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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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Park HE, Park JS, Park HT, Shin JI, Kim KM, Park SR, Choi JG, Jung M, Kang HL, Baik SC, Lee WK, Yoo HS, Shin MK. Fetuin as a potential serum biomarker to detect subclinical shedder of bovine paratuberculosis. Microb Pathog 2022; 169:105675. [PMID: 35820578 DOI: 10.1016/j.micpath.2022.105675] [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: 03/14/2022] [Revised: 06/25/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
Paratuberculosis (PTB) is a chronic contagious granulomatous enteritis of wild and domestic ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). PTB causes considerable economic losses to the dairy industry through decreased milk production and premature culling. PTB-affected cattle undergo a subclinical stage without clinical signs and initiate fecal shedding of MAP into the environment. Current diagnostic tools have low sensitivity for the detection of subclinical PTB infection. Therefore, alternative diagnostic tools are required to improve the diagnostic sensitivity of subclinical PTB infection. In this study, we performed ELISA for three previously identified host biomarkers (fetuin, alpha-1-acid glycoprotein, and apolipoprotein) and analyzed their diagnostic performance with conventional PTB diagnostic methods. We observed that serum fetuin levels were significantly lowered in the subclinical shedder and clinical shedder groups than in the healthy control group, indicating its potential utility as a diagnostic biomarker for bovine PTB. Also, fetuin showed an excellent discriminatory power with an AUC = 0.949, a sensitivity of 92.6%, and a specificity of 94.4% for the detection of subclinical MAP infection. In conclusion, our results demonstrated that fetuin could be used as a diagnostic biomarker for enhancing the diagnostic sensitivity for the detection of subclinical MAP infections that are difficult to detect based on current diagnostic methods.
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Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jin-Sik Park
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Hong-Tae Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jeong-Ih Shin
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Kyu-Min Kim
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Seo-Rin Park
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Jeong-Gyu Choi
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Myunghwan Jung
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Hyung-Lyun Kang
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Seung-Chul Baik
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Woo-Kon Lee
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea; BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
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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: 2] [Impact Index Per Article: 1.0] [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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Teklu T, Wondale B, Taye B, Hailemariam M, Bekele S, Tamirat M, Zewude A, Mohamed T, Medhin G, Legesse M, Yu Y, Ameni G, Pieper R. Differences in plasma proteomes for active tuberculosis, latent tuberculosis and non-tuberculosis mycobacterial lung disease patients with and without ESAT-6/CFP10 stimulation. Proteome Sci 2020; 18:10. [PMID: 33292280 PMCID: PMC7603755 DOI: 10.1186/s12953-020-00165-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is one of the world's most problematic infectious diseases. The pathogen Mycobacterium tuberculosis (Mtb) is contained by the immune system in people with latent TB infection (LTBI). No overt disease symptoms occur. The environmental and internal triggers leading to reactivation of TB are not well understood. Non-tuberculosis Mycobacteria (NTM) can also cause TB-like lung disease. Comparative analysis of blood plasma proteomes from subjects afflicted by these pathologies in an endemic setting may yield new differentiating biomarkers and insights into inflammatory and immunological responses to Mtb and NTM. METHODS Blood samples from 40 human subjects in a pastoral region of Ethiopia were treated with the ESAT-6/CFP-10 antigen cocktail to stimulate anti-Mtb and anti-NTM immune responses. In addition to those of active TB, LTBI, and NTM cohorts, samples from matched healthy control (HC) subjects were available. Following the generation of sample pools, proteomes were analyzed via LC-MS/MS. These experiments were also performed without antigen stimulation steps. Statistically significant differences using the Z-score method were determined and interpreted in the context of the proteins' functions and their contributions to biological pathways. RESULTS More than 200 proteins were identified from unstimulated and stimulated plasma samples (UPSs and SPSs, respectively). Thirty-four and 64 proteins were differentially abundant with statistical significance (P < 0.05; Benjamini-Hochberg correction with an FDR < 0.05) comparing UPS and SPS proteomic data of four groups, respectively. Bioinformatics analysis of such proteins via the Gene Ontology Resource was indicative of changes in cellular and metabolic processes, responses to stimuli, and biological regulations. The m7GpppN-mRNA hydrolase was increased in abundance in the LTBI group compared to HC subjects. Charged multivesicular body protein 4a and platelet factor-4 were increased in abundance in NTM as compared to HC and decreased in abundance in NTM as compared to active TB. C-reactive protein, α-1-acid glycoprotein 1, sialic acid-binding Ig-like lectin 16, and vitamin K-dependent protein S were also increased (P < 0.05; fold changes≥2) in SPSs and UPSs comparing active TB with LTBI and NTM cases. These three proteins, connected in a STRING functional network, contribute to the acute phase response and influence blood coagulation. CONCLUSION Plasma proteomes are different comparing LTBI, TB, NTM and HC cohorts. The changes are augmented following prior blood immune cell stimulation with the ESAT-6/CFP-10 antigen cocktail. The results encourage larger-cohort studies to identify specific biomarkers to diagnose NTM infection, LTBI, and to predict the risk of TB reactivation.
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Affiliation(s)
- Takele Teklu
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia.
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Biniam Wondale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Biruhalem Taye
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- European Molecular Biology Laboratory, Notkestraβe 85, 22607, Hamburg, Germany
| | | | | | - Mesfin Tamirat
- Laboratory department, Jinka General Hospital, Jinka, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public health Institute, P.O box 1242, Addis Ababa, Ethiopia
| | - Temesgen Mohamed
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, USA
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
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Babele P, Verma S, Kumar RB, Bhagyawant SS, Kamboj DV, Alam SI. Elucidation of protein biomarkers in plasma and urine for epsilon toxin exposure in mouse model. Anaerobe 2019; 59:76-91. [PMID: 31145997 DOI: 10.1016/j.anaerobe.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023]
Abstract
Epsilon toxin (ETX) is the major virulence determinant of C. perfringens type B or type D strains, causing diseases in animals, besides being a listed biological and toxin warfare (BTW) agent. Keeping in mind the high lethality and the rapid onset of clinical manifestations, early diagnosis of epsilon toxin exposure is of paramount importance for implementation of appropriate medical countermeasures. Using a 2DE-MS approach, the present study is the first comprehensive proteomic elucidation of ETX-induced protein markers in the mouse model, providing putative targets for early diagnosis of ETX exposure. A total of 52 unique proteins showing ETX-induced modulations were identified in plasma and urine samples. Fibrinogen, apolipoprotein, serum amyloid protein, plasminogen, serum albumin, glutathione peroxidase, transferrin, major urinary protein 2, haptoglobin, transthyretin, and vitamin D-binding protein were among the proteins observed in more than one dataset with altered abundance after the ETX-intoxication. The predicted localization, function, and interaction of the ETX-modulated proteins in the plasma and urine indicated involvement of multiple pathways; extracellular proteins, followed by macromolecular complexes associated with blood coagulation and plasminogen activating cascade, being the most prominent among others. The putative markers elucidated here warrants further validation and can be of immense value for the early diagnosis of ETX exposure.
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Affiliation(s)
- Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Smarti Verma
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | | | - Dev Vrat Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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6
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Stabel JR, Reinhardt TA, Hempel RJ. Short communication: Vitamin D status and responses in dairy cows naturally infected with Mycobacterium avium ssp. paratuberculosis. J Dairy Sci 2018; 102:1594-1600. [PMID: 30594355 DOI: 10.3168/jds.2018-15241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/26/2018] [Indexed: 01/15/2023]
Abstract
Serum samples were obtained from Holstein dairy control cows and cows naturally infected with Mycobacterium avium ssp. paratuberculosis (MAP) to evaluate the effects of disease status on serum 25-hydroxyvitamin D3 (25OHD3) levels. Disease status was stratified for infected cows into asymptomatic, subclinical infection (n = 25), and cows demonstrating clinical signs (n = 20), along with noninfected control (n = 12) cows for comparison. In addition, portions of the ileocecal valve were taken from a subsample of cows (n = 5 per treatment group) at necropsy and processed for RNA sequencing gene transcription studies. Genes associated with vitamin D metabolism were queried to determine any association between infection and gene expression. Serum 25OHD3 levels were significantly lower in cows in the clinical stage of disease compared with either cows in the subclinical stage and noninfected control cows. Differential expression for genes associated with the vitamin D pathway such as CYP27A1, CYP27B1, vitamin D-binding protein (DBP), and IFNG was dependent upon infection status. An upregulation of CYP27A1 was noted for cows in subclinical status, whereas CYP27B1 expression was enhanced for clinical cows. Increased expression of vitamin D-binding protein was observed for infected cattle, regardless of infection status. In summary, decreases in circulating 25OHD3 for animals with clinical disease may suggest that these cows have reduced innate immune responses, thereby influencing the ability of animals to fight infection.
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Affiliation(s)
- J R Stabel
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA 50010.
| | - T A Reinhardt
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA 50010
| | - R J Hempel
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA 50010
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7
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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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8
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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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9
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Bahr NC, Halupnick R, Linder G, Kiggundu R, Nabeta HW, Williams DA, Musubire AK, Morawski BM, Sreevatsan S, Meya DB, Rhein J, Boulware DR. Delta-like 1 protein, vitamin D binding protein and fetuin for detection of Mycobacterium tuberculosis meningitis. Biomark Med 2018; 12:707-716. [PMID: 29856234 DOI: 10.2217/bmm-2017-0373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AIM Tuberculosis meningitis (TBM) diagnosis is difficult, new biomarkers are needed. We evaluated the diagnostic utility of delta-like 1 protein (DLL1), vitamin D binding protein (VDBP) and fetuin. METHODS Biomarker concentrations were measured by ELISA in cryopreserved cerebrospinal fluid from 139 HIV-infected Ugandans with suspected meningitis. TBM was diagnosed by GeneXpert MTB/Rif or culture. Cohort diagnoses included TBM (n = 22), cryptococcal (n = 71), or aseptic meningitis (n = 16) and no meningitis (n = 30). RESULTS DLL1 (cut-off value 1150 pg/ml) provided 32% sensitivity and 98% specificity. Adding fetuin, cryptococcal antigen and IFN-γ resulted in sensitivities of 36, 63 and 76% with specificities of 98, 90 and 92%, respectively. VDBP (cut-off value 2.0 μg/ml) provided 81% sensitivity and 68% specificity while fetuin (cut-off value 2 μg/ml) provided a sensitivity of 86% and specificity of 68%. CONCLUSION CSF DLL1, VDBP and fetuin exhibited fair diagnostic performance for TBM diagnosis.
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Affiliation(s)
- Nathan C Bahr
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.,Infectious Diseases Institute, Makerere University, Kampala, Uganda.,Department of Medicine, Division of Infectious Diseases, University of Kansas, Kansas City, KS 66160, USA
| | - Ryan Halupnick
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Grace Linder
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben Kiggundu
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Henry W Nabeta
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Darlisha A Williams
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.,Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Abdu K Musubire
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Bozena M Morawski
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - David B Meya
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.,Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Joshua Rhein
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.,Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - David R Boulware
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
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Identification of potential urine proteins and microRNA biomarkers for the diagnosis of pulmonary tuberculosis patients. Emerg Microbes Infect 2018; 7:63. [PMID: 29636444 PMCID: PMC5893550 DOI: 10.1038/s41426-018-0066-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/23/2018] [Accepted: 03/02/2018] [Indexed: 12/31/2022]
Abstract
This study identified urinary biomarkers for tuberculosis (TB) diagnosis. The urine proteomic profiles of 45 pulmonary tuberculosis patients prior to anti-TB treatment and 45 healthy controls were analyzed and compared using two-dimensional electrophoresis with matrix-assisted laser desorption/ionization time of flight mass spectrometry. Nineteen differentially expressed proteins were identified preliminarily, and western blotting and qRT-PCR were performed to confirm these changes at the translational and transcriptional levels, respectively, using samples from 122 additional pulmonary tuberculosis patients and 73 additional healthy controls. Two proteins, mannose-binding lectin 2 and a 35-kDa fragment of inter-α-trypsin inhibitor H4, exhibited the highest differential expression. We constructed a protein-microRNA interaction network that primarily involved complement and inflammatory responses. Eleven microRNAs from microRNA-target protein interactions were screened and validated using qRT-PCR with some of the above samples, including 97 pulmonary tuberculosis patients and 48 healthy controls. Only miR-625-3p exhibited significant differential expression (p < 0.05). miR-625-3p was increased to a greater extent in samples of smear-positive than smear-negative patients. miR-625-3p was predicted to target mannose-binding lectin 2 protein. A binary logistic regression model based on miR-625-3p, mannose-binding lectin 2, and inter-α-trypsin inhibitor H4 was further established. This three-biomarker combination exhibited better performance for tuberculosis diagnosis than individual biomarkers or any two-biomarker combination and generated a diagnostic sensitivity of 85.87% and a specificity of 87.50%. These novel urine biomarkers may significantly improve tuberculosis diagnosis.
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11
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Parker WA, Mchiza ZJ, Sewpaul R, Job N, Chola L, Sithole M, Labadarios D. The impact of sociodemography, diet, and body size on serum retinol in women 16-35 years of age: SANHANES-1. Ann N Y Acad Sci 2017; 1416:48-65. [PMID: 29125179 DOI: 10.1111/nyas.13504] [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: 05/31/2017] [Revised: 08/25/2017] [Accepted: 09/04/2017] [Indexed: 11/30/2022]
Abstract
To determine the current vitamin A status of a nationally representative sample of women aged 16-35 years, compare it with previous national data, and determine the impact of sociodemography, diet, and body size on vitamin A status, we performed secondary analysis of data on South African women who participated in the first South African National Health and Nutrition Examination Survey (SANHANES-1). Vitamin A status was assessed by serum retinol, and the findings are reported as means and prevalences with corresponding 95% confidence intervals. Overall, the age-standardized vitamin A deficiency prevalence was 11.7%, a decrease from previous national data, but serum retinol levels remained lower than in other developing countries. Overall, unweighted, multilevel, multivariate logistic regression showed that vitamin A deficiency was influenced by race only (odds ratio (OR) = 1.89, P = 0.031), while weighted multiple logistic regression for 16- to 18-year-olds showed that vitamin A deficiency was influenced by locality (OR = 9.83, P = 0.005) and household income (intermediate (OR = 0.2, P = 0.022) and upper (OR = 0.25, P = 0.049)). Despite the decreased prevalence, vitamin A deficiency remains a moderate public health problem in the country. Opportunities for targeted interventions have been identified.
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Affiliation(s)
- Whadi-Ah Parker
- Population Health, Health Systems and Innovation, Human Sciences Research Council, Cape Town, South Africa
| | - Zandile J Mchiza
- Population Health, Health Systems and Innovation, Human Sciences Research Council, Cape Town, South Africa
| | - Ronel Sewpaul
- Population Health, Health Systems and Innovation, Human Sciences Research Council, Cape Town, South Africa
| | - Nophiwe Job
- Population Health, Health Systems and Innovation, Human Sciences Research Council, Cape Town, South Africa
| | - Lumbwe Chola
- PRICELESS SA, University of Witwatersrand School of Public Health, Parktown, South Africa
| | - Moses Sithole
- Centre for Science, Technology and Innovation Indicators, Human Sciences Research Council, Cape Town, South Africa
| | - Demetre Labadarios
- Population Health, Health Systems and Innovation, Human Sciences Research Council, Cape Town, South Africa
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12
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Li H, Wei S, Fang Y, Li M, Li X, Li Z, Zhang J, Zhu G, Li C, Bi L, Zhang G, Wang D, Zhang XE. Quantitative proteomic analysis of host responses triggered by Mycobacterium tuberculosis infection in human macrophage cells. Acta Biochim Biophys Sin (Shanghai) 2017; 49:835-844. [PMID: 28910983 DOI: 10.1093/abbs/gmx080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 02/03/2023] Open
Abstract
Macrophages are primary host of Mycobacterium tuberculosis (M.tb) and the central effector of in vivo innate immune responses against bacteria. Though the interaction between macrophages and mycobacteria has been widely investigated, the molecular mechanisms of M.tb pathogenesis in macrophages are still not clear. In this work, we investigated the altered protein expression profiles of macrophages after virulent H37Rv strain and avirulent H37Ra strain infection by tandem mass tag-based quantitative proteomics. Among 6762 identified proteins of macrophages, the expression levels of 235 proteins were significantly altered, which is supposed to be related to the infection of different strains. By bioinformatics analysis at systems level, we found that these proteins are mainly involved in the biological process of apoptosis, blood coagulation, oxidative phosphorylation, and others. The enormous variation in protein profiles between macrophages infected with H37Ra and H37Rv suggests the existence of four different immunity mechanisms that decide the fates of macrophages and M.tb. These data may provide a better understanding of M.tb pathogenesis within the host, which contributes to the prevention and clinical treatment of tuberculosis.
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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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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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Wang C, Li YY, Li X, Wei LL, Yang XY, Xu DD, Jiang TT, Li ZJ, Chen ZL, Zhang X, Liu JY, Ping ZP, Li JC. Serum complement C4b, fibronectin, and prolidase are associated with the pathological changes of pulmonary tuberculosis. BMC Infect Dis 2014; 14:52. [PMID: 24484408 PMCID: PMC3913605 DOI: 10.1186/1471-2334-14-52] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 01/30/2014] [Indexed: 11/15/2022] Open
Abstract
Background Mycobacterium tuberculosis infection can activate the immune system, leading to characteristic pathological changes such as inflammatory granuloma, caseous necrosis, and cavity formation. Methods Clinical data of 187 cases of pulmonary tuberculosis (PTB) were analyzed using statistical methods, while serum levels of complement C4b (C4b), fibronectin (FN), and prolidase (PEPD) were detected using the ELISA method among the control, minimal PTB, moderate PTB, and advanced PTB groups. Results We found significantly higher levels of serum C4b and PEPD (P = 0.018, P = 0.003), and significantly lower levels of serum FN (P < 0.001) in PTB patients. Furthermore, the serum levels of 3 proteins were significantly different among 3 PTB groups. FN level was significantly higher in the moderate PTB group, compared with patients in the minimal and advanced PTB groups (P < 0.05, P < 0.01). PEPD level was significantly higher in the moderate PTB group, compared with the minimal PTB group (P < 0.05). Analysis of clinical data showed that serum albumin, C-reactive protein (CRP), prealbumin, and C4 were significantly higher (P < 0.05), while serum globulin was significantly lower in patients with PTB (P < 0.001). A significant negative correlation was found between C4b and albumin, prealbumin. On the other hand, a significant positive correlation was found between C4b and globulin, CRP, PEPD, as well as between PEPD and CRP (P < 0.05). Conclusions Our study showed that C4b, FN, and PEPD are associated with tissue damage, granuloma formation, and cavity formation, respectively, in patients with PTB. The present study provides a new experimental basis to understand the pathogenesis and pathological changes of PTB.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, P,R, China.
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Xu DD, Deng DF, Li X, Wei LL, Li YY, Yang XY, Yu W, Wang C, Jiang TT, Li ZJ, Chen ZL, Zhang X, Liu JY, Ping ZP, Qiu YQ, Li JC. Discovery and identification of serum potential biomarkers for pulmonary tuberculosis using iTRAQ-coupled two-dimensional LC-MS/MS. Proteomics 2014; 14:322-31. [PMID: 24339194 DOI: 10.1002/pmic.201300383] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/22/2013] [Accepted: 11/29/2013] [Indexed: 11/08/2022]
Abstract
Pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis is a chronic disease. Currently, there are no sufficiently validated biomarkers for early diagnosis of TB infection. In this study, a panel of potential serum biomarkers was identified between patients with pulmonary TB and healthy controls by using iTRAQ-coupled 2D LC-MS/MS technique. Among 100 differentially expressed proteins screened, 45 proteins were upregulated (>1.25-fold at p < 0.05) and 55 proteins were downregulated (<0.8-fold at p < 0.05) in the TB serum. Bioinformatics analysis revealed that the differentially expressed proteins were related to the response to stimulus, the metabolic and immune system processes. The significantly differential expression of apolipoprotein CII (APOCII), CD5 antigen-like (CD5L), hyaluronan-binding protein 2 (HABP2), and retinol-binding protein 4 (RBP4) was further confirmed using immunoblotting and ELISA analysis. By forward stepwise multivariate regression analysis, a panel of serum biomarkers including APOCII, CD5L, and RBP4 was obtained to form the disease diagnostic model. The receiver operation characteristic curve of the diagnostic model was 0.98 (sensitivity = 93.42%, specificity = 92.86%). In conclusion, APOCII, CD5L, HABP2, and RBP4 may be potential protein biomarkers of pulmonary TB. Our research provides useful data for early diagnosis of TB.
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Affiliation(s)
- Dan-Dan Xu
- Institute of Cell Biology, Zhejiang University, Hangzhou, P. R. China
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Ray S, Patel SK, Kumar V, Damahe J, Srivastava S. Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures. Proteomics Clin Appl 2013; 8:53-72. [PMID: 24293340 PMCID: PMC7168033 DOI: 10.1002/prca.201300074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 01/26/2023]
Abstract
Apart from direct detection of the infecting organisms or biomarker of the pathogen itself, surrogate host markers are also useful for sensitive and early diagnosis of pathogenic infections. Early detection of pathogenic infections, discrimination among closely related diseases with overlapping clinical manifestations, and monitoring of disease progression can be achieved by analyzing blood biomarkers. Therefore, over the last decade large numbers of proteomics studies have been conducted to identify differentially expressed human serum/plasma proteins in different infectious diseases with the intent of discovering novel potential diagnostic/prognostic biomarkers. However, in-depth review of the literature indicates that many reported biomarkers are altered in the same way in multiple infectious diseases, regardless of the type of infection. This might be a consequence of generic acute phase reactions, while the uniquely modulated candidates in different pathogenic infections could be indicators of some specific responses. In this review article, we will provide a comprehensive analysis of differentially expressed serum/plasma proteins in various infectious diseases and categorize the protein markers associated with generic or specific responses. The challenges associated with the discovery, validation, and translational phases of serum/plasma biomarker establishment are also discussed.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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18
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Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection. J Clin Microbiol 2013; 52:536-43. [PMID: 24478485 DOI: 10.1128/jcm.02433-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis remains one of the most damaging diseases to agriculture, and there is also a concern for human spillover. A critical need exists for rapid, thorough, and inexpensive diagnostic methods capable of detecting and differentiating Mycobacterium bovis infection from other pathogenic and environmental mycobacteria at multiple surveillance levels. In a previous study, Seth et al. (PLoS One 4:e5478, 2009, doi:10.1371/journal.pone.0005478) identified 32 host peptides that specifically increased in the blood serum of M. bovis-infected animals). In the current study, 16 M. bovis proteins were discovered in the blood serum proteomics data sets. A large-scale validation analysis was undertaken for selected host and M. bovis proteins using a cattle serum repository containing M. bovis (n = 128), Mycobacterium kansasii (n = 10), and Mycobacterium avium subsp. paratuberculosis (n = 10), cases exposed to M. bovis (n = 424), and negative controls (n = 38). Of the host biomarkers, vitamin D binding protein (VDBP) showed the greatest sensitivity and specificity for M. bovis detection. Circulating M. bovis proteins, specifically polyketide synthetase 5, detected M. bovis-infected cattle with little to no seroreactivity against M. kansasii- and M. avium subsp. paratuberculosis-infected animals. These data indicate that host and pathogen serum proteins can serve as reliable biomarkers for tracking M. bovis infection in animal populations.
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Chegou NN, Detjen AK, Thiart L, Walters E, Mandalakas AM, Hesseling AC, Walzl G. Utility of host markers detected in Quantiferon supernatants for the diagnosis of tuberculosis in children in a high-burden setting. PLoS One 2013; 8:e64226. [PMID: 23691173 PMCID: PMC3655018 DOI: 10.1371/journal.pone.0064226] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/10/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The diagnosis of childhood tuberculosis (TB) disease remains a challenge especially in young and HIV-infected children. Recent studies have identified potential host markers which, when measured in Quantiferon (QFT-IT) supernatants, show promise in discriminating between Mycobacterium tuberculosis (M.tb) infection states. In this study, the utility of such markers was investigated in children screened for TB in a setting with high TB incidence. METHODOLOGY AND PRINCIPAL FINDINGS 76 children (29% HIV-infected) with or without active TB provided blood specimens collected directly into QFT-IT tubes. After overnight incubation, culture supernatants were harvested, aliquoted and frozen for future immunological research purposes. Subsequently, the levels of 12 host markers previously identified as potential TB diagnostic markers were evaluated in these supernatants for their ability to discriminate between M.tb infection and disease states using the Luminex platform. Of the 76 children included, 19 (25%) had culture confirmed TB disease; 26 (46%) of the 57 without TB had positive markers of M.tb infection defined by a positive QFT-IT test. The potentially most useful analytes for diagnosing TB disease included IFN-α2, IL-1Ra, sCD40L and VEGF and the most useful markers for discriminating between QFT-IT positive children as TB or latent infection included IL-1Ra, IP-10 and VEGF. When markers were used in combinations of four, 84% of all children were accurately classified into their respective groups (TB disease or no TB), after leave-one-out cross validation. CONCLUSIONS Measurement of the levels of IFN-α2, IL-1Ra, sCD40L, IP-10 and VEGF in QFT-IT supernatants may be a useful method for diagnosing TB disease and differentiating between active TB disease and M.tb infection in children. Our observations warrant further investigation in larger well-characterized clinical cohorts.
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Affiliation(s)
- Novel N Chegou
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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De Groote MA, Nahid P, Jarlsberg L, Johnson JL, Weiner M, Muzanyi G, Janjic N, Sterling DG, Ochsner UA. Elucidating novel serum biomarkers associated with pulmonary tuberculosis treatment. PLoS One 2013; 8:e61002. [PMID: 23637781 PMCID: PMC3630118 DOI: 10.1371/journal.pone.0061002] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/05/2013] [Indexed: 02/02/2023] Open
Abstract
In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in the Center for Disease Control and Prevention's Tuberculosis Trials Consortium (TBTC) Study 29. This work represents the first large-scale proteomic analysis employing modified DNA aptamers in a study of active tuberculosis (TB). We identified multiple proteins that exhibit significant expression differences during the intensive phase of TB therapy. There was enrichment for proteins in conserved networks of biological processes and function including antimicrobial defense, tissue healing and remodeling, acute phase response, pattern recognition, protease/anti-proteases, complement and coagulation cascade, apoptosis, immunity and inflammation pathways. Members of cytokine pathways such as interferon-gamma, while present, were not as highly represented as might have been predicted. The top proteins that changed between baseline and 8 weeks of therapy were TSP4, TIMP-2, SEPR, MRC-2, Antithrombin III, SAA, CRP, NPS-PLA2, LEAP-1, and LBP. The novel proteins elucidated in this work may provide new insights for understanding TB disease, its treatment and subsequent healing processes that occur in response to effective therapy.
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Affiliation(s)
- Mary A. De Groote
- SomaLogic, Inc., Boulder, Colorado, United States of America
- Department of Microbiology, Immunology and Pathology, Colorado State University Campus, Fort Collins, Colorado, United States of America
| | - Payam Nahid
- Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Leah Jarlsberg
- Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - John L. Johnson
- Tuberculosis Research Unit, Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Marc Weiner
- Division of Infectious Diseases, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Grace Muzanyi
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
| | - Nebojsa Janjic
- SomaLogic, Inc., Boulder, Colorado, United States of America
| | | | - Urs A. Ochsner
- SomaLogic, Inc., Boulder, Colorado, United States of America
- * E-mail:
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Abstract
BACKGROUND A major obstacle to effectively treat and control tuberculosis is the absence of an accurate, rapid, and low-cost diagnostic tool. A new approach for the screening of patients for tuberculosis is the use of rapid diagnostic classification algorithms. METHODS We tested a previously published diagnostic algorithm based on four biomarkers as a screening tool for tuberculosis in a Central European patient population using an assessor-blinded cross-sectional study design. In addition, we developed an improved diagnostic classification algorithm based on a study population at a tertiary hospital in Vienna, Austria, by supervised computational statistics. RESULTS The diagnostic accuracy of the previously published diagnostic algorithm for our patient population consisting of 206 patients was 54% (CI: 47%-61%). An improved model was constructed using inflammation parameters and clinical information. A diagnostic accuracy of 86% (CI: 80%-90%) was demonstrated by 10-fold cross validation. An alternative model relying solely on clinical parameters exhibited a diagnostic accuracy of 85% (CI: 79%-89%). CONCLUSION Here we show that a rapid diagnostic algorithm based on clinical parameters is only slightly improved by inclusion of inflammation markers in our cohort. Our results also emphasize the need for validation of new diagnostic algorithms in different settings and patient populations.
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Keicho N, Matsushita I, Tanaka T, Shimbo T, Hang NTL, Sakurada S, Kobayashi N, Hijikata M, Thuong PH, Lien LT. Circulating levels of adiponectin, leptin, fetuin-A and retinol-binding protein in patients with tuberculosis: markers of metabolism and inflammation. PLoS One 2012; 7:e38703. [PMID: 22685600 PMCID: PMC3369865 DOI: 10.1371/journal.pone.0038703] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/09/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Wasting is known as a prominent feature of tuberculosis (TB). To monitor the disease state, markers of metabolism and inflammation are potentially useful. We thus analyzed two major adipokines, adiponectin and leptin, and two other metabolic markers, fetuin-A and retinol-binding protein 4 (RBP4). METHODS The plasma levels of these markers were measured using enzyme-linked immunosorbent assays in 84 apparently healthy individuals (=no-symptom group) and 46 patients with active pulmonary TB around the time of treatment, including at the midpoint evaluation (=active-disease group) and compared them with body mass index (BMI), C-reactive protein (CRP), chest radiographs and TB-antigen specific response by interferon-γ release assay (IGRA). RESULTS In the no-symptom group, adiponectin and leptin showed negative and positive correlation with BMI respectively. In the active-disease group, at the time of diagnosis, leptin, fetuin-A and RBP4 levels were lower than in the no-symptom group [adjusted means 2.01 versus 4.50 ng/ml, P<0.0001; 185.58 versus 252.27 µg/ml, P<0.0001; 23.88 versus 43.79 µg/ml, P<0.0001, respectively]. High adiponectin and low leptin levels were associated with large infiltrates on chest radiographs even after adjustment for BMI and other covariates (P=0.0033 and P=0.0020). During treatment, adiponectin levels increased further and then decreased. Leptin levels remained low. Initial low levels of fetuin-A and RBP4 almost returned to the normal reference range in concert with reduced CRP. CONCLUSIONS Our data and recent literature suggest that low fat store and underlying inflammation may regulate these metabolic markers in TB in a different way. Decreased leptin, increased adiponectin, or this ratio may be a promising marker for severity of the disease independent of BMI. We should further investigate pathological roles of the balance between these adipokines.
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Affiliation(s)
- Naoto Keicho
- Department of Respiratory Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
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Chegou NN, Essone PN, Loxton AG, Stanley K, Black GF, van der Spuy GD, van Helden PD, Franken KL, Parida SK, Klein MR, Kaufmann SHE, Ottenhoff THM, Walzl G. Potential of host markers produced by infection phase-dependent antigen-stimulated cells for the diagnosis of tuberculosis in a highly endemic area. PLoS One 2012; 7:e38501. [PMID: 22693640 PMCID: PMC3367928 DOI: 10.1371/journal.pone.0038501] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/10/2012] [Indexed: 11/25/2022] Open
Abstract
Background Recent interferon gamma (IFN-γ)-based studies have identified novel Mycobacterium tuberculosis (M.tb) infection phase-dependent antigens as diagnostic candidates. In this study, the levels of 11 host markers other than IFN-γ, were evaluated in whole blood culture supernatants after stimulation with M.tb infection phase-dependent antigens, for the diagnosis of TB disease. Methodology and Principal Findings Five M.tb infection phase-dependent antigens, comprising of three DosR-regulon-encoded proteins (Rv2032, Rv0081, Rv1737c), and two resucitation promoting factors (Rv0867c and Rv2389c), were evaluated in a case-control study with 15 pulmonary TB patients and 15 household contacts that were recruited from a high TB incidence setting in Cape Town, South Africa. After a 7-day whole blood culture, supernatants were harvested and the levels of the host markers evaluated using the Luminex platform. Multiple antigen-specific host markers were identified with promising diagnostic potential. Rv0081-specific levels of IL-12(p40), IP-10, IL-10 and TNF-α were the most promising diagnostic candidates, each ascertaining TB disease with an accuracy of 100%, 95% confidence interval for the area under the receiver operating characteristics plots, (1.0 to 1.0). Conclusions Multiple cytokines other than IFN-γ in whole blood culture supernatants after stimulation with M.tb infection phase-dependent antigens show promise as diagnostic markers for active TB. These preliminary findings should be verified in well-designed diagnostic studies employing short-term culture assays.
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Affiliation(s)
- Novel N Chegou
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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