Li Hang, Zhao Caiping, Li Zeli, Yao Kainan, Zhang Jingjing, Si Wenwen, Liu Xiaohong, Jiang Yong, Zhu Meiling
Central Lab, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China.
Department of Respiratory, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China.
Front Genet. 2021 May 12;12:644143. doi: 10.3389/fgene.2021.644143. eCollection 2021.
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.
成纤维细胞异常分化为肌成纤维细胞是肺纤维化（PF）的关键病理机制。超级增强子是新发现的调控元件簇，被视为细胞身份的调节因子。我们推测超级增强子的异常激活必定参与了PF的病理过程。本研究旨在鉴定PF中潜在的致病性超级增强子驱动基因。从GEO数据集（GDS1492）中鉴定PF小鼠肺中的差异表达基因（DEG）。我们从SEA 3.0网络数据库收集人肺成纤维细胞和小鼠胚胎成纤维细胞中的超级增强子及其相关基因，该数据库提供有关超级增强子的全面信息。我们将成纤维细胞中上调的DEG与超级增强子相关基因进行交联，以预测PF中潜在的超级增强子驱动的致病基因。共有25个基因形成重叠，并通过STRING数据库构建这些基因的蛋白质-蛋白质相互作用网络。使用Cytoscape软件构建转录因子（TF）、超级增强子和相关基因的相互作用网络。对这些基因进行基因富集分析，包括KEGG通路和GO分析。潜在转化生长因子β（TGF-β）结合蛋白2（LTBP2）是预测的超级增强子驱动的致病基因之一，用于验证预测网络的准确性。在博来霉素诱导的PF小鼠模型以及TGF-β1刺激的小鼠和人成纤维细胞的肺中，LTBP2表达上调。Myc是与LTBP2超级增强子结合的TF之一。用CRISPR/Cas9质粒敲除超级增强子序列或抑制Myc均降低了NIH/3 T3细胞中TGF-β1诱导的LTBP2表达。鉴定和干扰超级增强子可能是探索PF潜在治疗方法的新途径。
