Bioinformatics and system biology approaches to determine the connection of SARS-CoV-2 infection and intrahepatic cholangiocarcinoma

Xinyi Zhou; Tengda Huang; Hongyuan Pan; Ao Du; Tian Wu; Jiang Lan; Yujia Song; Yue Lv; Fang He; Kefei Yuan

doi:10.1371/journal.pone.0300441

Bioinformatics and system biology approaches to determine the connection of SARS-CoV-2 infection and intrahepatic cholangiocarcinoma

PLoS One. 2024 Apr 22;19(4):e0300441. doi: 10.1371/journal.pone.0300441. eCollection 2024.

Authors

Xinyi Zhou¹, Tengda Huang¹, Hongyuan Pan¹, Ao Du¹, Tian Wu², Jiang Lan¹, Yujia Song¹, Yue Lv¹, Fang He³, Kefei Yuan¹

Affiliations

¹ Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
² NHC Key Laboratory of Transplant Engineering and Immunology, Regenerative Medicine Research Center, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, China.
³ Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.

Abstract

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19), has infected millions of individuals worldwide, which poses a severe threat to human health. COVID-19 is a systemic ailment affecting various tissues and organs, including the lungs and liver. Intrahepatic cholangiocarcinoma (ICC) is one of the most common liver cancer, and cancer patients are particularly at high risk of SARS-CoV-2 infection. Nonetheless, few studies have investigated the impact of COVID-19 on ICC patients.

Methods: With the methods of systems biology and bioinformatics, this study explored the link between COVID-19 and ICC, and searched for potential therapeutic drugs.

Results: This study identified a total of 70 common differentially expressed genes (DEGs) shared by both diseases, shedding light on their shared functionalities. Enrichment analysis pinpointed metabolism and immunity as the primary areas influenced by these common genes. Subsequently, through protein-protein interaction (PPI) network analysis, we identified SCD, ACSL5, ACAT2, HSD17B4, ALDOA, ACSS1, ACADSB, CYP51A1, PSAT1, and HKDC1 as hub genes. Additionally, 44 transcription factors (TFs) and 112 microRNAs (miRNAs) were forecasted to regulate the hub genes. Most importantly, several drug candidates (Periodate-oxidized adenosine, Desipramine, Quercetin, Perfluoroheptanoic acid, Tetrandrine, Pentadecafluorooctanoic acid, Benzo[a]pyrene, SARIN, Dorzolamide, 8-Bromo-cAMP) may prove effective in treating ICC and COVID-19.

Conclusion: This study is expected to provide valuable references and potential drugs for future research and treatment of COVID-19 and ICC.

Copyright: © 2024 Zhou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Betacoronavirus / genetics
Bile Duct Neoplasms* / genetics
Bile Duct Neoplasms* / virology
COVID-19* / genetics
COVID-19* / virology
Cholangiocarcinoma* / genetics
Cholangiocarcinoma* / virology
Computational Biology* / methods
Coronavirus Infections / genetics
Coronavirus Infections / virology
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Humans
Pandemics
Protein Interaction Maps / genetics
SARS-CoV-2* / genetics
Systems Biology* / methods

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by grants from the Natural Science Foundation of China (82370645, 82270643, 82070644 and 82170621), the National multidisciplinary collaborative diagnosis and treatment capacity building project for major diseases (TJZ202104), the Science and Technology Major Program of Sichuan Province (2022ZDZX0019), 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University (ZYJC18008, ZYGD22006).