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Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [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] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
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Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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Li H, Cao W, Chen S, Chen J, Xing Y, Yang H. Comparative interleukins and chemokines analysis of mice mesenchymal stromal cells infected with Mycobacterium tuberculosis H37Rv and H37Ra. Arch Biochem Biophys 2023:109673. [PMID: 37392994 DOI: 10.1016/j.abb.2023.109673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/03/2023]
Abstract
Inflammatory pathways involving Mesenchymal stromal cells (MSCs) play an important role in Mycobacterium tuberculosis (Mtb) infection. H37Rv (Rv) is a standard virulent strain, however, H37Ra (Ra) is a strain with reduced virulence. Interleukins and chemokines production are known to promote inflammation resistance in mammalian cells and is recently reported to regulate mycobacterial immunopathogenesis via inflammatory responses. MSCs are very important cells during Mtb infection. However, the different expressions of interleukins and chemokines in the process of Mtb-infected MSCs between Ra and Rv remain unclear. We used the techniques of RNA-Seq, Q-RT-PCR, ELISA, and Western Blotting. We have shown that Rv infection significantly increased mRNA expressions of Mndal, Gdap10, Bmp2, and Lif, thereby increasing more differentiation of MSCs compared with Ra infection in MSCs. Further investigation into the possible mechanisms, we found that Rv infection enhanced more inflammatory response (Mmp10, Mmp3, and Ptgs2) through more activation of the TLR2-MAP3K1-JNK pathway than did Ra infection in MSCs. Further action showed that Rv infection enhanced more Il1α, Il6, Il33, Cxcl2, Ccl3, and Ackr3 production than did Ra infection. Rv infection showed more expressions of Mmp10, Mmp3, Ptgs2, Il1α, Il6, Il33, Cxcl2, Ccl3, and Ackr3 possibly through more active TLR2-MAP3K1-JNK pathway than did Ra infection in MSCs. MSCs may therefore be a new candidate for the prevention and treatment of tuberculosis.
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Affiliation(s)
- Heng Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wei Cao
- Institute of health, Shanghai Institute of life Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shichao Chen
- College of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Jianxia Chen
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China; TB Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China; Shanghai TB Key Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yanchun Xing
- Department of Medicine, Anhui Huangshan Vocational and Technical College, Huangshan, Anhui, 245000, China.
| | - Hong Yang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China; TB Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China; Shanghai TB Key Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200092, China.
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Lu Y, Ning H, Kang J, Bai G, Zhou L, Kang Y, Wu Z, Tian M, Zhao J, Ma Y, Bai Y. Cyclic-di-AMP Phosphodiesterase Elicits Protective Immune Responses Against Mycobacterium tuberculosis H37Ra Infection in Mice. Front Cell Infect Microbiol 2022; 12:871135. [PMID: 35811674 PMCID: PMC9256937 DOI: 10.3389/fcimb.2022.871135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Many antigens from Mycobacterium tuberculosis (M. tuberculosis) have been demonstrated as strong immunogens and proved to have application potential as vaccine candidate antigens. Cyclic di-AMP (c-di-AMP) as a bacterial second messenger regulates various bacterial processes as well as the host immune responses. Rv2837c, the c-di-AMP phosphodiesterase (CnpB), was found to be relative to virulence of M. tuberculosis and interference with host innate immune response. In this study, recombinant CnpB was administered subcutaneously to mice. We found that CnpB had strong immunogenicity and induced high levels of humoral response and lung mucosal immunity after M. tuberculosis intranasally infection. CnpB immunization stimulated splenocyte proliferation and the increasing number of activated NK cells but had little effects on Th1/Th2 cellular immune responses in spleens. However, CnpB induced significant Th1/Th2 cellular immune responses with a decreased number of T and B cells in the lungs, and significantly recruits of CD4+ and CD8+ T cells after M. tuberculosis attenuated strain H37Ra infection. Besides, we first reported that CnpB could stimulate IFN-β expression transitorily and inhibit the autophagy of macrophages in vitro. In mice intranasally infection model, CnpB immunization alleviated pathological changes and reduced M. tuberculosis H37Ra loads in the lungs. Thus, our results suggested that CnpB interferes with host innate and adaptive immune responses and confers protection against M. tuberculosis respiratory infection, which should be considered in vaccine development as well as a drug target.
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Affiliation(s)
- Yanzhi Lu
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Huanhuan Ning
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
| | - Lei Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
| | - Yali Kang
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Zhengfeng Wu
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Maolin Tian
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Junhao Zhao
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Yueyun Ma
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, Beijing, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
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