Identification of Potential Pathogenic Super-Enhancers-Driven Genes in Pulmonary Fibrosis

Hang Li; Caiping Zhao; Zeli Li; Kainan Yao; Jingjing Zhang; Wenwen Si; Xiaohong Liu; Yong Jiang; Meiling Zhu

doi:10.3389/fgene.2021.644143

Identification of Potential Pathogenic Super-Enhancers-Driven Genes in Pulmonary Fibrosis

Front Genet. 2021 May 12:12:644143. doi: 10.3389/fgene.2021.644143. eCollection 2021.

Authors

Hang Li¹, Caiping Zhao¹, Zeli Li², Kainan Yao², Jingjing Zhang³, Wenwen Si¹, Xiaohong Liu⁴, Yong Jiang⁵, Meiling Zhu⁶

Affiliations

¹ Central Lab, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China.
² Department of Respiratory, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China.
³ Department of Pathology, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China.
⁴ Department of Respiratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
⁵ Department of Respiratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China.
⁶ Traditional Chinese Medicine Innovation Research Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China.

Abstract

Abnormal fibroblast differentiation into myofibroblast is a crucial pathological mechanism of pulmonary fibrosis (PF). Super-enhancers, a newly discovered cluster of regulatory elements, are regarded as the regulators of cell identity. We speculate that abnormal activation of super-enhancers must be involved in the pathological process of PF. This study aims to identify potential pathogenic super-enhancer-driven genes in PF. Differentially expressed genes (DEGs) in PF mouse lungs were identified from a GEO dataset (GDS1492). We collected super-enhancers and their associated genes in human lung fibroblasts and mouse embryonic fibroblasts from SEA version 3.0, a network database that provides comprehensive information on super-enhancers. We crosslinked upregulated DEGs and super-enhancer-associated genes in fibroblasts to predict potential super-enhancer-driven pathogenic genes in PF. A total of 25 genes formed an overlap, and the protein-protein interaction network of these genes was constructed by the STRING database. An interaction network of transcription factors (TFs), super-enhancers, and associated genes was constructed using the Cytoscape software. Gene enrichment analyses, including KEGG pathway and GO analysis, were performed for these genes. Latent transforming growth factor beta (TGF-β) binding protein 2 (LTBP2), one of the predicted super-enhancer-driven pathogenic genes, was used to verify the predicted network's accuracy. LTBP2 was upregulated in the lungs of the bleomycin-induced PF mouse model and TGF-β1-stimulated mouse and human fibroblasts. Myc is one of the TFs binding to the LTBP2 super-enhancer. Knockout of super-enhancer sequences with a CRISPR/Cas9 plasmid or inhibition of Myc all decreased TGF-β1-induced LTBP2 expression in NIH/3 T3 cells. Identifying and interfering super-enhancers might be a new way to explore possible therapeutic methods for PF.

Keywords: LTBP2; fibroblast; pulmonary fibrosis; super-enhancer; transcription factor.