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Peng B, Li H, Peng X. Understanding metabolic resistance strategy of clinically isolated antibiotic-resistant bacteria by proteomic approach. Expert Rev Proteomics 2024:1-10. [PMID: 39387182 DOI: 10.1080/14789450.2024.2413439] [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: 07/11/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/12/2024]
Abstract
INTRODUCTION Understanding the metabolic regulatory mechanisms leading to antibacterial resistance is important to develop effective control measures. AREAS COVERED In this review, we summarize the progress on metabolic mechanisms of antibiotic resistance in clinically isolated bacteria, as revealed using proteomic approaches. EXPERT OPINION Proteomic approaches are effective tools for uncovering clinically significant bacterial metabolic responses to antibiotics. Proteomics can disclose the associations between metabolic proteins, pathways, and networks with antibiotic resistance, and help identify their functional impact. The mechanisms by which metabolic proteins control the four generally recognized resistance mechanisms (decreased influx and targets, and increased efflux and enzymatic degradation) are particularly important. The proposed mechanism of reprogramming proteomics via key metabolites to enhance the killing efficiency of existing antibiotics needs attention.
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Affiliation(s)
- Bo Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui Li
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuanxian Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Wang L, Yang G, Guo L, Yao L, Liu Y, Sha W. Olink proteomics and lipidomics analysis of serum from patients infected with non-tuberculous mycobacteria and Mycobacterium tuberculosis. Inflamm Res 2024:10.1007/s00011-024-01943-z. [PMID: 39340659 DOI: 10.1007/s00011-024-01943-z] [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: 06/22/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Non-tuberculous mycobacterial (NTM) and Mycobacterium tuberculosis (MTB) infections are difficult to diagnose and treat, significantly burdening global health. The host immune status is generally believed to be associated with the onset and progression of NTM and MTB infections, but its specific impact remains unclear. METHODS In the present study, proteomics and lipidomics analysis of serum from normal controls (n = 26) and patients with MTB (n = 26), rapidly growing NTM (RGM, n = 15), and slowly growing NTM (SGM, n = 21) were conducted using the Olink technique based on a highly sensitive and specific neighborhood extension assay and the lipidomics technique. RESULTS IFN-γ, CXCL9, CXCL10, CXCL11, and CXCL13, etc. were simultaneously upregulated in MTB, RGM, and SGM, while lipids FAHFA 22:3, FAHFA 26:4, FAHFA 24:4, FAHFA 20:5, FAHFA 18:2 simultaneously downregulated. IL8, CCL3, CXCL5, and MCP-2, etc. were simultaneously upregulated in RGM and SGM compared to MTB, as well as PCs, LPCs, PEs, and LPEs. Compared with RGM, IL7, CD27, CCL17, CXCL12, and LPC 28:7-SN2 were downregulated in SGM. Pathway analyses revealed that tuberculosis, sphingolipid signaling pathway, and adipocytokine signaling pathway were regulated at the protein level and metabolite level. Diagnostic panels comprising immune-associated proteins and lipids greatly enhance diagnostic specificity and sensitivity. CONCLUSION This integrated multi-omics analysis provides a more comprehensive understanding of the molecular landscape of NTM and MTB, which may provide molecular targets for specialized therapies.
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Affiliation(s)
- Li Wang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guoling Yang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liang Guo
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lan Yao
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yidian Liu
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wei Sha
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
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Chen X, Wang J, Wang J, Ye J, Di P, Dong C, Lei H, Wang C. Several Potential Serum Proteomic Biomarkers for Diagnosis of Osteoarticular Tuberculosis Based on Mass Spectrometry. Clin Chim Acta 2023:117447. [PMID: 37353136 DOI: 10.1016/j.cca.2023.117447] [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: 12/21/2022] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Osteoarticular tuberculosis is one of the extrapulmonary tuberculosis (EPTB) diseases, which is mainly caused by infection of Mycobacterium tuberculosis (MTB) in bone and joints. The limitation of current clinical test methods is leading to a high misdiagnosis rate and affecting the treatment and prognosis. This study aims to search serum biomarkers that can assist in the diagnosis of osteoarticular tuberculosis. METHODS Proteomics can serve as an important method in the discovery of disease biomarkers. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to analyze proteins in 90 serum samples, which were collected from June 2020 to December 2021, then evaluated by statistical analysis to screen potential biomarkers. After that, potential biomarkers were validated by ELISA and diagnostic models were also established for observation of multi-index diagnostic efficacy. RESULTS 118 differential expressed proteins (DEPs) were obtained in serum after statistical analysis. After the diagnostic efficacy evaluation and clinical verification, inter-alpha-trypsin inhibitor heavy chain H2 (ITIH2), complement factor H-related protein 2 (CFHR2), complement factor H-related protein 3 (CFHR3) and complement factor H-related protein 5 (CFHR5) were found as potential biomarkers, with 0.7167 (95%CI: 0.5846-0.8487), 0.8600 (95%CI: 0.7701-0.9499), 0.8150 (95%CI: 0.6998-0.9302), and 0.9978 (95%CI: 0.9918-1.0040) AUC value, respectively. The remaining DEPs except CFHR5 were constructed as diagnostic models, the diagnostic model contained CFHR2 and CFHR3 had good diagnostic efficacy with 0.942 (95%CI: 0.872-0.980) AUC value compared to other models. CONCLUSION This study provides a reference for the discovery of serum protein markers for osteoarticular tuberculosis diagnosis, and the screened DEPs can also provide directions for subsequent pathogenesis research.
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Affiliation(s)
- Ximeng Chen
- Medical School of Chinese PLA, No.28 Fuxing Road, Haidian District, Beijing, China; Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China
| | - Jianan Wang
- Medical School of Chinese PLA, No.28 Fuxing Road, Haidian District, Beijing, China; Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China
| | - Jinyang Wang
- Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China
| | - Jingyun Ye
- Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China
| | - Ping Di
- Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China
| | - Chang Dong
- Department of Clinical Laboratory Medicine, The Eighth Medical Center, Chinese PLA General Hospital, No.17A Heishanhu Road, Haidian District, Beijing, China
| | - Hong Lei
- Department of Clinical Laboratory Medicine, The Eighth Medical Center, Chinese PLA General Hospital, No.17A Heishanhu Road, Haidian District, Beijing, China.
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, The First Medical Center, Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing, China.
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Guo Y, Liu K, Yang X, Lv Z, Zhao K, Wang X, Chu Y, Li J, Huang T. Multi-omics-based characterization of the influences of Mycobacterium tuberculosis virulence factors EsxB and PPE68 on host cells. Arch Microbiol 2023; 205:230. [PMID: 37162591 PMCID: PMC10170423 DOI: 10.1007/s00203-023-03576-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023]
Abstract
Mycobacterium tuberculosis, the ancient master of causing tuberculosis, is one of the most successful pathogens capable of persistently colonizing host lungs. The EsxB (CFP-10) of ESX-1 system and PPE68 of the PPE family contribute to the virulence of M. tuberculosis. However, the virulence potential and pathogenetic characteristics of these two proteins during M. tuberculosis infection remain unclear. In this study, two prokaryotic expression plasmids for EsxB or PPE68 of M. tuberculosis were constructed and the recombinant proteins His-EsxB or His-PPE68 were purified. The proteome and transcriptome of MH-S cells treated with His-EsxB or His-PPE68 were explored, followed by validating the expression of the identified differentially expressed genes (DEGs) using quantitative PCR. A total of 159/439 specific proteins or 633/1117 DEGs were obtained between control and His-EsxB or His-PPE68 treated groups in the MH-S proteomes and transcriptomes. Additionally, 37/60 signal pathways were predicted in the His-EsxB or His-PPE68 treated groups and "Cytokine-cytokine receptor interaction" was the most represented pathway. Furthermore, the expression of the DEGs (IL-1β, IL-6, and TNF-α) was significantly upregulated, suggesting that these DEGs contributed to the host response during EsxB or PPE68 treatment. These findings provide detailed information on developing an effective intervention strategy to control M. tuberculosis infection.
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Affiliation(s)
- Yidong Guo
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kanghua Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China
| | - Xiting Yang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Zheng Lv
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kelei Zhao
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Xinrong Wang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China.
| | - Ting Huang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China.
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Mass Spectrometry-Based Proteomic and Metabolomic Profiling of Serum Samples for Discovery and Validation of Tuberculosis Diagnostic Biomarker Signature. Int J Mol Sci 2022; 23:ijms232213733. [PMID: 36430211 PMCID: PMC9694769 DOI: 10.3390/ijms232213733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Tuberculosis (TB) is a transmissible disease listed as one of the 10 leading causes of death worldwide (10 million infected in 2019). A swift and precise diagnosis is essential to forestall its transmission, for which the discovery of effective diagnostic biomarkers is crucial. In this study, we aimed to discover molecular biomarkers for the early diagnosis of tuberculosis. Two independent cohorts comprising 29 and 34 subjects were assayed by proteomics, and 49 were included for metabolomic analysis. All subjects were arranged into three experimental groups—healthy controls (controls), latent TB infection (LTBI), and TB patients. LC-MS/MS blood serum protein and metabolite levels were submitted to univariate, multivariate, and ROC analysis. From the 149 proteins quantified in the discovery set, 25 were found to be differentially abundant between controls and TB patients. The AUC, specificity, and sensitivity, determined by ROC statistical analysis of the model composed of four of these proteins considering both proteomic sets, were 0.96, 93%, and 91%, respectively. The five metabolites (9-methyluric acid, indole-3-lactic acid, trans-3-indoleacrylic acid, hexanoylglycine, and N-acetyl-L-leucine) that better discriminate the control and TB patient groups (VIP > 1.75) from a total of 92 metabolites quantified in both ionization modes were submitted to ROC analysis. An AUC = 1 was determined, with all samples being correctly assigned to the respective experimental group. An integrated ROC analysis enrolling one protein and four metabolites was also performed for the common control and TB patients in the proteomic and metabolomic groups. This combined signature correctly assigned the 12 controls and 12 patients used only for prediction (AUC = 1, specificity = 100%, and sensitivity = 100%). This multiomics approach revealed a biomarker signature for tuberculosis diagnosis that could be potentially used for developing a point-of-care diagnosis clinical test.
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Kaushik A, Bandyopadhyay S, Porwal C, Srinivasan A, Rukmangadachar LA, Hariprasad G, Kola S, Kataria J, Singh UB. 2D-DIGE based urinary proteomics and functional enrichment studies to reveal novel Mycobacterium tuberculosis and human protein biomarker candidates for pulmonary tuberculosis. Biochem Biophys Res Commun 2022; 619:15-21. [PMID: 35728279 DOI: 10.1016/j.bbrc.2022.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
In the absence of a sensitive and specific diagnostic modality capable of detecting all forms of tuberculosis (TB), proteomics may identify specific Mycobacterium tuberculosis (M.tb) proteins in urine, with a potential as biomarkers. To identify candidate biomarkers for TB, proteome profile of urine from pulmonary TB patients was compared with non-disease controls (NDC) and disease controls (DC, Streptococcus pneumonia infected patients) using a combination of two-dimensional difference gel electrophoresis (2D-DIGE) and liquid chromatography tandem mass spectrometry (LCMS/MS). Eleven differentially expressed host proteins and Eighteen high abundant M.tb proteins were identified. Protein-protein interactome (PPI) and functional enrichment analyses like Gene Ontologies, Reactome pathway etc. demonstrated that the human proteins mainly belong to extracellular space and show physiological pathways for immune response and hematological disorders. Whereas, M.tb proteins belong to the cell periphery, plasma membrane and cell wall, and demonstrated catalytic, nucleotide binding and ATPase activities along with other functional processes. The study findings provide valuable inputs about the biomarkers of TB and shed light on the probable disease consequences as an outcome of the bacterial pathogenicity.
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Affiliation(s)
- Amit Kaushik
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | - Chhavi Porwal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Alagiri Srinivasan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Srujana Kola
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Jitender Kataria
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Sholeye AR, Williams AA, Loots DT, Tutu van Furth AM, van der Kuip M, Mason S. Tuberculous Granuloma: Emerging Insights From Proteomics and Metabolomics. Front Neurol 2022; 13:804838. [PMID: 35386409 PMCID: PMC8978302 DOI: 10.3389/fneur.2022.804838] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/24/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis infection, which claims hundreds of thousands of lives each year, is typically characterized by the formation of tuberculous granulomas — the histopathological hallmark of tuberculosis (TB). Our knowledge of granulomas, which comprise a biologically diverse body of pro- and anti-inflammatory cells from the host immune responses, is based mainly upon examination of lungs, in both human and animal studies, but little on their counterparts from other organs of the TB patient such as the brain. The biological heterogeneity of TB granulomas has led to their diverse, relatively uncoordinated, categorization, which is summarized here. However, there is a pressing need to elucidate more fully the phenotype of the granulomas from infected patients. Newly emerging studies at the protein (proteomics) and metabolite (metabolomics) levels have the potential to achieve this. In this review we summarize the diverse nature of TB granulomas based upon the literature, and amplify these accounts by reporting on the relatively few, emerging proteomics and metabolomics studies on TB granulomas. Metabolites (for example, trimethylamine-oxide) and proteins (such as the peptide PKAp) associated with TB granulomas, and knowledge of their localizations, help us to understand the resultant phenotype. Nevertheless, more multidisciplinary ‘omics studies, especially in human subjects, are required to contribute toward ushering in a new era of understanding of TB granulomas – both at the site of infection, and on a systemic level.
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Affiliation(s)
- Abisola Regina Sholeye
- Department of Biochemistry, Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Aurelia A. Williams
- Department of Biochemistry, Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Du Toit Loots
- Department of Biochemistry, Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - A. Marceline Tutu van Furth
- Department of Pediatric Infectious Diseases and Immunology, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Emma Children's Hospital, Amsterdam, Netherlands
| | - Martijn van der Kuip
- Department of Pediatric Infectious Diseases and Immunology, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Emma Children's Hospital, Amsterdam, Netherlands
| | - Shayne Mason
- Department of Biochemistry, Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
- *Correspondence: Shayne Mason
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Nabi B, Rehman S, Aggarwal S, Baboota S, Ali J. Nano-based anti-tubercular drug delivery: an emerging paradigm for improved therapeutic intervention. Drug Deliv Transl Res 2021; 10:1111-1121. [PMID: 32418158 PMCID: PMC7229880 DOI: 10.1007/s13346-020-00786-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB) classified as one of the most fatal contagious diseases is of prime concern globally. Mycobacterium tuberculosis is the causative agent that ingresses within the host cells. The approved conventional regimen, though the only viable option available, is unfavorably impacting the quality of life of the affected individual. Despite newer antibiotics gaining light, there is an unending demand for more therapeutic alternatives. Therefore, substantial continuous endeavors are been undertaken to come up with novel strategies to curb the disease, the stepping stone being nanotechnology. This approach is instrumental in overcoming the anomalies associated with conventional therapy owing to their intriguing attributes and leads to optimization of the therapeutic effect to a certain extent. This review focusses on the different types of nanocarrier systems that are being currently explored by the researchers for the delivery of anti-tubercular drugs, the outcomes achieved by them, and their prospects. Graphical abstract ![]()
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Affiliation(s)
- Bushra Nabi
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Saleha Rehman
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Sumit Aggarwal
- Division of ECD, Indian Council of Medical Research, New Delhi, India
| | - Sanjula Baboota
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Javed Ali
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India.
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Conde R, Laires R, Gonçalves LG, Rizvi A, Barroso C, Villar M, Macedo R, Simões MJ, Gaddam S, Lamosa P, Puchades-Carrasco L, Pineda-Lucena A, Patel AB, Mande SC, Barnejee S, Matzapetakis M, Coelho AV. Discovery of serum biomarkers for diagnosis of tuberculosis by NMR metabolomics including cross-validation with a second cohort. Biomed J 2021; 45:654-664. [PMID: 34314900 PMCID: PMC9486122 DOI: 10.1016/j.bj.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background Tuberculosis (TB) is a disease with worldwide presence and a major cause of death in several developing countries. Current diagnostic methodologies often lack specificity and sensitivity, whereas a long time is needed to obtain a conclusive result. Methods In an effort to develop better diagnostic methods, this study aimed at the discovery of a biomarker signature for TB diagnosis using a Nuclear Magnetic Resonance based metabolomics approach. In this study, we acquired 1H NMR spectra of blood serum samples of groups of healthy subjects, individuals with latent TB and of patients with pulmonary and extra-pulmonary TB. The resulting data were treated with uni- and multivariate statistical analysis. Results Six metabolites (inosine, hypoxanthine, mannose, asparagine, aspartate and glutamate) were validated by an independent cohort, all of them related with metabolic processes described as associated with TB infection. Conclusion The findings of the study are according with the WHO Target Product Profile recommendations for a triage test to rule-out active TB.
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Affiliation(s)
- R Conde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - R Laires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L G Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - C Barroso
- CDP Almada-Seixal, ARSLVT, Portugal.
| | - M Villar
- CDP Venda Nova, ARSLVT, Portugal.
| | | | | | - S Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research Center, Hyderabad, India; Department of Genetics, Osmania University, Hyderabad, India.
| | - P Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - A Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain.
| | - A B Patel
- CSIR- Centre for Cellular Molecular Biology, Hyderabad, India.
| | - S C Mande
- National Centre For Cell Science, Pune, India; Present address: Council of Scientific and Industrial Research, New Delhi, India.
| | - S Barnejee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - M Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
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Gautam S, Sharma D, Goel A, Patil SA, Bisht D. Insights into Mycobacterium leprae Proteomics and Biomarkers-An Overview. Proteomes 2021; 9:7. [PMID: 33573064 PMCID: PMC7931084 DOI: 10.3390/proteomes9010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Although leprosy is curable, the identification of biomarkers for the early diagnosis of leprosy would play a pivotal role in reducing transmission and the overall prevalence of the disease. Leprosy-specific biomarkers for diagnosis, particularly for the paucibacillary disease, are not well defined. Therefore, the identification of new biomarkers for leprosy is one of the prime themes of leprosy research. Studying Mycobacterium leprae, the causative agent of leprosy, at the proteomic level may facilitate the identification, quantification, and characterization of proteins that could be potential diagnostics or targets for drugs and can help in better understanding the pathogenesis. This review aims to shed light on the knowledge gained to understand leprosy or its pathogen employing proteomics and its role in diagnosis.
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Affiliation(s)
- Sakshi Gautam
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
- Department of Biotechnology, GLA University, NH-2, Mathura-Delhi Road, Mathura 281406, India;
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
| | - Anjana Goel
- Department of Biotechnology, GLA University, NH-2, Mathura-Delhi Road, Mathura 281406, India;
| | - Shripad A. Patil
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India; (S.G.); (D.S.); (S.A.P.)
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Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res 2021; 246:126674. [PMID: 33549960 DOI: 10.1016/j.micres.2020.126674] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
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Affiliation(s)
- Renuga Devi Kanabalan
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Le Jie Lee
- Prima Nexus Sdn. Bhd., Menara CIMB, Jalan Stesen Sentral 2, Kuala Lumpur, Malaysia
| | - Tze Yan Lee
- Perdana University School of Liberal Arts, Science and Technology (PUScLST), Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan Damansara Heights, Kuala Lumpur, 50490, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, Subang Jaya, 47500, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Rosnah Ismail
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia.
| | - Voon Kin Chin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam, Selangor, 42300, Malaysia.
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12
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Xu G, Xue J, Jiang J, Liang T, Yao Y, Liao S, Chen T, Li H, Liu C, Zhan X. Proteomic analysis reveals critical molecular mechanisms involved in the macrophage anti-spinal tuberculosis process. Tuberculosis (Edinb) 2020; 126:102039. [PMID: 33316736 DOI: 10.1016/j.tube.2020.102039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/20/2023]
Abstract
Tuberculosis infection activates the autoimmune system. However, the role of host-pathogen interactions involved in Mycobacterium tuberculosis infection is unclear. In this study, we analyzed 6 spinal tuberculosis tissues and 6 herniated disc tissues by using liquid chromatography-tandem mass spectrometry coupled with tandem mass spectrometry, and immunohistochemical staining was performed for validating the results. We identified 42 differential immune-related proteins and 3 hub genes that are primarily localised in the tertiary granule and involved in biological processes such as cellular response to the presence of cadmium ions, regulation of ion transmembrane transport, transmembrane transport, and inflammatory responses. Genes encoding cytochrome B-245 beta chain (CYBB), matrix metallopeptidase 9 (MMP9), and C-X-C motif chemokine ligand 10 (CXCL10) were identified as the hub genes that exhibited anti-tuberculosis activity and were responsible for macrophage resistance against M. tuberculosis. In conclusion, CYBB, MMP9, and CXCL10 resist M. tuberculosis infection through chemotaxis and macrophage activation. Our results indicate that CYBB, MMP9, and CXCL10 could be considered as molecular targets for spinal tuberculosis treatment, which may significantly improve patients' quality of life and prognosis.
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Affiliation(s)
- Guoyong Xu
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Jiang Xue
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Jie Jiang
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Tuo Liang
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Yuanlin Yao
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Shian Liao
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Tianyou Chen
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Hao Li
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China
| | - Chong Liu
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China.
| | - Xinli Zhan
- Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, PR China; Guangxi Medical University, Nanning, 530021, PR China.
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13
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Xuan WX, Li JJ, Zhang QC, Sun GN, Xu ZW, Sun ZF, Zhang XJ. Protein expression shift and potential diagnostic markers through proteomics profiling of tuberculous pleurisy biopsy tissues. Int J Infect Dis 2020; 99:245-252. [PMID: 32758691 DOI: 10.1016/j.ijid.2020.07.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/07/2020] [Accepted: 07/19/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Tuberculous pleurisy is a common type of tuberculosis (TB), but its diagnosis is challenging. This study aimed to profile the protein expression of this disease and identify new diagnostic makers. METHODS Biopsy tissues from patients with tuberculous pleurisy and controls were taken through thoracoscopy, and proteins were extracted for Tandem Mass Tag Mass Spectrometry. Differential protein expression was performed between patients and controls, and the identified proteins were analyzed for pathway enrichment. Selected proteins were further validated in another set of samples using a more quantitative method. RESULTS A total of 5101 proteins were detected and quantified in a discovery set of patients and controls. Overall protein expression was quite different between patients and controls. Most proteins were down-expressed, while a minority were overly expressed in the patient samples. At p value < 0.05 and absolute fold change >2, 295 proteins were found to be up-expressed and 608 down-expressed. The top enriched pathways included ECM-receptor interaction, complement and coagulation cascades and focal adhesion. All 19 selected candidates were validated in an independent set of patient and control samples. CONCLUSION This unbiased proteomics approach not only provided unique insights into protein expression and pathways, but also discovered potential diagnostic markers for tuberculous pleurisy.
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Affiliation(s)
- Wei-Xia Xuan
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Jin-Jin Li
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qun-Cheng Zhang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Guan-Nan Sun
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhi-Wei Xu
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhi-Fu Sun
- Department of Health Sciences Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Xiao-Ju Zhang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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