Association studies between COVID-19 and SSc-ILD

Severe COVID-19 patients may develop pulmonary fibrosis, similar to SSc-ILD disease, suggesting a potential link between the two diseases. However, there are limited treatment options for SSc-ILD-type diseases. Therefore, investigating pathological markers of the two diseases can provide valuable insights for treating related conditions. RNA sequencing technology offers high throughput and precision. However, the bimodal nature of RNA-Seq data cannot be accurately captured by commonly used algorithms such as DESeq2. To address this issue, the Beta-Poisson model has been developed to identify differentially expressed genes. Unlike the classical DESeq2 algorithm, the Beta-Poisson model introduces a Beta distribution to construct a new hybrid distribution in place of the Gamma distribution of the Gamma-Poisson distribution, effectively characterizing the bimodal features of RNA-Seq data. The transcriptomes of SARS-CoV infection and SSc-ILD disease in the lung epithelial cell dataset were analyzed to identify common differentially expressed genes of SARS-CoV and SSc-ILD disease. Gene function and signaling pathway enrichment analysis and protein-protein interaction (PPI) network were used to identify common pathways and drug targets for SSc-ILD with COVID-19 infection. The results show that there are 50 differentially expressed genes in common between COVID-19 and SSC-ILD. The functions of these genes are mainly enriched in immune system response, interferon signaling pathway and other related signaling pathways, and enriched in biological processes such as cell defense response to virus and interferon regulation. Based on the detection of hub genes based on PPIs network, it is predicted that STAT1, ISG15, IRF7, MX1, EIF2AK2, DDX58, OAS1, OAS2, IFIT1 and IFIT3 are the key genes involved in the pathological phenotype of the two diseases. Based on the key genes, the interaction of transcription factor (TF) and miRNA with common differentially expressed genes is also identified. The possible pathological markers of the two diseases and related molecular regulatory mechanisms of disease treatment are revealed to provide theoretical basis for the treatment of the two diseases. © 2023 Editorial Office of Journal of Shenzhen University. All rights reserved.