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Gong M, Zhang Y, Chen N, Ma LL, Feng XM, Yan YX. Proteomics in Cardiovascular disease. Clin Chim Acta 2024; 557:117877. [PMID: 38537675 DOI: 10.1016/j.cca.2024.117877] [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: 02/20/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
This study focuses on recent advances in proteomics and provides an up-to-date use of this technology in identifying cardiovascular disease (CVD) biomarkers. A total of eight electronic databases (PubMed, EMBASE, Web of Science, Cochrane Library, Wanfang, Vip, Sinomed, and CNKI) were searched and five were used for integrative analysis of sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic ratio (DOR) and 1 secondary indicator area under the curve (AUC). This systematic review and integrative analysis summarized potential biomarkers previously identified by proteomics. The integrative analysis suggested that proteomics technology had high clinical value in CVD diagnosis. The findings provided new possible directions for the prevention or diagnosis of CVD.
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Affiliation(s)
- Miao Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Yu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Ning Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Lin-Lin Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Xu-Man Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Yu-Xiang Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China.
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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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Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
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Mousavian Z, Folkesson E, Fröberg G, Foroogh F, Correia-Neves M, Bruchfeld J, Källenius G, Sundling C. A protein signature associated with active tuberculosis identified by plasma profiling and network-based analysis. iScience 2022; 25:105652. [PMID: 36561889 PMCID: PMC9763869 DOI: 10.1016/j.isci.2022.105652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/19/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Annually, approximately 10 million people are diagnosed with active tuberculosis (TB), and 1.4 million die of the disease. If left untreated, each person with active TB will infect 10-15 new individuals. The lack of non-sputum-based diagnostic tests leads to delayed diagnoses of active pulmonary TB cases, contributing to continued disease transmission. In this exploratory study, we aimed to identify biomarkers associated with active TB. We assessed the plasma levels of 92 proteins associated with inflammation in individuals with active TB (n = 20), latent TB (n = 14), or healthy controls (n = 10). Using co-expression network analysis, we identified one module of proteins with strong association with active TB. We removed proteins from the module that had low abundance or were associated with non-TB diseases in published transcriptomic datasets, resulting in a 12-protein plasma signature that was highly enriched in individuals with pulmonary and extrapulmonary TB and was further associated with disease severity.
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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
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
| | - Elin Folkesson
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Gabrielle Fröberg
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fariba Foroogh
- 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
| | - Margarida Correia-Neves
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga, Portugal
| | - Judith Bruchfeld
- Division of Infectious Diseases, Department of Medicine Solna, 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
- Corresponding author
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Kang YJ, Park H, Park SB, Lee J, Hyun H, Jung M, Lee EJ, Je MA, Kim J, Lee YS, Kim S. High Procalcitonin, C-Reactive Protein, and α-1 Acid Glycoprotein Levels in Whole Blood Samples Could Help Rapid Discrimination of Active Tuberculosis from Latent Tuberculosis Infection and Healthy Individuals. Microorganisms 2022; 10:microorganisms10101928. [PMID: 36296203 PMCID: PMC9611162 DOI: 10.3390/microorganisms10101928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) management is important for prompt discrimination of latent TB infection (LTBI) from active TB and proper treatment. Whole blood Interferon-gamma (IFN-γ) release assay (IGRA) is used to diagnose LTBI based on the secretion of IFN-γ by T-cells in the whole blood by using a specific antigen of Mycobacterium tuberculosis. However, the ability of IGRA to distinguish active TB from LTBI is considerably limited. Distinguishing active TB from LTBI is necessary to identify indicators that can be used to effectively manage TB and develop diagnostic methods. In the present study, we used a Luminex multiplex bead array (a bead-based antibody−antigen sandwich method). The whole blood level of acute phase proteins (APPs), such as endoglin (ENG), procalcitonin (PCT), C-reactive protein (CRP), and α1-acid glycoprotein (AGP), in active TB, LTBI, and healthy individuals were analyzed and quantified. The APP test results for the serum and whole blood samples showed that the levels of PCT, CRP, and AGP were significantly increased (p < 0.0500; area under curve = 0.955) in active TB. The level of these markers in the whole blood of active TB, LTBI, and healthy individuals could provide data for effective diagnosis and treatment of TB.
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Affiliation(s)
- Yun-Jeong Kang
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Department of Laboratory Medicine, Good Samsun Hospital, Busan 47007, Korea
| | - Heechul Park
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
| | - Sung-Bae Park
- Department of Biomedical Laboratory Science, Masan University, Changwon 51217, Korea
| | - Jiyoung Lee
- Research Institute of Dream DX Inc., Busan 46252, Korea
| | - Hyanglan Hyun
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
| | - Minju Jung
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan 46252, Korea
| | - Eun Ju Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
| | - Min-A Je
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
| | - Jungho Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
| | - Yong Sung Lee
- Department of Laboratory Medicine, Good Samsun Hospital, Busan 47007, Korea
- Correspondence: (Y.S.L.); (S.K.); Tel.: +82-10-6418-3619 (Y.S.L.); +82-51-510-0560 (S.K.); Fax: +82-51-510-0568 (S.K.)
| | - Sunghyun Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Korea
- Clinical Trial Specialist Program for In Vitro Diagnostics, Brain Busan 21 Plus Program, Graduate School, Catholic University of Pusan, Busan 46252, Korea
- Correspondence: (Y.S.L.); (S.K.); Tel.: +82-10-6418-3619 (Y.S.L.); +82-51-510-0560 (S.K.); Fax: +82-51-510-0568 (S.K.)
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Lu Q, Liu J, Yu Y, Liang HF, Zhang SQ, Li ZB, Chen JX, Xu QG, Li JC. ALB, HP, OAF and RBP4 as novel protein biomarkers for identifying cured patients with pulmonary tuberculosis by DIA. Clin Chim Acta 2022; 535:82-91. [PMID: 35964702 DOI: 10.1016/j.cca.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/09/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is a serious infectious disease that lacks robust blood-based biomarkers to identify cured TB. Some discharged patients are not fully cured and may relapse or even develop multidrug-resistant TB. This study is committed to finding proteomic-based plasma biomarkers to support establishing laboratory standards for clinical TB cure. METHODS Data-independent acquisition (DIA) was used to obtain the plasma protein expression profiles of TB patients at different treatment stages compared with healthy controls. Multivariate statistical methods and bioinformatics were used to analyze the data. RESULTS Bioinformatic analysis suggests coagulation dysfunction and vitamin and lipid metabolism disturbances in TB. Albumin (ALB), haptoglobin (HP), out at first protein homolog (OAF), and retinol-binding protein 4 (RBP4) can be used to establish a diagnostic model for the efficacy evaluation of TB with an area under the curve of 0.963, which could effectively distinguish untreated TB patients from cured patients. CONCLUSIONS Our research demonstrated that ALB, HP, OAF and RBP4 can be potential biomarkers for evaluating the efficacy of TB. These findings may provide experimental data for establishing the laboratory indicators of clinical TB cure and providing clinicians with new targets for exploring the underlying mechanisms of TB pathogenesis.
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Affiliation(s)
- Qiqi Lu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jun Liu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Yi Yu
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Hong-Feng Liang
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Shan-Qiang Zhang
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Zhi-Bin Li
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jia-Xi Chen
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou 318050, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiu-Gui Xu
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
| | - Ji-Cheng Li
- The Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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Du Y, Xin H, Cao X, Liu Z, He Y, Zhang B, Yan J, Wang D, Guan L, Shen F, Feng B, He Y, Liu J, Jin Q, Pan S, Zhang H, Gao L. Association Between Plasma Exosomes S100A9/C4BPA and Latent Tuberculosis Infection Treatment: Proteomic Analysis Based on a Randomized Controlled Study. Front Microbiol 2022; 13:934716. [PMID: 35935235 PMCID: PMC9355536 DOI: 10.3389/fmicb.2022.934716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundIdentifying host plasma exosome proteins associated with host response to latent tuberculosis infection (LTBI) treatment might promote our understanding of tuberculosis (TB) pathogenesis and provide useful tools for implementing the precise intervention.MethodsBased on an open-label randomized controlled trial (RCT) aiming to evaluate the short-course regimens for LTBI treatment, plasma exosomes from pre- and post-LTBI treatment were retrospectively detected by label-free quantitative protein mass spectrometry and validated by a parallel reaction monitoring method for participants with changed or not changed infection testing results after LTBI treatment. Eligible participants for both screening and verification sets were randomly selected from the based-RCT in a 1:1 ratio by age and gender. Reversion was defined as a decrease in IFN-γ levels from >0.70 IU/ml prior to treatment to 0.20 IU/ml within 1 week of treatment. The predictive ability of the candidate proteins was evaluated by receiver operating characteristic (ROC) analysis.ResultsTotally, two sample sets for screening (n = 40) and validation (n = 60) were included. Each of them included an equal number of subjects with persistent positive or reversed QuantiFERON-TB Gold In-Tube (QFT) results after LTBI. A total of 2,321 exosome proteins were detected and 102 differentially expressed proteins were identified to be associated with QFT reversion. Proteins with high confidence and original values intact were selected to be further verified. Totally, 9 downregulated proteins met the criteria and were validated. After verification, C4BPA and S100A9 were confirmed to be still significantly downregulated (fold change <0.67, p < 0.05). The respective areas under the ROC curve were 0.73 (95% CI: 0.57–0.89) and 0.69 (95% CI: 0.52–0.86) for C4BPA and S100A9, with a combined value of 0.78 (95% CI: 0.63–0.93). The positive and negative predictive values for combined markers were 70.10% (95% CI: 50.22–86.30%) and 55.63% (95% CI: 29.17–61.00%).ConclusionOur findings suggest that downregulated C4BPA and S100A9 in plasma exosomes might be associated with a host positive response to LTBI treatment. Further studies are warranted to verify the findings and potential underlying mechanisms in varied populations with a larger sample size.
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Affiliation(s)
- Ying Du
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Henan Xin
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefang Cao
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zisen Liu
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Yijun He
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Zhang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Jiaoxia Yan
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Dakuan Wang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Ling Guan
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, China
| | - Fei Shen
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, China
| | - Boxuan Feng
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongpeng He
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianmin Liu
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, China
| | - Qi Jin
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shouguo Pan
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
- Shouguo Pan
| | - Haoran Zhang
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Haoran Zhang
| | - Lei Gao
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Systems Biology of Pathogens, Center for Tuberculosis Research, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Lei Gao
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8
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Li X, Gao Y, Liu J, Xujian Q, Luo Q, Huang Z, Li J. Validation of Serotransferrin in the Serum as Candidate Biomarkers for the Diagnosis of Pulmonary Tuberculosis by Label-Free LC/MS. ACS OMEGA 2022; 7:24174-24183. [PMID: 35874208 PMCID: PMC9301696 DOI: 10.1021/acsomega.2c00837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aimed to identify secreted protein biomarkers in serum from the label-free LC/MS proteomics of neutrophils in pulmonary tuberculosis (TB) patients for the diagnosis biomarkers of TB label-free LC/MS. The proteomic profiles of neutrophils from 15 active TB patients and 15 healthy controls (HCs) were analyzed using label-free LC/MS. We identified 358 differentially expressed proteins preliminarily, including 279 up-regulated proteins and 79 down-regulated proteins. Thirty-eight differentially expressed secreted proteins involved in the progress of platelet degranulation between TB patients and HCs were focused. Of these, serotransferrin (TRF), alpha-2-macroglobulin (AMG), alpha-1-antitrypsin (AAT), alpha-1-acid glycoprotein 1 (AAG), alpha-1-acid glycoprotein 2 (AGP2), and alpha-1B-glycoprotein (A1BG) were selected for further verification in the serum of additional 134 TB patients and 138 HCs by nephelometry and ELISA in the training set. Statistically significant differences of TRF (P < 0.0001), AAT (P < 0.0001), AAG (P < 0.0001), AGP2 (P < 0.0001), and A1BG (P = 0.0003) were observed. The serum concentration of TRF was down-regulated in TB patients compared with healthy controls, which was coincident with the proteomics results. An additional validation of TRF was performed in an independent cohort of patients with active TB (n = 46), patients with lung cancer (n = 37), 20 HCs, and patients with pneumonia (n = 35) in the test set by nephelometry. The serum expression levels of TRF in the TB patients showed lower levels compared with those in patients with pneumonia (P = 0.0125), lung cancer (P = 0.0005), HCs (P < 0.0001), and the non-TB controls (P < 0.0001). Furthermore, the AUC value of TRF was 0.647 with 90.22% sensitivity and 42.86% specificity in discriminating the TB group from the pneumonia group, 0.702 with 93.48% sensitivity and 47.16% specificity in discriminating the TB group from the lung cancer group, 0.894 with 91.30% sensitivity and 71.62% specificity in discriminating the TB group from all HCs, and 0.792 with 91.30% sensitivity and 58.90% specificity in discriminating the TB group from the non-TB controls. This study obtained the proteomic profiles of neutrophils in the TB patients and HCs, which contribute to a better understanding of the pathogenesis molecules existing in the neutrophils of pulmonary tuberculosis and provide candidate biomarkers for the diagnosis of pulmonary tuberculosis.
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Affiliation(s)
- Xue Li
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yujie Gao
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jun Liu
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Qing Xujian
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Qing Luo
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zikun Huang
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
| | - Junming Li
- Department
of Clinical Laboratory, The First Affiliated
Hospital of Nanchang University; Institute of Infection and Immunity,
Nanchang University, Nanchang, Jiangxi 330006, China
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9
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Zhou H, Hwarari D, Zhang Y, Mo X, Luo Y, Ma H. Proteomic Analysis Reveals Salicylic Acid as a Pivotal Signal Molecule in Rice Response to Blast Disease Infection. PLANTS 2022; 11:plants11131702. [PMID: 35807653 PMCID: PMC9269340 DOI: 10.3390/plants11131702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/20/2022]
Abstract
Rice blast disease caused by a fungus, Magnaporthe grisea, is one of the most destructive diseases in rice production worldwide, and salicylic acid (SA) can efficiently decrease the damage of M. grisea. Here, we combined the 2-Dimensional-Liquid Chromatography and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (2D-LC-MALDI-TOF-TOF MS) techniques to compare and identify differentially expressed labelled proteins by the isobaric tags for relative and absolute quantitation (iTRAQ) between the blast-resistant cultivar Minghui and the susceptible rice cultivar Nipponbare in response to blast fungus infection. The group samples were treated with salicylic acid and compared to control samples. A total of 139 DEPs from the two cultivars showed either more than a two-fold change or alternating regulation patterns. Protein functionality analysis also exhibited that these proteins are involved in a wide range of molecular functions including: energy-related activity (30%), signal transduction (11%), redox homeostasis (15%), amino acid and nitrogen metabolism (4%), carbohydrate metabolism (5%), protein folding and assembly (10%), protein hydrolysis (9%), protein synthesis (12%), and other unknown functions (4%). Specifically, we demonstrated that exogenous treatment with salicylic acid promoted recovery in both rice cultivars from Magnaporthe grisea infection by enhancing: the regulation of signal transduction, increasing energy conversion and production through the regulation of the glycolytic pathway, and other various biochemical processes. These findings may facilitate future studies of the molecular mechanisms of rice blast resistance.
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Affiliation(s)
- Haiying Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an 223300, China;
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
| | - Yunhui Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Xiaosong Mo
- Jiangsu Grain and Oil Quality Monitoring Center, Nanjing 210031, China;
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an 223300, China;
- Correspondence: (Y.L.); (H.M.)
| | - Hongyu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
- Correspondence: (Y.L.); (H.M.)
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10
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Guo J, Zhang X, Chen X, Cai Y. Proteomics in Biomarker Discovery for Tuberculosis: Current Status and Future Perspectives. Front Microbiol 2022; 13:845229. [PMID: 35558124 PMCID: PMC9087271 DOI: 10.3389/fmicb.2022.845229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) continues to threaten many peoples' health worldwide, regardless of their country of residence or age. The current diagnosis of TB still uses mainly traditional, time-consuming, and/or culture-based techniques. Efforts have focused on discovering new biomarkers with higher efficiency and accuracy for TB diagnosis. Proteomics-the systematic study of protein diversity-is being applied to the discovery of novel protein biomarkers for different types of diseases. Mass spectrometry (MS) technology plays a revolutionary role in proteomics, and its applicability benefits from the development of other technologies, such as matrix-based and immune-based methods. MS and derivative strategies continuously contribute to disease-related discoveries, and some promising proteomic biomarkers for efficient TB diagnosis have been identified, but challenges still exist. For example, there are discrepancies in the biomarkers identified among different reports and the diagnostic accuracy of clinically applied proteomic biomarkers. The present review summarizes the current status and future perspectives of proteomics in the field of TB biomarker discovery and aims to elicit more promising findings for rapid and accurate TB diagnosis.
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Affiliation(s)
- Jiubiao Guo
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Ximeng Zhang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Xinchun Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Yi Cai
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
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11
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Manyelo CM, Solomons RS, Snyders CI, Kidd M, Kooblal Y, Leukes VN, Claassen C, Roos K, Stanley K, Walzl G, Chegou NN. Validation of host cerebrospinal fluid protein biomarkers for early diagnosis of tuberculous meningitis in children: a replication and new biosignature discovery study. Biomarkers 2022; 27:549-561. [PMID: 35506251 DOI: 10.1080/1354750x.2022.2071991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The diagnosis of tuberculous meningitis (TBM) in children is often delayed due to diagnostic difficulties. New tools are urgently needed to improve the diagnosis of the disease in this vulnerable group. The present study aimed to validate the accuracy of recently identified host cerebrospinal (CSF) biomarkers as candidates for the diagnosis of TBM in children. We collected CSF samples from 87 children aged 3 months to 13 years, that were consecutively admitted at a tertiary hospital in Cape Town, South Africa, on suspicion of having TBM. We evaluated the concentrations of 67 selected host protein biomarkers using a multiplex platform. Previously identified 3-marker (VEGF-A + IFN-γ + MPO) and 4-marker (IFN-γ + MPO + ICAM-1 + IL-8) signatures diagnosed TBM with AUCs of 0.89 (95% CI, 0.81-0.97) and 0.87 (95% CI, 0.79-0.95) respectively; sensitivities of 80.6% (95% CI, 62.5-92.5%) and 81.6% (95% CI, 65.7-92.3%), and specificities of 86.8% (71.9-95.6%) and 83.7% (70.4-92.7%) respectively. Furthermore, a new combination between the analytes (CC4b + CC4 + procalcitonin + CCL1) showed promise, with an AUC of 0.98 (95% CI, 0.94-1.00). We have shown that the accuracies of previously identified candidate CSF biomarkers for childhood TBM was reproducible. Our findings augur well for the future development of a simple bedside test for the rapid diagnosis of TBM in children.
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Affiliation(s)
- Charles M Manyelo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Regan S Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Candice I Snyders
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Martin Kidd
- Department of Statistics and Actuarial Sciences, Centre for Statistical Consultation, Stellenbosch University, Cape Town, South Africa
| | - Yajna Kooblal
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Vinzeigh N Leukes
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Conita Claassen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kelly Roos
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kim Stanley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Novel N Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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12
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Mohammed Y, Goodlett DR, Cheng MP, Vinh DC, Lee TC, Mcgeer A, Sweet D, Tran K, Lee T, Murthy S, Boyd JH, Singer J, Walley KR, Patrick DM, Quan C, Ismail S, Amar L, Pal A, Bassawon R, Fesdekjian L, Gou K, Lamontagne F, Marshall J, Haljan G, Fowler R, Winston BW, Russell JA. Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19. J Proteome Res 2022; 21:975-992. [PMID: 35143212 PMCID: PMC8864781 DOI: 10.1021/acs.jproteome.1c00863] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/15/2022]
Abstract
The host response to COVID-19 pathophysiology over the first few days of infection remains largely unclear, especially the mechanisms in the blood compartment. We report on a longitudinal proteomic analysis of acute-phase COVID-19 patients, for which we used blood plasma, multiple reaction monitoring with internal standards, and data-independent acquisition. We measured samples on admission for 49 patients, of which 21 had additional samples on days 2, 4, 7, and 14 after admission. We also measured 30 externally obtained samples from healthy individuals for comparison at baseline. The 31 proteins differentiated in abundance between acute COVID-19 patients and healthy controls belonged to acute inflammatory response, complement activation, regulation of inflammatory response, and regulation of protein activation cascade. The longitudinal analysis showed distinct profiles revealing increased levels of multiple lipid-associated functions, a rapid decrease followed by recovery for complement activation, humoral immune response, and acute inflammatory response-related proteins, and level fluctuation in the regulation of smooth muscle cell proliferation, secretory mechanisms, and platelet degranulation. Three proteins were differentiated between survivors and nonsurvivors. Finally, increased levels of fructose-bisphosphate aldolase B were determined in patients with exposure to angiotensin receptor blockers versus decreased levels in those exposed to angiotensin-converting enzyme inhibitors. Data are available via ProteomeXchange PXD029437.
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Affiliation(s)
- Yassene Mohammed
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
| | - David R. Goodlett
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
| | - Matthew P. Cheng
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Donald C. Vinh
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Todd C. Lee
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Allison Mcgeer
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
| | - David Sweet
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Karen Tran
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Terry Lee
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Srinivas Murthy
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
| | - John H. Boyd
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - Joel Singer
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Keith R. Walley
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - David M. Patrick
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
| | - Curtis Quan
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Sara Ismail
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Laetitia Amar
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Aditya Pal
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Rayhaan Bassawon
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Lara Fesdekjian
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Karine Gou
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | | | - John Marshall
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
| | - Greg Haljan
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
| | - Robert Fowler
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
| | - Brent W. Winston
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
| | - James A. Russell
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - ARBs CORONA I
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
- University of Sherbrooke,
Sherbrooke J1K 2R1, Quebec, Canada
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
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13
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Liu Q, Li R, Li Q, Luo B, Lin J, Lyu L. High levels of plasma S100A9 at admission indicate an increased risk of death in severe tuberculosis patients. J Clin Tuberc Other Mycobact Dis 2021; 25:100270. [PMID: 34849408 PMCID: PMC8609153 DOI: 10.1016/j.jctube.2021.100270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective This study aims to evaluate plasma S100A9 levels in tuberculosis (TB) patients with admission to the ICU as a marker to predict the risk of death for pulmonary severe TB. Methods This study enrolled 256 severe TB patients admitted to Beijing Chest Hospital from Jan to Dec 2019. The S100A9 levels were measured by ELISA. Standard clinical parameters were collected. The non-parametric Mann-Whitney test, t-test, and chi-square test were applied to statistical comparison. A multivariable analysis was performed to identify risk factors for death. Results The plasma S100A9 levels were higher in non-survivors (25.88, 16.77-44.64) compared to survivors (15.51, 13.67-19.94). S100A9 performed better than Acute Physiology and Chronic Health Evaluation (APACHE II) score in predicting death, with AUC of 0.725, sensitivity of 65.5%, and specificity of 80.3%. By combining APACHE II score together with the S100A9 levels we got an AUC of 0.754 (95% CI 0.68 to 0.82) in predicting death. Lastly, S100A9 levels were significantly higher in patients with APACHE II score >17.5, sputum smear-positive, early death, and high cavitary lesions numbers, all of which were related to TB progression. Conclusion Measurement and monitoring levels of plasma S100A9 in severe TB patients could facilitate the evaluation of patients with high risk at the early stage, which may help to improve the treatment outcome for TB patients.
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Affiliation(s)
- Qiuyue Liu
- Department of Intensive Care Unit, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ru Li
- Department of Anesthesiology, Stony Brook University Health Science Center, Stony Brook, NY 11794-8480, USA
| | - Qi Li
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Baojian Luo
- Department of Intensive Care Unit, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jun Lin
- Department of Anesthesiology, Stony Brook University Health Science Center, Stony Brook, NY 11794-8480, USA
| | - Lingna Lyu
- Department of Molecular Biology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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14
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Han B, Zhang L, Luo B, Ni Y, Bansal N, Zhou P. Comparison of milk fat globule membrane and whey proteome between Dromedary and Bactrian camel. Food Chem 2021; 367:130658. [PMID: 34343808 DOI: 10.1016/j.foodchem.2021.130658] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/22/2021] [Accepted: 07/19/2021] [Indexed: 12/20/2022]
Abstract
Camel milk is rich in nutrients and its impact on human medicine and nutrition cannot be ignored. We conducted an in-depth analysis of milk proteins obtained from two camel breed (Camelus bactrianus, CB and Camelus dromedarius, CD). Label-free proteomic technology was performed to analysis the MFGM and whey proteomes of CB and CD milk. In total, 1133 MFGM proteins and 627 whey proteins were identified from camel milk. Results revealed that 216 MFGM proteins and 109 whey proteins were significantly different between them. In addition, the cellular process, cell and binding were the predominately GO annotations of milk proteins. KEGG analysis shown that most proteins were involved in metabolic pathways. Furthermore, many proteins were found to be involved in PI3K/AKT signaling pathway, which could be the possible reason for hypoglycemic effect of camel milk. These results could provide a further understanding for unique biological characteristics of camel milk proteins.
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Affiliation(s)
- Binsong Han
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lina Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Baolong Luo
- School of Food Science and Technology, Shihezi University, Shihezi 832000, China
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi 832000, China
| | - Nidhi Bansal
- School of Agriculture and Food Science, Faculty of Science, The University of Queensland, St Lucia 4072, Australia
| | - Peng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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15
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Chatziparasidis G, Kantar A. Calprotectin: An Ignored Biomarker of Neutrophilia in Pediatric Respiratory Diseases. CHILDREN-BASEL 2021; 8:children8060428. [PMID: 34063831 PMCID: PMC8223968 DOI: 10.3390/children8060428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022]
Abstract
Calprotectin (CP) is a non-covalent heterodimer formed by the subunits S100A8 (A8) and S100A9 (A9). When neutrophils become activated, undergo disruption, or die, this abundant cytosolic neutrophil protein is released. By fervently chelating trace metal ions that are essential for bacterial development, CP plays an important role in human innate immunity. It also serves as an alarmin by controlling the inflammatory response after it is released. Extracellular concentrations of CP increase in response to infection and inflammation, and are used as a biomarker of neutrophil activation in a variety of inflammatory diseases. Although it has been almost 40 years since CP was discovered, its use in daily pediatric practice is still limited. Current evidence suggests that CP could be used as a biomarker in a variety of pediatric respiratory diseases, and could become a valuable key factor in promoting diagnostic and therapeutic capacity. The aim of this study is to re-introduce CP to the medical community and to emphasize its potential role with the hope of integrating it as a useful adjunct, in the practice of pediatric respiratory medicine.
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Affiliation(s)
| | - Ahmad Kantar
- Pediatric Asthma and Cough Centre, Instituti Ospedalieri Bergamaschi, University and Research Hospitals, 24046 Bergamo, Italy
- Correspondence:
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16
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Shi LY, Han YS, Chen J, Li ZB, Li JC, Jiang TT. Screening and identification of potential protein biomarkers for the early diagnosis of acute myocardial infarction. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:743. [PMID: 34268356 PMCID: PMC8246203 DOI: 10.21037/atm-20-7891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/12/2021] [Indexed: 01/01/2023]
Abstract
Background Acute myocardial infarction (AMI) is the most serious type of heart disease. Clinically, there is an urgent need to discover diagnostic biomarkers for the early diagnosis of AMI. Methods Serum proteomic profiles in AMI patients, healthy controls, and stable angina pectoris (SAP) patients were explored and compared by iTRAQ-2DLC-MS/MS. The clinical data of AMI patients were also analyzed. Differentially expressed proteins were validated by enzyme linked immunosorbent assay (ELISA), and diagnostic models were constructed. Results A total of 39 differentially expressed proteins were identified in AMI patients. The results showed that the serum levels of apolipoprotein E (APOE) in AMI patients were notably higher than those in the healthy controls (P=0.0172). The serum levels of aspartate aminotransferase (AATC) in AMI patients were markedly higher than those in the healthy controls and SAP patients (P<0.0001 and P<0.0001, respectively). The serum levels of fibronectin (FINC) in SAP patients were significantly higher than those in the healthy controls and AMI patients (P=0.0043 and P=0.0044, respectively). Clinical data analysis showed a considerable difference in blood glucose levels, troponin I (TNI), and creatine kinase (CK) in AMI patients compared with SAP patients and healthy controls. A diagnostic model consisting of AATC and clinical indicators [lactate dehydrogenase (LDH) and CK] was established to distinguish between AMI patients and healthy controls, with an area under the curve (AUC) value of 0.993 sensitivity and specificity of 96.2% and 96.3%, respectively. A diagnostic model consisting of AATC and CK was established to distinguish between AMI patients and SAP patients, with an AUC value of 0.975 and a sensitivity and specificity of 85.2% and 79.30%, respectively. Conclusions In this study, differentially expressed proteins in AMI patients were combined with clinical indexes, LDH and CK, and two diagnostic models were constructed. This study may provide meaningful data for the early diagnosis of AMI.
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Affiliation(s)
- Li-Ying Shi
- Clinical Laboratory Department, Zhejiang Hospital, Hangzhou, China
| | - Yu-Shuai Han
- Institute of Cell Biology, Zhejiang University, Hangzhou, China
| | - Jing Chen
- Institute of Cell Biology, Zhejiang University, Hangzhou, China
| | - Zhi-Bin Li
- Institute of Cell Biology, Zhejiang University, Hangzhou, China
| | - Ji-Cheng Li
- Institute of Cell Biology, Zhejiang University, Hangzhou, China
| | - Ting-Ting Jiang
- Department of Pathology, South China University of Technology School of Medicine, Guangzhou, China
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17
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Morris TC, Hoggart CJ, Chegou NN, Kidd M, Oni T, Goliath R, Wilkinson KA, Dockrell HM, Sichali L, Banda L, Crampin AC, French N, Walzl G, Levin M, Wilkinson RJ, Hamilton MS. Evaluation of Host Serum Protein Biomarkers of Tuberculosis in sub-Saharan Africa. Front Immunol 2021; 12:639174. [PMID: 33717190 PMCID: PMC7947659 DOI: 10.3389/fimmu.2021.639174] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
Accurate and affordable point-of-care diagnostics for tuberculosis (TB) are needed. Host serum protein signatures have been derived for use in primary care settings, however validation of these in secondary care settings is lacking. We evaluated serum protein biomarkers discovered in primary care cohorts from Africa reapplied to patients from secondary care. In this nested case-control study, concentrations of 22 proteins were quantified in sera from 292 patients from Malawi and South Africa who presented predominantly to secondary care. Recruitment was based upon intention of local clinicians to test for TB. The case definition for TB was culture positivity for Mycobacterium tuberculosis; and for other diseases (OD) a confirmed alternative diagnosis. Equal numbers of TB and OD patients were selected. Within each group, there were equal numbers with and without HIV and from each site. Patients were split into training and test sets for biosignature discovery. A nine-protein signature to distinguish TB from OD was discovered comprising fibrinogen, alpha-2-macroglobulin, CRP, MMP-9, transthyretin, complement factor H, IFN-gamma, IP-10, and TNF-alpha. This signature had an area under the receiver operating characteristic curve in the training set of 90% (95% CI 86–95%), and, after adjusting the cut-off for increased sensitivity, a sensitivity and specificity in the test set of 92% (95% CI 80–98%) and 71% (95% CI 56–84%), respectively. The best single biomarker was complement factor H [area under the receiver operating characteristic curve 70% (95% CI 64–76%)]. Biosignatures consisting of host serum proteins may function as point-of-care screening tests for TB in African hospitals. Complement factor H is identified as a new biomarker for such signatures.
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Affiliation(s)
- Thomas C Morris
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Clive J Hoggart
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Novel N Chegou
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Martin Kidd
- Centre for Statistical Consultation, Stellenbosch University, Cape Town, South Africa
| | - Tolu Oni
- Department of Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Rene Goliath
- Department of Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katalin A Wilkinson
- Department of Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, United Kingdom
| | - Hazel M Dockrell
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Lifted Sichali
- Malawi Epidemiology and Intervention Research Unit, Karonga Prevention Study, Lilongwe, Malawi
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Karonga Prevention Study, Lilongwe, Malawi
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Karonga Prevention Study, Lilongwe, Malawi.,Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Institute of Health and Wellbeing, University of Glasgow, Glasgow, United Kingdom
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Gerhard Walzl
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Robert J Wilkinson
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,Department of Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, United Kingdom
| | - Melissa S Hamilton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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18
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Kotsiou OS, Papagiannis D, Papadopoulou R, Gourgoulianis KI. Calprotectin in Lung Diseases. Int J Mol Sci 2021; 22:ijms22041706. [PMID: 33567747 PMCID: PMC7915440 DOI: 10.3390/ijms22041706] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Calprotectin (CLP) is a heterodimer formed by two S-100 calcium-binding cytosolic proteins, S100A8 and S100A9. It is a multifunctional protein expressed mainly by neutrophils and released extracellularly by activated or damaged cells mediating a broad range of physiological and pathological responses. It has been more than 20 years since the implication of S100A8/A9 in the inflammatory process was shown; however, the evaluation of its role in the pathogenesis of respiratory diseases or its usefulness as a biomarker for the appropriate diagnosis and prognosis of lung diseases have only gained attention in recent years. This review aimed to provide current knowledge regarding the potential role of CLP in the pathophysiology of lung diseases and describe how this knowledge is, up until now, translated into daily clinical practice. CLP is involved in numerous cellular processes in lung health and disease. In addition to its anti-microbial functions, CLP also serves as a molecule with pro- and anti-tumor properties related to cell survival and growth, angiogenesis, DNA damage response, and the remodeling of the extracellular matrix. The findings of this review potentially introduce CLP in daily clinical practice within the spectrum of respiratory diseases.
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Affiliation(s)
- Ourania S. Kotsiou
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
- Department of Nursing, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
- Correspondence:
| | - Dimitrios Papagiannis
- Department of Nursing, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, UK;
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19
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Kundu J, Bakshi S, Joshi H, Bhadada SK, Verma I, Sharma S. Proteomic profiling of peripheral blood mononuclear cells isolated from patients with tuberculosis and diabetes copathogenesis - A pilot study. PLoS One 2020; 15:e0233326. [PMID: 33156824 PMCID: PMC7647457 DOI: 10.1371/journal.pone.0233326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
Background Diabetes is an important risk factor for developing tuberculosis. This association leads to exacerbation of tuberculosis symptoms and delayed treatment of both the diseases. Molecular mechanism and biomarkers/drug targets related to copathogenesis of tuberculosis and diabetes are still poorly understood. In this study, proteomics based 2D-MALDI/MS approach was employed to identify host signature proteins which are altered during copathogenesis of tuberculosis and diabetes. Methods Comparative proteome of human peripheral blood mononuclear cells (PBMCs) from healthy controls, tuberculosis and diabetes patients in comparison to comorbid diabetes and tuberculosis patients was analyzed. Gel based proteomics approach followed by in gel trypsin digestion and peptide identification by mass spectrometry was used for signature protein identification. Results Total of 18 protein spots with differential expression in tuberculosis and diabetes copathogenesis (TBDM) patients in comparison to other groups were identified. These proteins belonged to four functional categories i.e. structural, cell cycle/growth regulation, signaling and intermediary metabolism. These include Vimentin, tubulin beta chain protein, Actin related protein 2/3 complex subunit 2, coffilin 1 (Structural), PDZ LIM domain protein, Rho-GDP dissociation inhibitor, Ras related protein Rab (signaling), superoxide dismutase, dCTPpyrophosphatase 1, Transcription initiation factor TFIID subunit 12, three isoforms of Peptidylprolylcis-trans isomerase A, SH3 domain containing protein (metabolism), three isoforms of Protein S100A9 and S100A8 (cell cycle progression/growth regulation). Conclusion Proteins identified to be differentially expressed in TBDM patient can act as potent biomarkers and as predictors for copathogenesis of tuberculosis and diabetes.
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Affiliation(s)
- Jyoti Kundu
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shikha Bakshi
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Himanshu Joshi
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjay K. Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sadhna Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
- * E-mail:
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20
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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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21
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Identification of Vinculin as a Potential Diagnostic Biomarker for Acute Aortic Dissection Using Label-Free Proteomics. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7806409. [PMID: 32766314 PMCID: PMC7388002 DOI: 10.1155/2020/7806409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/04/2020] [Accepted: 07/03/2020] [Indexed: 01/16/2023]
Abstract
Acute aortic dissection (AAD) is an emergent vascular disease. Currently, its diagnosis depends on clinical and radiological investigations but lacking of serum biomarkers. In this study, we aimed to identify potential serum biomarkers for AAD using label-free proteomics approach. A total of 90 serum samples were collected from three groups: patients with acute aortic dissection (AAD, n = 30), patients with acute myocardial infarction (AMI, n = 30), and healthy controls (n = 30), and the first four samples from each group were selected for label-free proteomics analysis. Using label-free approach, a total of 22 differentially expressed proteins were identified in the serum samples of the AAD group, of which 15 were upregulated and 7 were downregulated as compared to the AMI and healthy control groups. The most prominent increased protein was vinculin, which was selected to validate in total samples. The level of vinculin was significantly elevated in AAD patients (15.8 ng/ml, IQR: 9.3-19.9 ng/ml) than that in AMI patients (8.6 ng/ml, IQR:5.3-11.4 ng/ml) and healthy volunteers (5.3 ng/ml, IQR:2.8-7.6 ng/ml), P < 0.0001. Furthermore, the concentration of vinculin both increased in type A and B dissection. At the early stage of AAD, vinculin maintained a high level to 48 hours compared with that of AMI. Our study demonstrated that vinculin may play a role in the early diagnosis of AAD.
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Yamauchi M, Kinjo T, Parrott G, Miyagi K, Haranaga S, Nakayama Y, Chibana K, Fujita K, Nakamoto A, Higa F, Owan I, Yonemoto K, Fujita J. Diagnostic performance of serum interferon gamma, matrix metalloproteinases, and periostin measurements for pulmonary tuberculosis in Japanese patients with pneumonia. PLoS One 2020; 15:e0227636. [PMID: 31917802 PMCID: PMC6952104 DOI: 10.1371/journal.pone.0227636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022] Open
Abstract
Serum markers that differentiate between tuberculous and non-tuberculous pneumonia would be clinically useful. However, few serum markers have been investigated for their association with either disease. In this study, serum levels of interferon gamma (IFN-γ), matrix metalloproteinases 1 and 9 (MMP-1 and MMP-9, respectively), and periostin were compared between 40 pulmonary tuberculosis (PTB) and 28 non-tuberculous pneumonia (non-PTB) patients. Diagnostic performance was assessed by analysis of receiver-operating characteristic (ROC) curves and classification trees. Serum IFN-γ and MMP-1 levels were significantly higher and serum MMP-9 levels significantly lower in PTB than in non-PTB patients (p < 0.001, p = 0.002, p < 0.001, respectively). No significant difference was observed in serum periostin levels between groups. ROC curve analysis could not determine the appropriate cut-off value with high sensitivity and specificity; therefore, a classification tree method was applied. This method identified patients with limited infiltration into three groups with statistical significance (p = 0.01), and those with MMP-1 levels < 0.01 ng/mL and periostin levels ≥ 118.8 ng/mL included only non-PTB patients (95% confidence interval 0.0–41.0). Patients with extensive infiltration were also divided into three groups with statistical significance (p < 0.001), and those with MMP-9 levels < 3.009 ng/mL included only PTB patients (95% confidence interval 76.8–100.0). In conclusion, the novel classification tree developed using MMP-1, MMP-9, and periostin data distinguished PTB from non-PTB patients. Further studies are needed to validate our cut-off values and the overall clinical usefulness of these markers.
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Affiliation(s)
- Momoko Yamauchi
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Takeshi Kinjo
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- * E-mail:
| | - Gretchen Parrott
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kazuya Miyagi
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Shusaku Haranaga
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Center for General Clinical Training and Education, University of the Ryukyus Hospital, Okinawa, Japan
| | - Yuko Nakayama
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Kenji Chibana
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Kaori Fujita
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Atsushi Nakamoto
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Futoshi Higa
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Isoko Owan
- Department of Respiratory Medicine, National Hospital Organization Okinawa Hospital, Okinawa, Japan
| | - Koji Yonemoto
- Division of Biostatistics, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Biostatistics, Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jiro Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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23
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Hu YT, Yi WJ, Jiang TT, Tu HH, Wei LL, Shi LY, Liu CM, Chen J, Han YS, Gan L, Li ZB, Huang H, Li JC. Serum proteins TGFBI, PCSK9, and CCL14 are potential biomarkers for different traditional Chinese medicine syndromes of multidrug-resistant tuberculosis. Anat Rec (Hoboken) 2020; 303:2131-2143. [PMID: 31909895 DOI: 10.1002/ar.24353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
Patients with multidrug-resistant tuberculosis (MDR-TB) tend to have a long course of anti-TB treatment and severe side effects. Traditional Chinese Medicine (TCM) has a synergistic effect in attenuation of MDR-TB. However, the lack of objective biological standards to classify and diagnose MDR-TB TCM syndromes could result in less effective TCM treatment. Therefore, in this study, we identified differentially expressed proteins (DEPs) in serum of individuals with MDR-TB TCM syndromes by applying isobaric tags for relative and absolute quantification coupled with two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS) method and bioinformatics analysis. The functional analysis of DEPs was also performed. Additionally, DEPs among three different TCM syndromes of MDR-TB were validated by enzyme-linked immunosorbent assay (ELISA). Finally, a receiver operating characteristic (ROC) curve was performed to estimate the diagnostic ability of DEPs. A total of 71 DEPs were identified in the three different MDR-TB TCM syndrome groups such as the pulmonary Yin deficiency (PYD) syndrome group, the Hyperactivity of Fire due to Yin deficiency (HFYD) syndrome group, and the deficiency of Qi and Yin (DQY) syndrome group. The results showed that the expression level of transforming growth factor-beta-induced protein ig-h3 (TGFBI) was lower in the PYD syndrome group (p = .002), the proprotein convertase subtilisin/kexin type 9 (PCSK9) was overexpressed in the HFYD syndrome group (p < .0001), and the C-C motif chemokine ligand 14 (CCL14) expression level was reduced in the DQY syndrome group (p = .004). Our study demonstrated that serum TGFBI, PCSK9, and CCL14 may serve as potential novel biomarkers for PYD syndrome, HFYD syndrome and DQY syndrome of MDR-TB, respectively. The study provides a biological basis for MDR-TB TCM syndromes classification and can be of great significance for the treatment of different TCM syndromes.
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Affiliation(s)
- Yu-Ting Hu
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Wen-Jing Yi
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Ting-Ting Jiang
- South China University of Technology School of Medicine, Guangzhou, China
| | - Hui-Hui Tu
- Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Chang-Ming Liu
- Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
| | - Jing Chen
- Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
| | - Yu-Shuai Han
- Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
| | - Lin Gan
- South China University of Technology School of Medicine, Guangzhou, China
| | - Zhi-Bin Li
- Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
| | - Huai Huang
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Ji-Cheng Li
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China.,Department of Anatomy and Embryology, Zhejiang University, Hangzhou, China
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24
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Lu Y, Fang Z, Zeng T, Li M, Chen Q, Zhang H, Zhou Q, Hu Y, Chen L, Su S. Chronic hepatitis B: dynamic change in Traditional Chinese Medicine syndrome by dynamic network biomarkers. Chin Med 2019; 14:52. [PMID: 31768187 PMCID: PMC6873721 DOI: 10.1186/s13020-019-0275-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background In traditional Chinese medicine (TCM) clinical practice, TCM syndromes help to understand human homeostasis and guide individualized treatment. However, the TCM syndrome changes with disease progression, of which the scientific basis and mechanism remain unclear. Methods To demonstrate the underlying mechanism of dynamic changes in the TCM syndrome, we applied a dynamic network biomarker (DNB) algorithm to obtain the DNBs of changes in the TCM syndrome, based on the transcriptomic data of patients with chronic hepatitis B and typical TCM syndromes, including healthy controls and patients with liver-gallbladder dampness-heat syndrome (LGDHS), liver-depression spleen-deficiency syndrome (LDSDS), and liver-kidney yin-deficiency syndrome (LKYDS). The DNB model exploits collective fluctuations and correlations of the observed genes, then diagnoses the critical state. Results Our results showed that the DNBs of TCM syndromes were comprised of 52 genes and the tipping point occurred at the LDSDS stage. Meanwhile, there were numerous differentially expressed genes between LGDHS and LKYDS, which highlighted the drastic changes before and after the tipping point, implying the 52 DNBs could serve as early-warning signals of the upcoming change in the TCM syndrome. Next, we validated DNBs by cytokine profiling and isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that PLG (plasminogen) and coagulation factor XII (F12) were significantly expressed during the progression of TCM syndrome from LGDHS to LKYDS. Conclusions This study provides a scientific understanding of changes in the TCM syndrome. During this process, the cytokine system was involved all the time. The DNBs PLG and F12 were confirmed to significantly change during TCM-syndrome progression and indicated a potential value of DNBs in auxiliary diagnosis of TCM syndrome in CHB. Trial registration Identifier: NCT03189992. Registered on June 4, 2017. Retrospectively registered (http://www.clinicaltrials.gov)
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Affiliation(s)
- Yiyu Lu
- 1Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Zhaoyuan Fang
- 2Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Tao Zeng
- 2Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Meiyi Li
- 5Minhang Branch, Zhongshan Hospital, Fudan University/Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199 China
| | - Qilong Chen
- 1Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Hui Zhang
- 1Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Qianmei Zhou
- 1Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Yiyang Hu
- 4Institute of Liver Disease, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Luonan Chen
- 2Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China.,3CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
| | - Shibing Su
- 1Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
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25
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Wu T, Bai H, Zhao Z, Wang M, Hu X, Jiao L, Wu Q, Liu T, Zhang C, Chen H, Zhang J, Song J, Wu L, Zhou W, Tong C, Ying B. A prospective study on associations between superoxide dismutase gene polymorphisms and antituberculosis drug‐induced liver injury in a Chinese Han population. J Gene Med 2019; 21:e3121. [PMID: 31415712 DOI: 10.1002/jgm.3121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Tao Wu
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Hao Bai
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Minjin Wang
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Xuejiao Hu
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Lin Jiao
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Qian Wu
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Tangyuheng Liu
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Chunying Zhang
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Hao Chen
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Jingwei Zhang
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Jiajia Song
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Lijuan Wu
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Wenjing Zhou
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
| | - Chongxiang Tong
- Department of Laboratory MedicinePulmonary Hospital of Lanzhou Lanzhou China
| | - Binwu Ying
- Department of Laboratory Medicine and National Clinical Research Center for GeriatricsWest China Hospital of Sichuan University Chengdu China
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26
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Cowman SA, Jacob J, Hansell DM, Kelleher P, Wilson R, Cookson WOC, Moffatt MF, Loebinger MR. Whole-Blood Gene Expression in Pulmonary Nontuberculous Mycobacterial Infection. Am J Respir Cell Mol Biol 2019; 58:510-518. [PMID: 29206475 DOI: 10.1165/rcmb.2017-0230oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The factors predisposing toward the development of pulmonary nontuberculous mycobacterial (pNTM) disease and influencing disease progression remain unclear. Impaired immune responses have been reported in individuals with pNTM disease, but data are limited and inconsistent. In this study, we sought to use gene expression profiling to examine the host response to pNTM disease. Microarray analysis of whole-blood gene expression was performed on 25 subjects with pNTM disease and 27 uninfected control subjects with respiratory disease. Gene expression results were compared with phenotypic variables and survival data. Compared with uninfected control subjects, pNTM disease was associated with downregulation of 213 transcripts enriched for terms related to T cell signaling, including IFNG. Reduced IFNG expression was associated with more severe computed tomography changes and impaired lung function. Mortality was associated with the expression of transcripts related to the innate immune response and inflammation, whereas transcripts related to T and B cell function were associated with improved survival. These findings suggest that pNTM disease is associated with an aberrant immune response, which may reflect an underlying propensity to infection or result from NTM infection itself. There were important differences in the immune response associated with survival and mortality in pNTM disease.
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Affiliation(s)
- Steven A Cowman
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - Joseph Jacob
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,3 Department of Radiology, Royal Brompton Hospital, London, United Kingdom
| | - David M Hansell
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,3 Department of Radiology, Royal Brompton Hospital, London, United Kingdom
| | - Peter Kelleher
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - Robert Wilson
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - William O C Cookson
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Miriam F Moffatt
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Michael R Loebinger
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
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27
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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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28
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MacLean E, Broger T, Yerlikaya S, Fernandez-Carballo BL, Pai M, Denkinger CM. A systematic review of biomarkers to detect active tuberculosis. Nat Microbiol 2019; 4:748-758. [PMID: 30804546 DOI: 10.1038/s41564-019-0380-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 01/18/2019] [Indexed: 12/12/2022]
Abstract
Millions of cases of tuberculosis (TB) go undiagnosed each year. Better diagnostic tools are urgently needed. Biomarker-based or multiple marker biosignature-based tests, ideally performed on blood or urine, for the detection of active TB might help to meet target product profiles proposed by the World Health Organization for point-of-care testing. We conducted a systematic review to summarize evidence on proposed biomarkers and biosignatures and evaluate their quality and level of evidence. We screened the titles and abstracts of 7,631 citations and included 443 publications that fulfilled the inclusion criteria and were published in 2010-2017. The types of biomarkers identified included antibodies, cytokines, metabolic activity markers, mycobacterial antigens and volatile organic compounds. Only 47% of studies reported a culture-based reference standard and diagnostic sensitivity and specificity. Forty-four biomarkers (4%) were identified in high-quality studies and met the target product profile minimum criteria, of which two have been incorporated into commercial assays. Of the 44 highest-quality biomarkers, 24 (55%) were multiple marker biosignatures. No meta-analyses were performed owing to between-study heterogeneity. In conclusion, TB biomarker discovery studies are often poorly designed and findings are rarely confirmed in independent studies. Few markers progress to a further developmental stage. More validation studies that consider the intended diagnostic use cases and apply rigorous design are needed. The extracted data from this review are currently being used by FIND as the foundation of a dynamic database in which biomarker data and developmental status will be presented.
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Affiliation(s)
- Emily MacLean
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Québec, Canada
| | | | | | | | - Madhukar Pai
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
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29
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Dynamic matrisome: ECM remodeling factors licensing cancer progression and metastasis. Biochim Biophys Acta Rev Cancer 2018; 1870:207-228. [DOI: 10.1016/j.bbcan.2018.09.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/07/2018] [Accepted: 09/30/2018] [Indexed: 01/04/2023]
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30
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Bartáková E, Štefan M, Stráníková A, Pospíšilová L, Arientová S, Beran O, Blahutová M, Máca J, Holub M. Calprotectin and calgranulin C serum levels in bacterial sepsis. Diagn Microbiol Infect Dis 2018; 93:219-226. [PMID: 30420210 DOI: 10.1016/j.diagmicrobio.2018.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 01/18/2023]
Abstract
The aim of this study was to evaluate the serum levels of calprotectin and calgranulin C and routine biomarkers in patients with bacterial sepsis (BS). The initial serum concentrations of calprotectin and calgranulin C were significantly higher in patients with BS (n = 66) than in those with viral infections (n = 24) and the healthy controls (n = 26); the level of calprotectin was found to be the best predictor of BS, followed by the neutrophil-lymphocyte count ratio (NLCR) and the level of procalcitonin (PCT). The white blood cell (WBC) count and the NLCR rapidly returned to normal levels, whereas PCT levels normalized later and the increased levels of calprotectin, calgranulin C, and C-reactive protein persisted until the end of follow-up. Our results suggest that the serum levels of calprotectin are a reliable biomarker of BS and that the WBC count and the NLCR are rapid predictors of the efficacy of antimicrobial therapy.
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Affiliation(s)
- Eva Bartáková
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Marek Štefan
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Alžběta Stráníková
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Lenka Pospíšilová
- Department of Clinical Biochemistry, Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Simona Arientová
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Ondřej Beran
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Marie Blahutová
- Department of Clinical Biochemistry, Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
| | - Jan Máca
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic; Department of Anesthesiology and Intensive Care Medicine, University Hospital of Ostrava, 17. listopadu 1790/5, 708 52 Ostrava-Poruba, Czech Republic.
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6, Czech Republic.
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31
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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32
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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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33
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Zhang HL, Liu CY, Ma W, Huang L, Li CJ, Li CS, Zhang ZW. Identification of differentially expressed proteins in the gastric mucosal atypical hyperplasia tissue microenvironment. Oncol Lett 2018; 16:2355-2365. [PMID: 30008939 PMCID: PMC6036401 DOI: 10.3892/ol.2018.8941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 04/05/2018] [Indexed: 11/06/2022] Open
Abstract
In the present study, the interaction of proteins in the microenvironment of gastric mucosal atypical hyperplasia was analyzed. The stromata of normal gastric mucosa (NGM) and gastric mucosal atypical hyperplasia (GMAH) tissues were purified with laser capture microdissection (LCM). The differentially expressed GMAH proteins of the NGM and GMAH tissues were identified by quantitative proteomic techniques with isotope labeling. The cross-talk between differentially expressed proteins in NGM and GMAH tissues was then analyzed by bioinformatics. There were 165 differentially expressed proteins identified from the stromata of NGM and GMAH tissues. Among them, 99 proteins were upregulated and 66 were downregulated in GMAH tissue. The present study demonstrated that these proteins in gastric mucosal atypical hyperplasia were involved in cancer-associated signaling pathways, including the p53, mitogen-activated protein kinase (MAPK), cell cycle and apoptosis signaling pathways, and were involved in cellular growth, cellular proliferation, apoptosis and the humoral immune response. The results of the present study suggest that the 165 differentially expressed proteins, including S100 calcium-binding protein A6 (S100A6) and superoxide dismutase 3 (SOD3) in the microenvironment of gastric mucosal atypical hyperplasia, are involved in the p53, MAPK, cell cycle and apoptosis signaling pathways, and serve a function in the pathogenesis of gastric cancer.
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Affiliation(s)
- He-Liang Zhang
- Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute of Medical College, University of South China, Hengyang, Hunan 421001, P.R. China.,Medical Company, Troops 66028 of People's Liberation Army, Chengde, Hebei 067000, P.R. China
| | - Chong-Yuan Liu
- Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute of Medical College, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Wei Ma
- Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute of Medical College, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Lin Huang
- Department of Pediatrics, Shaoyang Medical School, Shaoyang, Hunan 422000, P.R. China
| | - Chang-Jian Li
- Clinical Medicine Undergraduate Program, Medical College, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Cheng-Song Li
- Clinical Medicine Undergraduate Program, Medical College, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Zhi-Wei Zhang
- Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute of Medical College, University of South China, Hengyang, Hunan 421001, P.R. China
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34
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Quantitative Proteomic Analysis Provides Insights into Rice Defense Mechanisms against Magnaporthe oryzae. Int J Mol Sci 2018; 19:ijms19071950. [PMID: 29970857 PMCID: PMC6073306 DOI: 10.3390/ijms19071950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/21/2018] [Accepted: 06/28/2018] [Indexed: 11/30/2022] Open
Abstract
Blast disease is one of the major rice diseases, and causes nearly 30% annual yield loss worldwide. Resistance genes that have been cloned, however, are effective only against specific strains. In cultivation practice, broad-spectrum resistance to various strains is highly valuable, and requires researchers to investigate the basal defense responses that are effective for diverse types of pathogens. In this study, we took a quantitative proteomic approach and identified 634 rice proteins responsive to infections by both Magnaporthe oryzae strains Guy11 and JS153. These two strains have distinct pathogenesis mechanisms. Therefore, the common responding proteins represent conserved basal defense to a broad spectrum of blast pathogens. Gene ontology analysis indicates that the “responding to stimulus” biological process is explicitly enriched, among which the proteins responding to oxidative stress and biotic stress are the most prominent. These analyses led to the discoveries of OsPRX59 and OsPRX62 that are robust callose inducers, and OsHSP81 that is capable of inducing both ROS production and callose deposition. The identified rice proteins and biological processes may represent a conserved rice innate immune machinery that is of great value for breeding broad-spectrum resistant rice in the future.
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35
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Zhang Y, Xin Q, Wu Z, Wang C, Wang Y, Wu Q, Niu R. Application of Isobaric Tags for Relative and Absolute Quantification (iTRAQ) Coupled with Two-Dimensional Liquid Chromatography/Tandem Mass Spectrometry in Quantitative Proteomic Analysis for Discovery of Serum Biomarkers for Idiopathic Pulmonary Fibrosis. Med Sci Monit 2018; 24:4146-4153. [PMID: 29909421 PMCID: PMC6036962 DOI: 10.12659/msm.908702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background The present study was performed to explore the presence of informative protein biomarkers of human serum proteome in idiopathic pulmonary fibrosis (IPF). Material/Methods Serum samples were profiled using iTRAQ coupled with two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS) technique, and ELISA was used to validate candidate biomarkers. Results A total of 394 proteins were identified and 97 proteins were associated with IPF. Four biomarker candidates generated from iTRAQ experiments – CRP, fibrinogen-α chain, haptoglobin, and kininogen-1 – were successfully verified using ELISA. Conclusions The present study demonstrates that levels of CRP and fibrinogen-α are higher and levels of haptoglobin and kininogen-1 are lower in patients with IPF compared to levels in healthy controls. We found they are useful candidate biomarkers for IPF.
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Affiliation(s)
- Ying Zhang
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Qian Xin
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Zhen Wu
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Chaochao Wang
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Yongbin Wang
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Qian Wu
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Rui Niu
- Department of Respiratory Medicine, The Second Hospital of Shandong University, Jinan, Shandong, China (mainland)
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36
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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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37
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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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38
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Nakiwala JK, Walker NF, Diedrich CR, Worodria W, Meintjes G, Wilkinson RJ, Mayanja-Kizza H, Colebunders R, Kestens L, Wilkinson KA, Lowe DM. Neutrophil Activation and Enhanced Release of Granule Products in HIV-TB Immune Reconstitution Inflammatory Syndrome. J Acquir Immune Defic Syndr 2018; 77:221-229. [PMID: 29135655 PMCID: PMC5765966 DOI: 10.1097/qai.0000000000001582] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Tuberculosis immune reconstitution inflammatory syndrome (TB-IRIS) remains incompletely understood. Neutrophils are implicated in tuberculosis pathology but detailed investigations in TB-IRIS are lacking. We sought to further explore the biology of TB-IRIS and, in particular, the role of neutrophils. SETTING Two observational, prospective cohort studies in HIV/TB coinfected patients starting antiretroviral therapy (ART), 1 to analyze gene expression and subsequently 1 to explore neutrophil biology. METHODS nCounter gene expression analysis was performed in patients with TB-IRIS (n = 17) versus antiretroviral-treated HIV/TB coinfected controls without IRIS (n = 17) in Kampala, Uganda. Flow cytometry was performed in patients with TB-IRIS (n = 18) and controls (n = 11) in Cape Town, South Africa to determine expression of neutrophil surface activation markers, intracellular cytokines, and human neutrophil peptides (HNPs). Plasma neutrophil elastase and HNP1-3 were quantified using enzyme-linked immunosorbent assay. Lymph node immunohistochemistry was performed on 3 further patients with TB-IRIS. RESULTS There was a significant increase in gene expression of S100A9 (P = 0.002), NLRP12 (P = 0.018), COX-1 (P = 0.025), and IL-10 (P = 0.045) 2 weeks after ART initiation in Ugandan patients with TB-IRIS versus controls, implicating neutrophil recruitment. Patients with IRIS in both cohorts demonstrated increases in blood neutrophil count, plasma HNP and elastase concentrations from ART initiation to week 2. CD62L (L-selectin) expression on neutrophils increased over 4 weeks in South African controls whereas patients with IRIS demonstrated the opposite. Intense staining for the neutrophil marker CD15 and IL-10 was seen in necrotic areas of the lymph nodes of the patients with TB-IRIS. CONCLUSIONS Neutrophils in TB-IRIS are activated, recruited to sites of disease, and release granule contents, contributing to pathology.
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Affiliation(s)
- Justine K Nakiwala
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Naomi F Walker
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Collin R Diedrich
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Pediatrics, Division of Infectious Disease, Children's Hospital of UPMC, University of Pittsburgh, Pittsburgh, PA
| | - William Worodria
- Department of Medicine, Mulago Hospital, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Graeme Meintjes
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Robert J Wilkinson
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Harriet Mayanja-Kizza
- Department of Medicine, Mulago Hospital, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Robert Colebunders
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Luc Kestens
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Katalin A Wilkinson
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- The Francis Crick Institute, London, United Kingdom
| | - David M Lowe
- Department of Medicine, Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, Imperial College London, London, United Kingdom
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
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39
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Xu X, Liu Z, Wang J, Xie H, Li J, Cao J, Zhou L, Zheng S. Global proteomic profiling in multistep hepatocarcinogenesis and identification of PARP1 as a novel molecular marker in hepatocellular carcinoma. Oncotarget 2017; 7:13730-41. [PMID: 26883192 PMCID: PMC4924674 DOI: 10.18632/oncotarget.7316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/23/2016] [Indexed: 12/18/2022] Open
Abstract
The more accurate biomarkers have long been desired for hepatocellular carcinoma (HCC). Here, we characterized global large-scale proteomics of multistep hepatocarcinogenesis in an attempt to identify novel biomarkers for HCC. Quantitative data of 37874 sequences and 3017 proteins during hepatocarcinogenesis were obtained in cohort 1 of 75 samples (5 pooled groups: normal livers, hepatitis livers, cirrhotic livers, peritumoral livers, and HCC tissues) by iTRAQ 2D LC-MS/MS. The diagnostic performance of the top six most upregulated proteins in HCC group and HSP70 as reference were subsequently validated in cohort 2 of 114 samples (hepatocarcinogenesis from normal livers to HCC) using immunohistochemistry. Of seven candidate protein markers, PARP1, GS and NDRG1 showed the optimal diagnostic performance for HCC. PARP1, as a novel marker, showed comparable diagnostic performance to that of classic markers GS and NDRG1 in HCC (AUCs = 0.872, 0.856 and 0.792, respectively). A significant higher AUC of 0.945 was achieved when three markers combined. For diagnosis of HCC, the sensitivity and specificity were 88.2% and 81.0% when at least two of the markers were positive. Similar diagnostic values of PARP1, GS and NDRG1 were confirmed by immunohistochemistry in cohort 3 of 180 HCC patients. Further analysis indicated that PARP1 and NDRG1 were associated with some clinicopathological features, and the independent prognostic factors for HCC patients. Overall, global large-scale proteomics on spectrum of multistep hepatocarcinogenesis are obtained. PARP1 is a novel promising diagnostic/prognostic marker for HCC, and the three-marker panel (PARP1, GS and NDRG1) with excellent diagnostic performance for HCC was established.
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Affiliation(s)
- Xiao Xu
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhikun Liu
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Jianguo Wang
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Haiyang Xie
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Jie Li
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Jili Cao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Lin Zhou
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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40
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Schaible UE, Linnemann L, Redinger N, Patin EC, Dallenga T. Strategies to Improve Vaccine Efficacy against Tuberculosis by Targeting Innate Immunity. Front Immunol 2017; 8:1755. [PMID: 29312298 PMCID: PMC5732265 DOI: 10.3389/fimmu.2017.01755] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/27/2017] [Indexed: 01/08/2023] Open
Abstract
The global tuberculosis epidemic is the most common cause of death after infectious disease worldwide. Increasing numbers of infections with multi- and extensively drug-resistant variants of the Mycobacterium tuberculosis complex, resistant even to newly discovered and last resort antibiotics, highlight the urgent need for an efficient vaccine. The protective efficacy to pulmonary tuberculosis in adults of the only currently available vaccine, M. bovis BCG, is unsatisfactory and geographically diverse. More importantly, recent clinical studies on new vaccine candidates did not prove to be better than BCG, yet. Here, we propose and discuss novel strategies to improve efficacy of existing anti-tuberculosis vaccines. Modulation of innate immune responses upon vaccination already provided promising results in animal models of tuberculosis. For instance, neutrophils have been shown to influence vaccine efficacy, both, positively and negatively, and stimulate specific antibody secretion. Modulating immune regulatory properties after vaccination such as induction of different types of innate immune cell death, myeloid-derived suppressor or regulatory T cells, production of anti-inflammatory cytokines such as IL-10 may have beneficial effects on protection efficacy. Incorporation of lipid antigens presented via CD1 molecules to T cells have been discussed as a way to enhance vaccine efficacy. Finally, concepts of dendritic cell-based immunotherapies or training the innate immune memory may be exploitable for future vaccination strategies against tuberculosis. In this review, we put a spotlight on host immune networks as potential targets to boost protection by old and new tuberculosis vaccines.
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Affiliation(s)
- Ulrich E Schaible
- Cellular Microbiology, Priority Program Infections, Research Center Borstel, Borstel, Germany.,Thematic Translation Unit Tuberculosis, German Center for Infection Research, Research Center Borstel, Borstel, Germany
| | - Lara Linnemann
- Cellular Microbiology, Priority Program Infections, Research Center Borstel, Borstel, Germany
| | - Natalja Redinger
- Cellular Microbiology, Priority Program Infections, Research Center Borstel, Borstel, Germany
| | - Emmanuel C Patin
- Cellular Microbiology, Priority Program Infections, Research Center Borstel, Borstel, Germany.,Retroviral Immunology, The Francis Crick Institute, London, United Kingdom
| | - Tobias Dallenga
- Cellular Microbiology, Priority Program Infections, Research Center Borstel, Borstel, Germany.,Thematic Translation Unit Tuberculosis, German Center for Infection Research, Research Center Borstel, Borstel, Germany
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41
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Screening and identification of lncRNAs as potential biomarkers for pulmonary tuberculosis. Sci Rep 2017; 7:16751. [PMID: 29196714 PMCID: PMC5711916 DOI: 10.1038/s41598-017-17146-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/22/2017] [Indexed: 11/21/2022] Open
Abstract
Pulmonary tuberculosis (TB) is among the diseases with the highest morbidity and mortality worldwide. Effective diagnostic methods for TB are lacking. In this study, we investigated long non-coding RNAs (lncRNAs) in plasma using microarray and the potential diagnostic value of lncRNAs for TB. We found a total of 163 up-regulated lncRNAs and 348 down-regulated lncRNAs. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and coding-noncoding co-expression (CNC) analyses showed that functions of differentially expressed lncRNAs were mainly enriched in the regulation of alpha-beta T cell activation and the T cell receptor signalling pathway. Four differentially expressed lncRNAs, NR_038221 (fold change = 3.79, P < 0.01), NR_003142 (fold change = 1.69, P < 0.05), ENST00000570366 (fold change = 3.04, P < 0.05), and ENST00000422183 (fold change = 2.11, P < 0.001), were verified using RT-qPCR. Among those, NR_038221, NR_003142, and ENST00000570366 were found to be up-regulated, while ENST00000422183 was down-regulated. The value of the area under the curve (AUC) for the diagnostic model consisting of the four lncRNAs was 0.845 (sensitivity = 79.2%, specificity = 75%). We further predicted 85 mRNAs and 404 miRNAs that potentially interact with these lncRNAs. Our study revealed the potential value of lncRNAs as biomarkers for early diagnosis of TB and the underlying mechanisms of these abnormally expressed lncRNAs in the pathogenesis of TB.
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42
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Isolation and Characterization of Serum Extracellular Vesicles (EVs) from Atlantic Salmon Infected with Piscirickettsia Salmonis. Proteomes 2017; 5:proteomes5040034. [PMID: 29194379 PMCID: PMC5748569 DOI: 10.3390/proteomes5040034] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
Secretion of extracellular vesicles (EVs) is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is known, however, of EV secretion in fish, or the effect of infection on EV release and content. In the present study, EVs were isolated from the serum of healthy and Piscirickettsia salmonis infected Atlantic salmon in order to evaluate the effect of infection on EV secretion. P. salmonis is facultative intracellular bacterium that causes a systemic infection disease in farmed salmonids. EVs isolated from both infected and non-infected fish had an average diameter of 230–300 nm, as confirmed by transmission electron microscopy, nanoparticle tracking, and flow cytometry. Mass spectrometry identified 180 proteins in serum EVs from both groups of fish. Interestingly, 35 unique proteins were identified in serum EVs isolated from the fish infected with P. salmonis. These unique proteins included proteasomes subunits, granulins, and major histocompatibility class I and II. Our results suggest that EV release could be part of a mechanism in which host stimulatory molecules are released from infected cells to promote an immune response.
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43
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Li J, Sun L, Xu F, Xiao J, Jiao W, Qi H, Shen C, Shen A. Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics. Oncotarget 2017; 8:103290-103301. [PMID: 29262562 PMCID: PMC5732728 DOI: 10.18632/oncotarget.21179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/29/2017] [Indexed: 02/02/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is an infectious disease found worldwide. Children infected with MTB are more likely to progress to active TB (ATB); however, the molecular mechanism behind this process has long been a mystery. We employed the label-free quantitative proteomic technology to identify and characterize differences in plasma proteins between ATB and latent TB infection (LTBI) in children. To detect differences that are indicative of MTB infection, we first selected proteins whose expressions were markedly different between the ATB and LTBI groups and the control groups (inflammatory disease control (IDC) and healthy control (HC) groups). A total of 521 proteins differed (> 1.5-fold or < 0.6-fold) in the LTBI group, and 318 proteins in the ATB group when compared with the control groups. Of these, 49 overlapping proteins were differentially expressed between LTBI and ATB. Gene Ontology (GO) analysis revealed most proteins had a cellular and organelle distribution. The MTB infection status was mainly related to differences in binding, cellular and metabolic processes. XRCC4, PCF11, SEMA4A and ATP11A were selected and further verified by qPCR and western blot. At the mRNA level, the expression of XRCC4, PCF11and SEMA4A presented an increased trend in ATB group compare with LTBI. At the protein level, the expression of all these proteins by western blot in ATB/LTBI was consistent with the trends from proteomic detection. Our results provide important data for future mechanism studies and biomarker selection for MTB infection in children.
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Affiliation(s)
- Jieqiong Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Lin Sun
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Fang Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Jing Xiao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Weiwei Jiao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Hui Qi
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chen Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Adong Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
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44
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Strbenac D, Zhong L, Raftery MJ, Wang P, Wilson SR, Armstrong NJ, Yang JYH. Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods. J Proteome Res 2017; 16:2359-2369. [DOI: 10.1021/acs.jproteome.6b00882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dario Strbenac
- School
of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ling Zhong
- Bioanalytical
Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark J. Raftery
- Bioanalytical
Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Penghao Wang
- School
of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Susan R. Wilson
- School of Mathematics & Statistics, University of New South Wales, Sydney, New South Wales 2052, Australia
- Centre
for Mathematics and its Applications, Mathematical Sciences Institute, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Nicola J. Armstrong
- School
of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jean Y. H. Yang
- School
of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
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45
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Wu L, Sun Y, Wan J, Luan T, Cheng Q, Tan Y. A proteomic analysis identifies candidate early biomarkers to predict ovarian hyperstimulation syndrome in polycystic ovarian syndrome patients. Mol Med Rep 2017; 16:272-280. [PMID: 28534980 PMCID: PMC5482139 DOI: 10.3892/mmr.2017.6604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/08/2017] [Indexed: 12/13/2022] Open
Abstract
Ovarian hyperstimulation syndrome (OHSS) is a potentially life‑threatening, iatrogenic complication that occurs during assisted reproduction. Polycystic ovarian syndrome (PCOS) significantly increases the risk of OHSS during controlled ovarian stimulation. Therefore, a more effective early prediction technique is required in PCOS patients. Quantitative proteomic analysis of serum proteins indicates the potential diagnostic value for disease. In the present study, the authors revealed the differentially expressed proteins in OHSS patients with PCOS as new diagnostic biomarkers. The promising proteins obtained from liquid chromatography‑mass spectrometry were subjected to ELISA and western blotting assay for further confirmation. A total of 57 proteins were identified with significant difference, of which 29 proteins were upregulated and 28 proteins were downregulated in OHSS patients. Haptoglobin, fibrinogen and lipoprotein lipase were selected as candidate biomarkers. Receiver operating characteristic curve analysis demonstrated all three proteins may have potential as biomarkers to discriminate OHSS in PCOS patients. Haptoglobin, fibrinogen and lipoprotein lipase have never been reported as a predictive marker of OHSS in PCOS patients, and their potential roles in OHSS occurrence deserve further studies. The proteomic results reported in the present study may gain deeper insights into the pathophysiology of OHSS.
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Affiliation(s)
- Lan Wu
- First Clinical Medicine College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, P.R. China
| | - Yazhou Sun
- Department of Pediatrics, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Jun Wan
- Department of Obstetrics, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital, Nanjing, Jiangsu 210004, P.R. China
| | - Ting Luan
- Department of Obstetrics, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital, Nanjing, Jiangsu 210004, P.R. China
| | - Qing Cheng
- Department of Obstetrics, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital, Nanjing, Jiangsu 210004, P.R. China
| | - Yong Tan
- First Clinical Medicine College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, P.R. China
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46
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Jiang TT, Shi LY, Wei LL, Li X, Yang S, Wang C, Liu CM, Chen ZL, Tu HH, Li ZJ, Li JC. Serum amyloid A, protein Z, and C4b-binding protein β chain as new potential biomarkers for pulmonary tuberculosis. PLoS One 2017; 12:e0173304. [PMID: 28278182 PMCID: PMC5344400 DOI: 10.1371/journal.pone.0173304] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/17/2017] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to discover novel biomarkers for pulmonary tuberculosis (TB). Differentially expressed proteins in the serum of patients with TB were screened and identified by iTRAQ-two dimensional liquid chromatography tandem mass spectrometry analysis. A total of 79 abnormal proteins were discovered in patients with TB compared with healthy controls. Of these, significant differences were observed in 47 abnormally expressed proteins between patients with TB or pneumonia and chronic obstructive pulmonary disease (COPD). Patients with TB (n = 136) exhibited significantly higher levels of serum amyloid A (SAA), vitamin K-dependent protein Z (PROZ), and C4b-binding protein β chain (C4BPB) than those in healthy controls (n = 66) (P<0.0001 for each) albeit significantly lower levels compared with those in patients with pneumonia (n = 72) (P<0.0001 for each) or COPD (n = 72) (P<0.0001, P<0.0001, P = 0.0016, respectively). After 6 months of treatment, the levels of SAA and PROZ were significantly increased (P = 0.022, P<0.0001, respectively), whereas the level of C4BPB was significantly decreased (P = 0.0038) in treated TB cases (n = 72). Clinical analysis showed that there were significant differences in blood clotting and lipid indices in patients with TB compared with healthy controls, patients with pneumonia or COPD, and treated TB cases (P<0.05). Correlation analysis revealed significant correlations between PROZ and INR (rs = 0.414, P = 0.044), and between C4BPB and FIB (rs = 0.617, P = 0.0002) in patients with TB. Receiver operating characteristic curve analysis revealed that the area under the curve value of the diagnostic model combining SAA, PROZ, and C4BPB to discriminate the TB group from the healthy control, pneumonia, COPD, and cured TB groups was 0.972, 0.928, 0.957, and 0.969, respectively. Together, these results suggested that SAA, PROZ, and C4BPB may serve as new potential biomarkers for TB. Our study may thus provide experimental data for the differential diagnosis of TB.
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Affiliation(s)
- Ting-Ting Jiang
- South China University of Technology School of Medicine, Guangzhou, P.R. China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, P.R. China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, P.R. China
| | - Xiang Li
- Key Laboratory of Gastroenteropathy, Zhejiang Province People’s Hospital, Hangzhou, China
| | - Su Yang
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Chong Wang
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Chang-Ming Liu
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Zhong-Liang Chen
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Zhong-Jie Li
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
| | - Ji-Cheng Li
- South China University of Technology School of Medicine, Guangzhou, P.R. China
- Institute of Cell Biology, Zhejiang University, Hangzhou, P.R. China
- * E-mail:
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Pang Z, Chen L, Mu W, Liu L, Liu X. Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph. Sci Rep 2016; 6:24103. [PMID: 27050922 PMCID: PMC4822174 DOI: 10.1038/srep24103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/21/2016] [Indexed: 01/11/2023] Open
Abstract
Phytophthora capsici is an important oomycete plant pathogen that causes significant losses worldwide. The carboxylic acid amide fungicide flumorph has shown excellent activity against oomycete plant pathogens. Despite its potential, there remains concern that the sexual reproduction of oomycete pathogens, which results in genetic recombination, could result in the rapid development of resistance to flumorph. The current study utilized an iTRAQ (isobaric tags for relative and absolute quantitation) based method to compare differences between the proteome of the parental P. capsici isolate PCAS1 and its sexual progeny S2-838, which exhibits significant resistance to flumorph. A total of 2396 individual proteins were identified, of these, 181 were considered to be associated with the adaptive response of P. capsici to flumorph. The subsequent bioinformatic analysis revealed that the adaptive response of P. capsici to flumorph was complex and regulated by multiple mechanisms, including utilising carbohydrate from the host environment to compensate for the cell wall stress induced by flumorph, a shift in energy generation, decreased amino acids biosynthesis, and elevated levels of proteins associated with the pathogen's response to stimulus and transmembrane transport. Moreover, the results of the study provided crucial data that could provide the basis for early monitoring of flumorph resistance in field populations of P. capsici.
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Affiliation(s)
- Zhili Pang
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Lei Chen
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
- College of Forestry, Beijing Forestry University, Beijing, P. R. China
| | - Wenjun Mu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
- Zhengzhou Tobacco Research Institute of CNTC, P. R. China
| | - Li Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Xili Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
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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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Zhao X, Xu L, Zheng L, Yin L, Qi Y, Han X, Xu Y, Peng J. Potent effects of dioscin against gastric cancer in vitro and in vivo. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:274-282. [PMID: 26969381 DOI: 10.1016/j.phymed.2016.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 01/24/2016] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND We previously reported the effect of dioscin on human gastric carcinoma SGC-7901 cells, but its effects on other gastric cancers are still unknown. PURPOSE The present paper aimed to demonstrate the activity of dioscin against human gastric carcinoma MGC-803 and MKN-45. STUDY DESIGN In our study, MGC-803 and MKN-45 cells were used to examine the effects of dioscin on human gastric carcinoma in vitro. The effects of dioscin against human gastric carcinoma in vivo were accomplished by the xenografts of MGC-803 cells in BALB/c nude mice. METHODS AO/EB and DAPI staining, TEM, single cell gel electrophoresis and flow cytometry assays were used in cell experiments. Then, an iTRAQ-based proteomics approach, DNA and siRNA transfection experiments were carried out for mechanism investigation. RESULTS In MGC-803 cells, dioscin caused DNA damage and mitochondrial change, induced ROS generation, Ca(2+) release and cell apoptosis, and blocked cell cycle at S phase. In vivo results showed that dioscin significantly suppressed the tumor growth of MGC-803 cell xenografts in nude mice. In addition, dioscin markedly inhibited cell migration, caused Cytochrome c release and adjusted mitochondrial signal pathway. Then, an iTRAQ-based proteomics approach was carried out and 121 differentially expressed proteins were found, in which five biomarkers associated with cell cycle, apoptosis and migration were evaluated. Dioscin significantly up-regulated the levels of GALR-2 and RBM-3, and down-regulated CAP-1, Tribbles-2 and CliC-3. Furthermore, overexpressed DNA transfection of CAP-1 enhanced cell migration and invasion, which was decreased by dioscin. SiRNA to Tribbles-2 affected the protein levels of Bcl-2, Bax and MAPKs, suggesting that dioscin decreased Tribbles-2 level leading to cell apoptosis. CONCLUSION Our works confirmed the activity of dioscin against gastric cancer. In addition, this work also provided that dioscin is a new potent candidate for treating gastric cancer in the future.
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Affiliation(s)
- Xinwei Zhao
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lina Xu
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lingli Zheng
- Department of Pharmaceuticals, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Lianhong Yin
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Yan Qi
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Xu Han
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Youwei Xu
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Jinyong Peng
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China.
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Bates M, Zumla A. The development, evaluation and performance of molecular diagnostics for detection of Mycobacterium tuberculosis. Expert Rev Mol Diagn 2016; 16:307-22. [PMID: 26735769 DOI: 10.1586/14737159.2016.1139457] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The unique pathogenesis of tuberculosis (TB) poses several barriers to the development of accurate diagnostics: a) the establishment of life-long latency by Mycobacterium tuberculosis (M.tb) after primary infection confounds the development of classical antibody or antigen based assays; b) our poor understanding of the molecular pathways that influence progression from latent to active disease; c) the intracellular nature of M.tb infection in tissues means that M.tb and/or its components, are not readily detectable in peripheral specimens; and d) the variable presence of M.tb bacilli in specimens from patients with extrapulmonary TB or children. The literature on the current portfolio of molecular diagnostics tests for TB is reviewed here and the developmental pipeline is summarized. Also reviewed are data from recently published operational research on the GeneXpert MTB/RIF assay and discussed are the lessons that can be taken forward for the design of studies to evaluate the impact of TB diagnostics.
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Affiliation(s)
- Matthew Bates
- a UNZA-UCLMS Research & Training Programme , University Teaching Hospital , Lusaka , Zambia.,b Centre for Clinical Microbiology, Division of Infection and Immunity , University College London , London , UK
| | - Alimuddin Zumla
- a UNZA-UCLMS Research & Training Programme , University Teaching Hospital , Lusaka , Zambia.,b Centre for Clinical Microbiology, Division of Infection and Immunity , University College London , London , UK.,c NIHR Biomedical Research Centre , University College London Hospitals , London , UK
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