1
|
Zhong J, Yuan H, Yang J, Du Y, Li Z, Liu X, Yang H, Wang Z, Wang Z, Jiang L, Ren Z, Li H, Li Z, Liu Y. Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and sarcopenia. Front Med (Lausanne) 2024; 11:1378846. [PMID: 38978778 PMCID: PMC11228343 DOI: 10.3389/fmed.2024.1378846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Sarcopenia is a condition characterized by age-related loss of muscle mass and strength. Increasing evidence suggests that patients with sarcopenia have higher rates of coronavirus 2019 (COVID-19) infection and poorer post-infection outcomes. However, the exact mechanism and connections between the two is unknown. In this study, we used high-throughput data from the GEO database for sarcopenia (GSE111016) and COVID-19 (GSE171110) to identify common differentially expressed genes (DEGs). We conducted GO and KEGG pathway analyses, as well as PPI network analysis on these DEGs. Using seven algorithms from the Cytoscape plug-in cytoHubba, we identified 15 common hub genes. Further analyses included enrichment, PPI interaction, TF-gene and miRNA-gene regulatory networks, gene-disease associations, and drug prediction. Additionally, we evaluated immune cell infiltration with CIBERSORT and assessed the diagnostic accuracy of hub genes for sarcopenia and COVID-19 using ROC curves. In total, we identified 66 DEGs (34 up-regulated and 32 down-regulated) and 15 hub genes associated with sarcopenia and COVID-19. GO and KEGG analyses revealed functions and pathways between the two diseases. TF-genes and TF-miRNA regulatory network suggest that FOXOC1 and hsa-mir-155-5p may be identified as key regulators, while gene-disease analysis showed strong correlations with hub genes in schizophrenia and bipolar disorder. Immune infiltration showed a correlation between the degree of immune infiltration and the level of infiltration of different immune cell subpopulations of hub genes in different datasets. The ROC curves for ALDH1L2 and KLF5 genes demonstrated their potential as diagnostic markers for both sarcopenia and COVID-19. This study suggests that sarcopenia and COVID-19 may share pathogenic pathways, and these pathways and hub genes offer new targets and strategies for early diagnosis, effective treatment, and tailored therapies for sarcopenia patients with COVID-19.
Collapse
Affiliation(s)
- Jun Zhong
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Hui Yuan
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jinghong Yang
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Yimin Du
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Zheng Li
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xu Liu
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Haibo Yang
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Zhaojun Wang
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Zi Wang
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Lujun Jiang
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Zhiqiang Ren
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Hongliang Li
- School of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Zhong Li
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yanshi Liu
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|
2
|
Vaswani CM, Simone J, Pavelick JL, Wu X, Tan GW, Ektesabi AM, Gupta S, Tsoporis JN, Dos Santos CC. Tiny Guides, Big Impact: Focus on the Opportunities and Challenges of miR-Based Treatments for ARDS. Int J Mol Sci 2024; 25:2812. [PMID: 38474059 DOI: 10.3390/ijms25052812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is characterized by lung inflammation and increased membrane permeability, which represents the leading cause of mortality in ICUs. Mechanical ventilation strategies are at the forefront of supportive approaches for ARDS. Recently, an increasing understanding of RNA biology, function, and regulation, as well as the success of RNA vaccines, has spurred enthusiasm for the emergence of novel RNA-based therapeutics. The most common types of RNA seen in development are silencing (si)RNAs, antisense oligonucleotide therapy (ASO), and messenger (m)RNAs that collectively account for 80% of the RNA therapeutics pipeline. These three RNA platforms are the most mature, with approved products and demonstrated commercial success. Most recently, miRNAs have emerged as pivotal regulators of gene expression. Their dysregulation in various clinical conditions offers insights into ARDS pathogenesis and offers the innovative possibility of using microRNAs as targeted therapy. This review synthesizes the current state of the literature to contextualize the therapeutic potential of miRNA modulation. It considers the potential for miR-based therapeutics as a nuanced approach that incorporates the complexity of ARDS pathophysiology and the multifaceted nature of miRNA interactions.
Collapse
Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Julia Simone
- Department of Medicine, McMaster University, Hamilton, ON L8V 5C2, Canada
| | - Jacqueline L Pavelick
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xiao Wu
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Greaton W Tan
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sahil Gupta
- Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Interdepartmental Division of Critical Care, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| |
Collapse
|
3
|
Gao H, Wang S, Duan H, Wang Y, Zhu H. Biological analysis of the potential pathogenic mechanisms of Infectious COVID-19 and Guillain-Barré syndrome. Front Immunol 2023; 14:1290578. [PMID: 38115996 PMCID: PMC10728822 DOI: 10.3389/fimmu.2023.1290578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Background Guillain-Barré syndrome (GBS) is a medical condition characterized by the immune system of the body attacking the peripheral nerves, including those in the spinal nerve roots, peripheral nerves, and cranial nerves. It can cause limb weakness, abnormal sensations, and facial nerve paralysis. Some studies have reported clinical cases associated with the severe coronavirus disease 2019 (COVID-19) and GBS, but how COVID-19 affects GBS is unclear. Methods We utilized bioinformatics techniques to explore the potential genetic connection between COVID-19 and GBS. Differential expression of genes (DEGs) related to COVID-19 and GBS was collected from the Gene Expression Omnibus (GEO) database. By taking the intersection, we obtained shared DEGs for COVID-19 and GBS. Subsequently, we utilized bioinformatics analysis tools to analyze common DEGs, conducting functional enrichment analysis and constructing Protein-protein interaction networks (PPI), Transcription factors (TF) -gene networks, and TF-miRNA networks. Finally, we validated our findings by constructing the Receiver Operating Characteristic (ROC) curves. Results This study utilizes bioinformatics tools for the first time to investigate the close genetic relationship between COVID-19 and GBS. CAMP, LTF, DEFA1B, SAMD9, GBP1, DDX60, DEFA4, and OAS3 are identified as the most significant interacting genes between COVID-19 and GBS. In addition, the signaling pathway of NOD-like receptors is believed to be essential in the link between COVID-19 and GBS.
Collapse
Affiliation(s)
| | | | | | | | - Hui Zhu
- Department of Neurology, The First Teaching Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|