.

AB - BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.

KW - coronary artery disease

KW - gene expression

KW - lipoportein

KW - macrophages

KW - subcutaneous fat

UR - http://www.scopus.com/inward/record.url?scp=85194216306&partnerID=8YFLogxK

U2 - 10.1161/CIRCRESAHA.123.323184

DO - 10.1161/CIRCRESAHA.123.323184

M3 - Article

C2 - 38639096

SN - 0009-7330

VL - 134

SP - 1405

EP - 1423

JO - Circulation research

JF - Circulation research

IS - 11

ER -

Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

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