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Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16410-16419. doi: 10.1073/pnas.1904108116. Epub 2019 Jul 26.

Regulation of CCL2 expression in human vascular endothelial cells by a neighboring divergently transcribed long noncoding RNA.

Khyzha N1,2,3, Khor M1,2,3, DiStefano PV1,2,3, Wang L4,5, Matic L6, Hedin U6, Wilson MD4,5, Maegdefessel L7,8,9, Fish JE10,2,3.

Author information

1
Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada.
2
Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada.
3
Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2C4, Canada.
4
Genetics and Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada.
5
Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.
6
Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institute, 17176 Stockholm, Sweden.
7
Department of Vascular and Endovascular Surgery, Technical University Munich, 81675 Munich, Germany.
8
Partner Site Munich, Deutsches Zentrum für Herz-Kreislauf-Forschung, 80636 Munich, Germany.
9
Department of Medicine, Karolinska Institute, 17164 Stockholm, Sweden.
10
Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada; jason.fish@utoronto.ca.

Abstract

Atherosclerosis is a chronic inflammatory disease that is driven, in part, by activation of vascular endothelial cells (ECs). In response to inflammatory stimuli, the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway orchestrates the expression of a network of EC genes that contribute to monocyte recruitment and diapedesis across the endothelium. Although many long noncoding RNAs (lncRNAs) are dysregulated in atherosclerosis, they remain poorly characterized, especially in the context of human vascular inflammation. Prior studies have illustrated that lncRNAs can regulate their neighboring protein-coding genes via interaction with protein complexes. We therefore identified and characterized neighboring interleukin-1β (IL-1β)-regulated messenger RNA (mRNA)-lncRNA pairs in ECs. We found these pairs to be highly correlated in expression, especially when located within the same chromatin territory. Additionally, these pairs were predominantly divergently transcribed and shared common gene regulatory elements, characterized by active histone marks and NF-κB binding. Further analysis was performed on lncRNA-CCL2, which is transcribed divergently to the gene, CCL2, encoding a proatherosclerotic chemokine. LncRNA-CCL2 and CCL2 showed coordinate up-regulation in response to inflammatory stimuli, and their expression was correlated in unstable symptomatic human atherosclerotic plaques. Knock-down experiments revealed that lncRNA-CCL2 positively regulated CCL2 mRNA levels in multiple primary ECs and EC cell lines. This regulation appeared to involve the interaction of lncRNA-CCL2 with RNA binding proteins, including HNRNPU and IGF2BP2. Hence, our approach has uncovered a network of neighboring mRNA-lncRNA pairs in the setting of inflammation and identified the function of an lncRNA, lncRNA-CCL2, which may contribute to atherogenesis in humans.

KEYWORDS:

atherosclerosis; chromatin; endothelium; epigenetics; long noncoding RNA

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