Discovery of novel genes of macrophages related to lung fibrosis pathways based on single-cell RNA sequencing
Gmail - ATS 2022_ Abstract Notification.pdf
JongHyun Kim , MinDong Sung, Kyeong-Seob Jeong, Yu-Rand Park
Rationale: In severe Coronavirus Disease 2019 (COVID-19), the infected lung becomes fibrosis. Macrophages have been identified as pathogenic fibrotic response regulators. This study aims to discover lung fibrosis related genes in COVID-19 by using single-cell RNA sequencing (scRNA-seq).
Methods: The healthy control, idiopathic pulmonary fibrosis (IPF), and severe COVID-19 lung scRNA-seq data, was obtained from the Gene Expression Omnibus (GEO) database (GSE135893, GSE149878). In addition, we used control, moderate and severe COVID-19 broncho-alveolar lavage fluid (BALF) scRNA-seq data (GSE145926). The expression matrices were preprocessed, integrated, and clustered with Seurat (v.4.0.4) package. To find lung fibrosis related novel genes in severe COVID-19 lung, differential expression analysis among control, COVID-19, and IPF lung was done. Both up or down regulated genes in IPF and COVID-19 were selected as candidates gens. Using these genes, we also performed differential expression analysis between moderate and severe COVID-19. Finally, we selected significant up or down- regulated genes of macrophages. For semantic verification of these significant genes of lung fibrosis, pathway analysis was performed based on Reactome DB.
Results: Totally 114,153 cells were profiled from 10 control, 20 IPF, 4 COVID-19 lungs. Main cell types were annotated as: immune, endothelial, epithelial, and mesenchymal cell, and the macrophages were sub-clustered in 25 subclusters as previously published method. The macrophages were sub-clustered as follows: FABP4, SPP1, FCN1, and mixed macrophages. The level of expression in COVID19 was larger in SPP1+ macrophages (COVID-19 (58%), IPF (32%), control (8%)), and it dropped in FABP4+( COVID-19 (7%), IPF (42%), control (59%)) and FCN1+ macrophages (COVID-19 (31%), IPF (18%), control (22%). Finally, (SGK1, C15orf48, IL1RN, CCL2, SPP1, CCL3, CXCL8) genes were up-regulated; and (NUPR1, APOC1, FABP4, C1QB, C1QA, C1QC) genes were down-regulated in severe COVID-19. The reactome pathway analysis showed that up-regulated genes were related to interleukin 10, 4, 7 pathways; down-regulated genes were related to vitamin A related pathway, which was known that vitamin A deficiency exacerbate lung fibrosis.
Conclusions: In this study, we discovered that the genes associated with lung fibrosis in severe COVID-19. Some of these genes were already reported relating to lung fibrosis, but also there were newly detected genes in this study. The discovered genes can be targeted to prevent to progress lung fibrosis in COVID19 infection.