1
|
Hkimi C, Kamoun S, Khamessi O, Ghedira K. Mycobacterium tuberculosis-THP-1 like macrophages protein-protein interaction map revealed through dual RNA-seq analysis and a computational approach. J Med Microbiol 2024; 73. [PMID: 38314675 DOI: 10.1099/jmm.0.001803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Introduction. Infection caused by Mycobacterium tuberculosis (M. tb) is still a leading cause of mortality worldwide with estimated 1.4 million deaths annually.Hypothesis/Gap statement. Despite macrophages' ability to kill bacterium, M. tb can grow inside these innate immune cells and the exploration of the infection has traditionally been characterized by a one-sided relationship, concentrating solely on the host or examining the pathogen in isolation.Aim. Because of only a handful of M. tb-host interactions have been experimentally characterized, our main goal is to predict protein-protein interactions during the early phases of the infection.Methodology. In this work, we performed an integrative computational approach that exploits differentially expressed genes obtained from Dual RNA-seq analysis combined with known domain-domain interactions.Results. A total of 2381 and 7214 genes were identified as differentially expressed in M. tb and in THP-1-like macrophages, respectively, revealing different transcriptional profiles in response to infection. Over 48 h of infection, the host-pathogen network revealed 25 016 PPIs. Analysis of the resulting predicted network based on cellular localization information of M. tb proteins, indicated the implication of interacting nodes including the bacterial PE/PPE/PE_PGRS family. In addition, M. tb proteins interacted with host proteins involved in NF-kB signalling pathway as well as interfering with the host apoptosis ability via the potential interaction of M. tb TB16.3 with human TAB1 and M. tb GroEL2 with host protein kinase C delta, respectively.Conclusion. The prediction of the full range of interactions between M. tb and host will contribute to better understanding of the pathogenesis of this bacterium and may provide advanced approaches to explore new therapeutic targets against tuberculosis.
Collapse
Affiliation(s)
- Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Selim Kamoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Oussema Khamessi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
| |
Collapse
|
2
|
Huang T, He J, Zhou X, Pan H, He F, Du A, Yu B, Jiang N, Li X, Yuan K, Wang Z. Discovering common pathogenetic processes between COVID-19 and tuberculosis by bioinformatics and system biology approach. Front Cell Infect Microbiol 2023; 13:1280223. [PMID: 38162574 PMCID: PMC10757339 DOI: 10.3389/fcimb.2023.1280223] [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: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic, stemming from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has persistently threatened the global health system. Meanwhile, tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) still continues to be endemic in various regions of the world. There is a certain degree of similarity between the clinical features of COVID-19 and TB, but the underlying common pathogenetic processes between COVID-19 and TB are not well understood. Methods To elucidate the common pathogenetic processes between COVID-19 and TB, we implemented bioinformatics and systematic research to obtain shared pathways and molecular biomarkers. Here, the RNA-seq datasets (GSE196822 and GSE126614) are used to extract shared differentially expressed genes (DEGs) of COVID-19 and TB. The common DEGs were used to identify common pathways, hub genes, transcriptional regulatory networks, and potential drugs. Results A total of 96 common DEGs were selected for subsequent analyses. Functional enrichment analyses showed that viral genome replication and immune-related pathways collectively contributed to the development and progression of TB and COVID-19. Based on the protein-protein interaction (PPI) network analysis, we identified 10 hub genes, including IFI44L, ISG15, MX1, IFI44, OASL, RSAD2, GBP1, OAS1, IFI6, and HERC5. Subsequently, the transcription factor (TF)-gene interaction and microRNA (miRNA)-gene coregulatory network identified 61 TFs and 29 miRNAs. Notably, we identified 10 potential drugs to treat TB and COVID-19, namely suloctidil, prenylamine, acetohexamide, terfenadine, prochlorperazine, 3'-azido-3'-deoxythymidine, chlorophyllin, etoposide, clioquinol, and propofol. Conclusion This research provides novel strategies and valuable references for the treatment of tuberculosis and COVID-19.
Collapse
Affiliation(s)
- Tengda Huang
- 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
| | - Jinyi He
- 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
| | - Xinyi Zhou
- 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
| | - Hongyuan Pan
- 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
| | - Fang He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ao Du
- 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
| | - Bingxuan Yu
- 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
| | - Nan Jiang
- 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
| | - Xiaoquan Li
- 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
| | - Kefei Yuan
- 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
| | - Zhen Wang
- 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
| |
Collapse
|