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Pandey D, Ghosh D. Proteomics-based host-specific biomarkers for tuberculosis: The future of TB diagnosis. J Proteomics 2024; 305:105245. [PMID: 38942234 DOI: 10.1016/j.jprot.2024.105245] [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: 03/24/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Tuberculosis (TB) is an infectious disease that remains one of the major global public health concerns. Early detection of Active Pulmonary TB is therefore of utmost importance for controlling lethality and disease spreading. Currently available TB diagnostics can be broadly categorized into microscopy, culture-based, and molecular approaches, all of which come with compromised sensitivity, limited efficacy, and high expenses. Hence, rapid, sensitive, and affordable diagnostic methods for TB is the current prerequisite for disease management. This review summarizes the proteomics investigations for host-specific biomarkers from serum, sputum, saliva, and urine samples of TB patients, along with patients having comorbidity. Thorough data mining from available literature led us to conclude that the host-specific proteins involved in immunity and defense, metabolic regulation, cellular adhesion, and motility, inflammatory responses, and tissue remodelling have shown significant deregulation upon Mycobacterium tuberculosis (Mtb) infection. Notably, the immunoregulatory protein orosomucoid (ORM) was up-regulated in active TB compared to non-TB individuals, as observed in multiple studies from diverse sample types. Mannose receptor C type 2 (MRC2) was identified as an upregulated, treatment response biomarker in two independent serum proteomics investigations. Thorough mechanistic investigation on these candidate proteins would be fascinating to dig into potential drug targets and customized therapeutics for TB patients, along with their diagnostic potentials.
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Affiliation(s)
- Divya Pandey
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun 248007, Uttarakhand, India
| | - Dipanjana Ghosh
- School of Biomolecular Engineering & Biotechnology, Rajiv Gandhi Technological University, Airport Bypass Road, Bhopal 462033, India.
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Mousavian Z, Källenius G, Sundling C. From simple to complex: Protein-based biomarker discovery in tuberculosis. Eur J Immunol 2023; 53:e2350485. [PMID: 37740950 DOI: 10.1002/eji.202350485] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/15/2023] [Accepted: 09/22/2023] [Indexed: 09/25/2023]
Abstract
Tuberculosis (TB) is a deadly infectious disease that affects millions of people globally. TB proteomics signature discovery has been a rapidly growing area of research that aims to identify protein biomarkers for the early detection, diagnosis, and treatment monitoring of TB. In this review, we have highlighted recent advances in this field and how it is moving from the study of single proteins to high-throughput profiling and from only using proteomics to include additional types of data in multi-omics studies. We have further covered the different sample types and experimental technologies used in TB proteomics signature discovery, focusing on studies of HIV-negative adults. The published signatures were defined as either coming from hypothesis-based protein targeting or from unbiased discovery approaches. The methodological approaches influenced the type of proteins identified and were associated with the circulating protein abundance. However, both approaches largely identified proteins involved in similar biological pathways, including acute-phase responses and T-helper type 1 and type 17 responses. By analysing the frequency of proteins in the different signatures, we could also highlight potential robust biomarker candidates. Finally, we discuss the potential value of integration of multi-omics data and the importance of control cohorts and signature validation.
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Affiliation(s)
- Zaynab Mousavian
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Gunilla Källenius
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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3
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Khamchun S, Pongtussanahem O. Coronin-1A serves as a serum biomarker for supportive diagnosis of Mycobacterium tuberculosis infection. Germs 2023; 13:20-31. [PMID: 38023959 PMCID: PMC10659747 DOI: 10.18683/germs.2023.1363] [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: 05/08/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 12/01/2023]
Abstract
Introduction The severity and spread of tuberculosis, a major burden, can be prevented by more rapid and accurate laboratory diagnosis. The purpose of this study is to systematically explore candidate serum proteins in patients with Mycobacterium tuberculosis infection for further application as novel biomarkers. Methods Our study was performed in two major steps: screening of the literature for potential biomarkers, and then validation of their levels in patients and controls. Many serum/plasma proteins previously reported to be abnormally expressed in patients with tuberculosis between 2012 and 2021 were comprehensively assembled. The biological role in tuberculosis was also predicted for each using the bioinformatics tool STRING. Candidate proteins found to have the same expression in other related diseases were excluded. Subsequently, the serum level of the candidate serum/plasma protein that met the aforementioned criteria was validated by sandwich ELISA; diagnostic performance was analysed by the area under the curve (AUC) of the receiver operating characteristic (ROC). Results From 103 collected serum/plasma proteins, coronin-1A was found to have abnormal expression only in patients with tuberculosis and was associated with tuberculosis. In addition, the validation of coronin-1A in the serum of patients with pulmonary tuberculosis revealed a higher level than in that of healthy individuals. Furthermore, the area under the ROC curve for diagnostic power of coronin-1A was 0.866, with high sensitivity and specificity at a cut-point of approximately 52.7 ng/mL. Conclusions We concluded that the level of serum coronin-1A might serve as a novel biomarker for alternative laboratory examination to effectively distinguish patients with tuberculosis from those with other related diseases and healthy individuals.
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Affiliation(s)
- Supaporn Khamchun
- PhD, Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phaholyothin road, Phayao 56000, Thailand and Unit of Excellence in Cellular and Molecular Immunodiagnosis and Therapy, University of Phayao, Phaholyothin road, Phayao 56000, Thailand
| | - Orathai Pongtussanahem
- MSc, Laboratory of Medical Technology, Dokkhamtai Hospital, Dokkhamtai-Chaingmai road, Phayao 56000, Thailand
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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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Huang M, Ding Z, Li W, Chen W, Du Y, Jia H, Sun Q, Du B, Wei R, Xing A, Li Q, Chu N, Pan L. Identification of protein biomarkers in host cerebrospinal fluid for differential diagnosis of tuberculous meningitis and other meningitis. Front Neurol 2022; 13:886040. [PMID: 36003300 PMCID: PMC9393334 DOI: 10.3389/fneur.2022.886040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background and purpose The diagnosis of tuberculous meningitis (TBM) is difficult due to the lack of sensitive methods. Identification of TBM-specific biomarkers in the cerebrospinal fluid (CSF) may help diagnose and improve our understanding of TBM pathogenesis. Patients and methods Of the 112 suspected patients with TBM prospectively enrolled in the study, 32 patients with inconclusive diagnosis, non-infectious meningitis, and long-term treatment with hormones and immunosuppressants were excluded. The expression of 8 proteins in the CSF was analyzed using ELISA in 22 patients with definite TBM, 18 patients with probable TBM, and 40 patients with non-TBM. Results Significant differences in the expression of 7 proteins were detected between the TBM and non-TBM groups (P < 0.01). Unsupervised hierarchical clustering (UHC) analysis revealed a disease-specific profile consisting of 7 differentially expressed proteins for TBM diagnosis, with an accuracy of 82.5% (66/80). Logistic regression with forward stepwise analysis indicated that a combination of 3 biomarkers (APOE_APOAI_S100A8) showed a better ability to discriminate TBM from patients with non-TBM [area under the curve (AUC) = 0.916 (95%CI: 0.857–0.976)], with a sensitivity of 95.0% (95%CI: 83.1–99.4%) and a specificity of 77.5% (95%CI: 61.5–89.2%). Conclusion Our results confirmed the potential ability of CSF proteins to distinguish TBM from patients with non-TBM and provided a useful panel for the diagnosis of TBM.
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Affiliation(s)
- Mailing Huang
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zeyu Ding
- Neurology Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wensheng Li
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Emergency Medicine, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weibi Chen
- Neurology Department, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yadong Du
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongyan Jia
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Boping Du
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Rongrong Wei
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Aiying Xing
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Naihui Chu
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China
- Naihui Chu
| | - Liping Pan
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
- *Correspondence: Liping Pan
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Jin Y, Wang W, Wang Q, Zhang Y, Zahid KR, Raza U, Gong Y. Alpha-1-antichymotrypsin as a novel biomarker for diagnosis, prognosis, and therapy prediction in human diseases. Cancer Cell Int 2022; 22:156. [PMID: 35439996 PMCID: PMC9019971 DOI: 10.1186/s12935-022-02572-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
The glycoprotein alpha-1-antichymotrypsin (AACT), a serine protease inhibitor, is mainly synthesized in the liver and then secreted into the blood and is involved in the acute phase response, inflammation, and proteolysis. The dysregulation of AACT and its glycosylation levels are associated with tumor progression and recurrence, and could be used as a biomarker for tumor monitoring. In this review, we summarized the expression level, glycosylation modification, and biological characteristics of AACT during inflammation, neurodegenerative or other elderly diseases, and tumorigenesis, as well as, focused on the biological roles of AACT in cancer. The aberrant expression of AACT in cancer might be due to genetic alterations and/or immune by bioinformatics analysis. Moreover, AACT may serve as a diagnostic or prognostic biomarker or therapeutic target in tumors. Furthermore, we found that the expression of AACT was associated with the overall survival of patients with human cancers. Decreased AACT expression was associated with poor survival in patients with liver cancer, increased AACT expression was associated with shorter survival in patients with pancreatic cancer, and decreased AACT expression was associated with shorter survival in patients with early lung cancer. The review confirmed the key roles of AACT in tumorigenesis, suggesting that the glycoprotein AACT may serve as a biomarker for tumor diagnosis and prognosis, and could be a potential therapeutic target for human diseases.
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Affiliation(s)
- Yanxia Jin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Weidong Wang
- College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China.
| | - Qiyun Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Yueyang Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Kashif Rafiq Zahid
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), PWD Campus, Rawalpindi, Pakistan
| | - Yongsheng Gong
- Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, No.26 Daoqian Street, Suzhou, 215002, China.
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HaileMariam M, Yu Y, Singh H, Teklu T, Wondale B, Worku A, Zewude A, Mounaud S, Tsitrin T, Legesse M, Gobena A, Pieper R. Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort. Front Cell Infect Microbiol 2021; 11:595554. [PMID: 34150670 PMCID: PMC8212885 DOI: 10.3389/fcimb.2021.595554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 01/01/2023] Open
Abstract
Differential diagnosis of tuberculosis (TB) and latent TB infection (LTBI) remains a public health priority in high TB burden countries. Pulmonary TB is diagnosed by sputum smear microscopy, chest X-rays, and PCR tests for distinct Mycobacterium tuberculosis (Mtb) genes. Clinical tests to diagnose LTBI rely on immune cell stimulation in blood plasma with TB-specific antigens followed by measurements of interferon-γ concentrations. The latter is an important cytokine for cellular immune responses against Mtb in infected lung tissues. Sputum smear microscopy and chest X-rays are not sufficiently sensitive while both PCR and interferon-γ release assays are expensive. Alternative biomarkers for the development of diagnostic tests to discern TB disease states are desirable. This study's objective was to discover sputum diagnostic biomarker candidates from the analysis of samples from 161 human subjects including TB patients, individuals with LTBI, negative community controls (NCC) from the province South Omo, a pastoral region in Ethiopia. We analyzed 16S rRNA gene-based bacterial taxonomies and proteomic profiles. The sputum microbiota did not reveal statistically significant differences in α-diversity comparing the cohorts. The genus Mycobacterium, representing Mtb, was only identified for the TB group which also featured reduced abundance of the genus Rothia in comparison with the LTBI and NCC groups. Rothia is a respiratory tract commensal and may be sensitive to the inflammatory milieu generated by infection with Mtb. Proteomic data supported innate immune responses against the pathogen in subjects with pulmonary TB. Ferritin, an iron storage protein released by damaged host cells, was markedly increased in abundance in TB sputum compared to the LTBI and NCC groups, along with the α-1-acid glycoproteins ORM1 and ORM2. These proteins are acute phase reactants and inhibit excessive neutrophil activation. Proteomic data highlight the effector roles of neutrophils in the anti-Mtb response which was not observed for LTBI cases. Less abundant in the sputum of the LTBI group, compared to the NCC group, were two immunomodulatory proteins, mitochondrial TSPO and the extracellular ribonuclease T2. If validated, these proteins are of interest as new biomarkers for diagnosis of LTBI.
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Affiliation(s)
- Milkessa HaileMariam
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, United States
| | - Harinder Singh
- J. Craig Venter Institute, Rockville, MD, United States
| | - Takele Teklu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia
| | - Biniam Wondale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Adane Worku
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Tamara Tsitrin
- J. Craig Venter Institute, Rockville, MD, United States
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ameni Gobena
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Rembert Pieper
- J. Craig Venter Institute, Rockville, MD, United States
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8
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Garay-Baquero DJ, White CH, Walker NF, Tebruegge M, Schiff HF, Ugarte-Gil C, Morris-Jones S, Marshall BG, Manousopoulou A, Adamson J, Vallejo AF, Bielecka MK, Wilkinson RJ, Tezera LB, Woelk CH, Garbis SD, Elkington P. Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis. JCI Insight 2020; 5:137427. [PMID: 32780727 PMCID: PMC7526553 DOI: 10.1172/jci.insight.137427] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDTuberculosis (TB) kills more people than any other infection, and new diagnostic tests to identify active cases are required. We aimed to discover and verify novel markers for TB in nondepleted plasma.METHODSWe applied an optimized quantitative proteomics discovery methodology based on multidimensional and orthogonal liquid chromatographic separation combined with high-resolution mass spectrometry to study nondepleted plasma of 11 patients with active TB compared with 10 healthy controls. Prioritized candidates were verified in independent UK (n = 118) and South African cohorts (n = 203).RESULTSWe generated the most comprehensive TB plasma proteome to date, profiling 5022 proteins spanning 11 orders-of-magnitude concentration range with diverse biochemical and molecular properties. We analyzed the predominantly low-molecular weight subproteome, identifying 46 proteins with significantly increased and 90 with decreased abundance (peptide FDR ≤ 1%, q ≤ 0.05). Verification was performed for novel candidate biomarkers (CFHR5, ILF2) in 2 independent cohorts. Receiver operating characteristics analyses using a 5-protein panel (CFHR5, LRG1, CRP, LBP, and SAA1) exhibited discriminatory power in distinguishing TB from other respiratory diseases (AUC = 0.81).CONCLUSIONWe report the most comprehensive TB plasma proteome to date, identifying novel markers with verification in 2 independent cohorts, leading to a 5-protein biosignature with potential to improve TB diagnosis. With further development, these biomarkers have potential as a diagnostic triage test.FUNDINGColciencias, Medical Research Council, Innovate UK, NIHR, Academy of Medical Sciences, Program for Advanced Research Capacities for AIDS, Wellcome Centre for Infectious Diseases Research.
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Affiliation(s)
- Diana J Garay-Baquero
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA
| | - Cory H White
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Naomi F Walker
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Tebruegge
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom.,Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Hannah F Schiff
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Cesar Ugarte-Gil
- TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Instituto de Medicina Tropical Alexander von Humboldt, School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stephen Morris-Jones
- Department of Microbiology, University College London Hospitals NHS Trust, London, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben G Marshall
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
| | | | - John Adamson
- Pharmacology Core, Africa Health Research Institute (AHRI), Durban, South Africa
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | | | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Liku B Tezera
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Spiros D Garbis
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA.,Cancer Sciences Division, Faculty of Medicine, University of Southampton, United Kingdom
| | - Paul Elkington
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
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9
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Li K, Ran R, Jiang Z, Fan C, Li T, Yin Z. Changes in T-lymphocyte subsets and risk factors in human immunodeficiency virus-negative patients with active tuberculosis. Infection 2020; 48:585-595. [PMID: 32472529 PMCID: PMC7395032 DOI: 10.1007/s15010-020-01451-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/21/2020] [Indexed: 11/08/2022]
Abstract
Purpose Immune function imbalance is closely associated with the occurrence and development of infectious diseases. We studied the characteristics of changes in T-lymphocyte subsets and their risk factors in HIV-negative patients with active tuberculosis (ATB). Methods T-lymphocyte subsets in 275 HIV-negative ATB patients were quantitatively analyzed and compared with an Mycobacteriumtuberculosis-free control group. Single-factor and multifactor analyses of clinical and laboratory characteristics of patients were also conducted. Results In ATB patients, CD4 and CD8 T-cell counts decreased, and the levels were positively interrelated (r = 0.655, P < 0.0001). After 4 weeks of antituberculosis treatment, CD4 and CD8 T-cell counts increased significantly but remained lower than in the control group. CD4 and CD8 cell counts were negatively associated with the extent of lesions detected in the chest by computed tomography (all P < 0.05). Although not reflected in the CD4/CD8 ratio, CD4 and CD8 cell counts differed between drug-resistant TB patients and drug-susceptible TB patients (P = 0.030). The multivariate analysis showed prealbumin, alpha-1 globulin, body mass index, and platelet count were independent risk factors for decreased CD4 cell count (all P < 0.05), while age and platelet count were independent risk factors for decreased CD8 cell count (all P < 0.05). Conclusion CD4 and CD8 T-cell counts showed the evident value in predicting ATB severity. An increase in the CD4/CD8 ratio may be a critical clue of drug resistance in ATB. Although the factors influencing CD4 and CD8 are not identical, our results indicated the importance of serum protein and platelets to ATB patients’ immune function. Electronic supplementary material The online version of this article (10.1007/s15010-020-01451-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kui Li
- Department of Infectious Diseases, Ankang Central Hospital, Ankang, Shaanxi, China.,Department of Infectious Diseases, Ankang Central Hospital, Hubei University of Medicine, Hubei, China
| | - Renyu Ran
- Department of Infectious Diseases, Ankang Central Hospital, Ankang, Shaanxi, China
| | - Zicheng Jiang
- Department of Infectious Diseases, Ankang Central Hospital, Ankang, Shaanxi, China.,Department of Infectious Diseases, Ankang Central Hospital, Hubei University of Medicine, Hubei, China
| | - Chuanqi Fan
- Department of Infectious Diseases, Ankang Central Hospital, Ankang, Shaanxi, China
| | - Tao Li
- Department of Infectious Diseases, Ankang Central Hospital, Ankang, Shaanxi, China
| | - Zhiguo Yin
- Department of Pharmacy, Ankang Central Hospital, No. 85, South Jinzhou Road, Hanbin District, Ankang, 725000, Shaanxi, China.
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10
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Bisht D, Sharma D, Sharma D, Singh R, Gupta VK. Recent insights intoMycobacterium tuberculosisthrough proteomics and implications for the clinic. Expert Rev Proteomics 2019; 16:443-456. [DOI: 10.1080/14789450.2019.1608185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
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11
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Chen Y, Huang A, Ao W, Wang Z, Yuan J, Song Q, Wei D, Ye H. Proteomic analysis of serum proteins from HIV/AIDS patients with Talaromyces marneffei infection by TMT labeling-based quantitative proteomics. Clin Proteomics 2018; 15:40. [PMID: 30598657 PMCID: PMC6302400 DOI: 10.1186/s12014-018-9219-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Talaromyces marneffei (TM) is an emerging pathogenic fungus that can cause a fatal systemic mycosis in patients infected with human immunodeficiency virus (HIV). Although global awareness regarding HIV/TM coinfection is increasing little is known about the mechanism that mediates the rapid progression to HIV/AIDS disease in coinfected individuals. The aim of this study was to analyze the serum proteome of HIV/TM coinfected patients and to identify the associated protein biomarkers for TM in patients with HIV/AIDS. METHODS We systematically used multiplexed isobaric tandem mass tag labeling combined with liquid chromatography mass spectrometry (LC-MS/MS) to screen for differentially expressed proteins in the serum samples from HIV/TM-coinfected patients. RESULTS Of a total data set that included 1099 identified proteins, approximately 86% of the identified proteins were quantified. Among them, 123 proteins were at least 1.5-fold up-or downregulated in the serum between HIV/TM-coinfected and HIV-mono-infected patients. Furthermore, our results indicate that two selected proteins (IL1RL1 and THBS1) are potential biomarkers for distinguishing HIV/TM-coinfected patients. CONCLUSIONS This is the first report to provide a global proteomic profile of serum samples from HIV/TM-coinfected patients. Our data provide insights into the proteins that are involved as host response factors during infection. These data shed new light on the molecular mechanisms that are dysregulated and contribute to the pathogenesis of HIV/TM coinfection. IL1RL1 and THBS1 are promising diagnostic markers for HIV/TM-coinfected patients although further large-scale studies are needed. Thus, quantitative proteomic analysis revealed molecular differences between the HIV/TM-coinfected and HIV-mono-infected individuals, and might provide fundamental information for further detailed investigations.
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Affiliation(s)
- Yahong Chen
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
| | - Aiqiong Huang
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
| | - Wen Ao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
| | - Zhengwu Wang
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
| | - Jinjin Yuan
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
| | - Qing Song
- Shanxi Institute of Flexible Electronics, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 People’s Republic of China
| | - Dahai Wei
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- The First Affiliated Hospital of Jiaxing University, 1882 Zhonghuan Road, Jiaxing, 314001 People’s Republic of China
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025 People’s Republic of China
| | - Hanhui Ye
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
- Fuzhou Infectious Disease Hospital, Fujian Medical University, 312 Xihong Road, Fuzhou, 350025 Fujian Province People’s Republic of China
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12
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Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis (Edinb) 2018; 112:52-61. [PMID: 30205969 PMCID: PMC6181582 DOI: 10.1016/j.tube.2018.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/22/2023]
Abstract
Rationale: The monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. Objective: We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Methods: Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. Results: A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status. Conclusion: A comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care.
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Affiliation(s)
- Komal Kedia
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason P Wendler
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Leah G Jarsberg
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kelly G Stratton
- Computational and Statistical Analysis Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aaron T Wright
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | | | - Marc H Weiner
- University of Texas Health Science Center at San Antonio and the South Texas VAMC, San Antonio, TX, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
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13
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Sun H, Pan L, Jia H, Zhang Z, Gao M, Huang M, Wang J, Sun Q, Wei R, Du B, Xing A, Zhang Z. Label-Free Quantitative Proteomics Identifies Novel Plasma Biomarkers for Distinguishing Pulmonary Tuberculosis and Latent Infection. Front Microbiol 2018; 9:1267. [PMID: 29951049 PMCID: PMC6008387 DOI: 10.3389/fmicb.2018.01267] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
The lack of effective differential diagnostic methods for active tuberculosis (TB) and latent infection (LTBI) is still an obstacle for TB control. Furthermore, the molecular mechanism behind the progression from LTBI to active TB has been not elucidated. Therefore, we performed label-free quantitative proteomics to identify plasma biomarkers for discriminating pulmonary TB (PTB) from LTBI. A total of 31 overlapping proteins with significant difference in expression level were identified in PTB patients (n = 15), compared with LTBI individuals (n = 15) and healthy controls (HCs, n = 15). Eight differentially expressed proteins were verified using western blot analysis, which was 100% consistent with the proteomics results. Statistically significant differences of six proteins were further validated in the PTB group compared with the LTBI and HC groups in the training set (n = 240), using ELISA. Classification and regression tree (CART) analysis was employed to determine the ideal protein combination for discriminating PTB from LTBI and HC. A diagnostic model consisting of alpha-1-antichymotrypsin (ACT), alpha-1-acid glycoprotein 1 (AGP1), and E-cadherin (CDH1) was established and presented a sensitivity of 81.2% (69/85) and a specificity of 95.2% (80/84) in discriminating PTB from LTBI, and a sensitivity of 81.2% (69/85) and a specificity of 90.1% (64/81) in discriminating PTB from HCs. Additional validation was performed by evaluating the diagnostic model in blind testing set (n = 113), which yielded a sensitivity of 75.0% (21/28) and specificity of 96.1% (25/26) in PTB vs. LTBI, 75.0% (21/28) and 92.3% (24/26) in PTB vs. HCs, and 75.0% (21/28) and 81.8% (27/33) in PTB vs. lung cancer (LC), respectively. This study obtained the plasma proteomic profiles of different M.TB infection statuses, which contribute to a better understanding of the pathogenesis involved in the transition from latent infection to TB activation and provide new potential diagnostic biomarkers for distinguishing PTB and LTBI.
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Affiliation(s)
- Huishan Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zhiguo Zhang
- Changping Tuberculosis Prevent and Control Institute of Beijing, Beijing, China
| | - Mengqiu Gao
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Mailing Huang
- Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Rongrong Wei
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Boping Du
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Aiying Xing
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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14
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Muthu M, Deenadayalan A, Ramachandran D, Paul D, Gopal J, Chun S. A state-of-art review on the agility of quantitative proteomics in tuberculosis research. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Determination of dehydroepiandrosterone and its biologically active oxygenated metabolites in human plasma evinces a hormonal imbalance during HIV-TB coinfection. Sci Rep 2018; 8:6692. [PMID: 29703963 PMCID: PMC5923237 DOI: 10.1038/s41598-018-24771-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022] Open
Abstract
An estimated one third of the world's population is affected by latent tuberculosis (TB), which once active represents a leading cause of death among infectious diseases. Human immunodeficiency virus (HIV) infection is a main predisposing factor to TB reactivation. Individuals HIV-TB co-infected develop a chronic state of inflammation associated with hypothalamic-pituitary-adrenal (HPA) axis dysregulation. This results in a hormonal imbalance, disturbing the physiological levels of cortisol and dehydroepiandrosterone (DHEA). DHEA and its oxygenated metabolites androstenediol (AED), androstenetriol (AET) and 7-oxo-DHEA are immunomodulatory compounds that may regulate physiopathology in HIV-TB co-infection. In order to study possible changes in plasma levels of these hormones, we developed an approach based on high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). To our knowledge, this represents the first report of their simultaneous measurement in HIV-TB individuals and the comparison with healthy donors, obtaining statistically higher plasma levels of DHEA, AET and 7-oxo-DHEA in patients. Moreover, we found that concentrations of 7-oxo-DHEA positively correlated with absolute CD4+ T cell counts, nadir CD4+ T cell values and with individuals who presented TB restricted to the lungs. This research contributes to understanding the role of these hormones in HIV-TB and emphasizes the importance of deepening their study in this context.
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16
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Chen C, Yan T, Liu L, Wang J, Jin Q. Identification of a Novel Serum Biomarker for Tuberculosis Infection in Chinese HIV Patients by iTRAQ-Based Quantitative Proteomics. Front Microbiol 2018. [PMID: 29535695 PMCID: PMC5834467 DOI: 10.3389/fmicb.2018.00330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tuberculosis (TB) is a major comorbidity in HIV patients as well as a serious co-epidemic. Traditional detection methods are not effective or sensitive for the detection of Mycobacterium tuberculosis at the early stage. TB has become a major cause of lethal on HIV patients. We employed isobaric tags for relative and absolute quantitation (iTRAQ) technology to identify the different host responses in HIV-noTB and HIV-TB patients’ sera. Given the diversity of HIV subtypes, which results in a variety of host responses in different human populations, we focused on the Chinese patients. Of the 25 proteins identified, 7 were increased and 18 were decreased in HIV-TB co-infected patients. These proteins were found to be involved in host immune response processes. We identified a candidate protein, endoglin (ENG), which showed an 4.9 times increase by iTRAQ and 11.5 times increase by ELISA. ENG demonstrated the diagnostic efficacy and presented a novel molecular biomarker for TB in HIV-infected Chinese patients. This study provides new insight into the challenges in the diagnosis and effective management of patients with HIV-TB.
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Affiliation(s)
- Cong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Yan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianmin Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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17
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López-Hernández Y, Patiño-Rodríguez O, García-Orta ST, Pinos-Rodríguez JM. Mass spectrometry applied to the identification of Mycobacterium tuberculosis and biomarker discovery. J Appl Microbiol 2017; 121:1485-1497. [PMID: 27718305 DOI: 10.1111/jam.13323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/28/2016] [Accepted: 08/08/2016] [Indexed: 12/31/2022]
Abstract
An adequate and effective tuberculosis (TB) diagnosis system has been identified by the World Health Organization as a priority in the fight against this disease. Over the years, several methods have been developed to identify the bacillus, but bacterial culture remains one of the most affordable methods for most countries. For rapid and accurate identification, however, it is more feasible to implement molecular techniques, taking advantage of the availability of public databases containing protein sequences. Mass spectrometry (MS) has become an interesting technique for the identification of TB. Here, we review some of the most widely employed methods for identifying Mycobacterium tuberculosis and present an update on MS applied for the identification of mycobacterial species.
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Affiliation(s)
| | - O Patiño-Rodríguez
- CONACyT, Centro de Desarrollo de Productos Bióticos del Instituto Politécnico Nacional, Morelos, México
| | - S T García-Orta
- Centro de Biociencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J M Pinos-Rodríguez
- Centro de Biociencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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18
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Souza GHMF, Guest PC, Martins-de-Souza D. LC-MS E, Multiplex MS/MS, Ion Mobility, and Label-Free Quantitation in Clinical Proteomics. Methods Mol Biol 2017; 1546:57-73. [PMID: 27896757 DOI: 10.1007/978-1-4939-6730-8_4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MSE (HDMSE and UDMSE) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC). Label free UPLC-HDMSE is less expensive than labeled-based quantitative proteomics and has no limits regarding the number of samples that can be analyzed and compared, which is an important requirement for supporting clinical applications.
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Affiliation(s)
- Gustavo Henrique Martins Ferreira Souza
- Mass Spectrometry Applications & Development Laboratory, Waters Corporation, 125, Alphaville Industrial, Barueri, 06455-020, Campinas, São Paulo, SP, Brazil.
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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19
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Haas CT, Roe JK, Pollara G, Mehta M, Noursadeghi M. Diagnostic 'omics' for active tuberculosis. BMC Med 2016; 14:37. [PMID: 27005907 PMCID: PMC4804573 DOI: 10.1186/s12916-016-0583-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022] Open
Abstract
The decision to treat active tuberculosis (TB) is dependent on microbiological tests for the organism or evidence of disease compatible with TB in people with a high demographic risk of exposure. The tuberculin skin test and peripheral blood interferon-γ release assays do not distinguish active TB from a cleared or latent infection. Microbiological culture of mycobacteria is slow. Moreover, the sensitivities of culture and microscopy for acid-fast bacilli and nucleic acid detection by PCR are often compromised by difficulty in obtaining samples from the site of disease. Consequently, we need sensitive and rapid tests for easily obtained clinical samples, which can be deployed to assess patients exposed to TB, discriminate TB from other infectious, inflammatory or autoimmune diseases, and to identify subclinical TB in HIV-1 infected patients prior to commencing antiretroviral therapy. We discuss the evaluation of peripheral blood transcriptomics, proteomics and metabolomics to develop the next generation of rapid diagnostics for active TB. We catalogue the studies published to date seeking to discriminate active TB from healthy volunteers, patients with latent infection and those with other diseases. We identify the limitations of these studies and the barriers to their adoption in clinical practice. In so doing, we aim to develop a framework to guide our approach to discovery and development of diagnostic biomarkers for active TB.
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Affiliation(s)
- Carolin T Haas
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Jennifer K Roe
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Meera Mehta
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK.
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20
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Achkar JM, Cortes L, Croteau P, Yanofsky C, Mentinova M, Rajotte I, Schirm M, Zhou Y, Junqueira-Kipnis AP, Kasprowicz VO, Larsen M, Allard R, Hunter J, Paramithiotis E. Host Protein Biomarkers Identify Active Tuberculosis in HIV Uninfected and Co-infected Individuals. EBioMedicine 2015; 2:1160-8. [PMID: 26501113 PMCID: PMC4588417 DOI: 10.1016/j.ebiom.2015.07.039] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 01/28/2023] Open
Abstract
Biomarkers for active tuberculosis (TB) are urgently needed to improve rapid TB diagnosis. The objective of this study was to identify serum protein expression changes associated with TB but not latent Mycobacterium tuberculosis infection (LTBI), uninfected states, or respiratory diseases other than TB (ORD). Serum samples from 209 HIV uninfected (HIV−) and co-infected (HIV+) individuals were studied. In the discovery phase samples were analyzed via liquid chromatography and mass spectrometry, and in the verification phase biologically independent samples were analyzed via a multiplex multiple reaction monitoring mass spectrometry (MRM-MS) assay. Compared to LTBI and ORD, host proteins were significantly differentially expressed in TB, and involved in the immune response, tissue repair, and lipid metabolism. Biomarker panels whose composition differed according to HIV status, and consisted of 8 host proteins in HIV− individuals (CD14, SEPP1, SELL, TNXB, LUM, PEPD, QSOX1, COMP, APOC1), or 10 host proteins in HIV+ individuals (CD14, SEPP1, PGLYRP2, PFN1, VASN, CPN2, TAGLN2, IGFBP6), respectively, distinguished TB from ORD with excellent accuracy (AUC = 0.96 for HIV− TB, 0.95 for HIV+ TB). These results warrant validation in larger studies but provide promise that host protein biomarkers could be the basis for a rapid, blood-based test for TB. Active tuberculosis leads to the differential expression of serum proteins involved in associated host processes. Serum protein expression changes in tuberculosis involve the immune response, tissue repair, and lipid metabolism. Panels of 8–10 host proteins can distinguish active tuberculosis from latent infection, and other respiratory diseases.
Accurate biomarkers for active tuberculosis (TB) are urgently needed to improve rapid diagnosis. Current diagnostics for TB rely on microbiologic or molecular confirmation of M. tuberculosis, and are therefore dependent on a specimen from the site of disease which is not always accessible. This study demonstrates that human host proteins are differentially expressed in TB compared to latent M. tuberculosis infection, or respiratory diseases other than TB. Our data thus provide promise that host proteins have the potential to become the basis of rapid blood tests that do not require a sample from the site of disease.
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Affiliation(s)
- Jacqueline M Achkar
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Laetitia Cortes
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Pascal Croteau
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Corey Yanofsky
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Marija Mentinova
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Isabelle Rajotte
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Michael Schirm
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Yiyong Zhou
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Ana Paula Junqueira-Kipnis
- Department of Microbiology, Immunology, Parasitology and Pathology, Public Health and Tropical Medicine Institute, Federal University of Goias, Rua 235 esq. Primeira avenida, Goiania, Goias, 74605-050, Brazil
| | - Victoria O Kasprowicz
- KwaZulu-Natal Research Institute for TB HIV (K-RITH), KwaZulu-Natal, Durban, South Africa ; The Ragon Institute of MGH, MIT and Harvard, Charlestown, Boston, USA ; HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Larsen
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - René Allard
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
| | - Joanna Hunter
- Caprion Proteomics Inc., 201 President-Kennedy Ave., Montreal H2X 3Y7, Quebec, Canada
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Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment. PLoS One 2015. [PMID: 26214306 PMCID: PMC4516286 DOI: 10.1371/journal.pone.0134168] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Biomarkers for determining clearance of Mycobacterium tuberculosis (Mtb) infection during anti-tuberculosis therapy or following exposure could facilitate enhanced monitoring and treatment. We screened for biomarkers indicating clearance of Mtb infection in vitro. A comparative proteomic analysis was performed using GeLC MSI/MS. Intracellular and secreted proteomes from activated THP-1 cells infected with the Mtb H37Rv strain (MOI = 1) and treated with isoniazid and rifampicin for 1 day (infection stage) and 5 days (clearance stage) were analyzed. Host proteins associated with early infection (n = 82), clearance (n = 121), sustained in both conditions (n = 34) and suppressed by infection (n = 46) were elucidated. Of the potential clearance markers, SSFA2 and CAECAM18 showed the highest and lowest protein intensities, respectively. A western blot of CAECAM18 validated the LC MS/MS result. For three clearance markers (SSFA2, PARP14 and PSME4), in vivo clinical validation was concordantly reported in previous patient cohorts. A network analysis revealed that clearance markers were enriched amongst four protein interaction networks centered on: (i) CD44/CCND1, (ii) IFN-β1/NF-κB, (iii) TP53/TGF-β and (iv) IFN-γ/CCL2. After infection, proteins associated with proliferation, and recruitment of immune cells appeared to be enriched possibly reflecting recruitment of defense mechanisms. Counteracting proteins (CASP3 vs. Akt and NF-κB vs. TP53) associated with apoptosis regulation and its networks were enriched among the early and sustained infection biomarkers, indicating host-pathogen competition. The BRCA1/2 network was suppressed during infection, suggesting that cell proliferation suppression is a feature of Mtb survival. Our study provides insights into the mechanisms of host-Mtb interaction by comparing the stages of infection clearance. The identified clearance biomarkers may be useful in monitoring tuberculosis treatment.
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