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Rezaeeyan H, Arabfard M, Rasouli HR, Shahriary A, Gh BFNM. Evaluation of common protein biomarkers involved in the pathogenesis of respiratory diseases with proteomic methods: A systematic review. Immun Inflamm Dis 2023; 11:e1090. [PMID: 38018577 PMCID: PMC10659759 DOI: 10.1002/iid3.1090] [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: 05/15/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023] Open
Abstract
AIM Respiratory disease (RD) is one of the most common diseases characterized by lung dysfunction. Many diagnostic mechanisms have been used to identify the pathogenic agents of responsible for RD. Among these, proteomics emerges as a valuable diagnostic method for pinpointing the specific proteins involved in RD pathogenesis. Therefore, in this study, for the first time, we examined the protein markers involved in the pathogenesis of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), asthma, bronchiolitis obliterans (BO), and chemical warfare victims exposed to mustard gas, using the proteomics method as a systematic study. MATERIALS AND METHODS A systematic search was performed up to September 2023 on several databases, including PubMed, Scopus, ISI Web of Science, and Cochrane. In total, selected 4246 articles were for evaluation according to the criteria. Finally, 119 studies were selected for this systematic review. RESULTS A total of 13,806 proteins were identified, 6471 in COPD, 1603 in Asthma, 5638 in IPF, three in BO, and 91 in mustard gas exposed victims. Alterations in the expression of these proteins were observed in the respective diseases. After evaluation, the results showed that 31 proteins were found to be shared among all five diseases. CONCLUSION Although these 31 proteins regulate different factors and molecular pathways in all five diseases, they ultimately lead to the regulation of inflammatory pathways. In other words, the expression of some proteins in COPD and mustard-exposed patients increases inflammatory reactions, while in IPF, they cause lung fibrosis. Asthma, causes allergic reactions due to T-cell differentiation toward Th2.
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Affiliation(s)
- Hadi Rezaeeyan
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion MedicineIranian Blood Transfusion Organization (IBTO)TehranIran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Hamid R. Rasouli
- Trauma Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - B. Fatemeh Nobakht M. Gh
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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Unravelling the molecular mechanisms underlying chronic respiratory diseases for the development of novel therapeutics via in vitro experimental models. Eur J Pharmacol 2022; 919:174821. [DOI: 10.1016/j.ejphar.2022.174821] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
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Chen Z, Xu SL, Ge LY, Zhu J, Zheng T, Zhu Z, Zhou L. Sialic acid-binding immunoglobulin-like lectin 9 as a potential therapeutic target for chronic obstructive pulmonary disease. Chin Med J (Engl) 2021; 134:757-764. [PMID: 33595976 PMCID: PMC8104259 DOI: 10.1097/cm9.0000000000001381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT Chronic obstructive pulmonary disease (COPD) has become the third-leading cause of death worldwide, which is a severe economic burden to the healthcare system. Chronic bronchitis is the most common condition that contributes to COPD, both locally and systemically. Neutrophilic inflammation predominates in the COPD airway wall and lumen. Logically, repression of neutrophilia is an essential fashion to COPD treatment. However, currently available anti-neutrophilic therapies provide little benefit in COPD patients and may have serious side effects. Thus, there is an urgent need to explore an effective and safe anti-neutrophilic approach that might delay progression of the disease. Sialic acid-binding immunoglobulin-like lectin (Siglec)-9 is a member of the Siglec cell surface immunoglobulin family. It is noteworthy that Siglec-9 is highly expressed on human neutrophils and monocytes. Ligation of Siglec-9 by chemical compounds or synthetic ligands induced apoptosis and autophagic-like cell death in human neutrophils. Furthermore, administration of antibody to Siglec-E, mouse functional ortholog of Siglec-9, restrained recruitment and activation of neutrophils in mouse models of airway inflammation in vivo. Given the critical role that neutrophils play in chronic bronchitis and emphysema, targeting Siglec-9 could be beneficial for the treatment of COPD, asthma, fibrosis, and related chronic inflammatory lung diseases.
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Affiliation(s)
- Zi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shuang-Lan Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lin-Yang Ge
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jin Zhu
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, Jiangsu 210002, China
| | - Tao Zheng
- Department of Pediatrics and Department of Molecular Microbiology and Immunology, Brown University Warren Alpert Medical School, Providence, RI 02912, USA
| | - Zhou Zhu
- Department of Pediatrics and Department of Molecular Microbiology and Immunology, Brown University Warren Alpert Medical School, Providence, RI 02912, USA
| | - Linfu Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Loi ALT, Hoonhorst S, van Aalst C, Langereis J, Kamp V, Sluis-Eising S, ten Hacken N, Lammers JW, Koenderman L. Proteomic profiling of peripheral blood neutrophils identifies two inflammatory phenotypes in stable COPD patients. Respir Res 2017; 18:100. [PMID: 28532454 PMCID: PMC5440930 DOI: 10.1186/s12931-017-0586-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/16/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND COPD is a heterogeneous chronic inflammatory disease of the airways and it is well accepted that the GOLD classification does not fully represent the complex clinical manifestations of COPD and this classification therefore is not well suited for phenotyping of individual patients with COPD. Besides the chronic inflammation in the lung compartment, there is also a systemic inflammation present in COPD patients. This systemic inflammation is associated with elevated levels of cytokines in the peripheral blood, but the precise composition is unknown. Therefore, differences in phenotype of peripheral blood neutrophils in vivo could be used as a read out for the overall systemic inflammation in COPD. METHOD Our aim was to utilize an unsupervised method to assess the proteomic profile of peripheral neutrophils of stable COPD patients and healthy age matched controls to find potential differences in these profiles as read-out of inflammatory phenotypes. We performed fluorescence two-dimensional difference gel electrophoresis with the lysates of peripheral neutrophils of controls and stable COPD patients. RESULTS We identified two groups of COPD patients based on the differentially regulated proteins and hierarchical clustering whereas there was no difference in lung function between these two COPD groups. The neutrophils from one of the COPD groups were less responsive to bacterial peptide N-formyl-methionyl-leucyl-phenylalanine (fMLF). CONCLUSION This illustrates that systemic inflammatory signals do not necessarily correlate with the GOLD classification and that inflammatory phenotyping can significantly add in an improved diagnosis of single COPD patients. TRIAL REGISTRATION Clinicaltrials.gov: NCT00807469 registered December 11th 2008.
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Affiliation(s)
- Adèle Lo Tam Loi
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Hoonhorst
- Departments of Respiratory Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Corneli van Aalst
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen Langereis
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vera Kamp
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone Sluis-Eising
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nick ten Hacken
- Departments of Respiratory Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan-Willem Lammers
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leo Koenderman
- Departments of Respiratory Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Department Respiratory Medicine and Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3583CX Utrecht, The Netherlands
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Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R. Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections. PLoS Pathog 2017; 13:e1006151. [PMID: 28129394 PMCID: PMC5298345 DOI: 10.1371/journal.ppat.1006151] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 02/08/2017] [Accepted: 12/24/2016] [Indexed: 12/15/2022] Open
Abstract
Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs. The effector proteins were further enriched in DNA-protein complexes isolated in native PAGE gels. Immunofluorescence microscopy revealed a flattened morphology of neutrophils associated with decondensed chromatin, remnants of granules in the cell periphery, and myeloperoxidase co-localized with extracellular DNA, features consistent with early-phase NETs. Nuclear staining revealed that a considerable fraction of bacterial cells in these structures were dead. The proteomes of two pathogens, Staphylococcus aureus and Escherichia coli, were indicative of adaptive responses to early-phase NETs, specifically the release of virulence factors and arrest of ribosomal protein synthesis. Finally, we discovered patterns of proteolysis consistent with widespread cleavage of proteins by neutrophil elastase, proteinase 3 and cathepsin G and evidence of citrullination in many nuclear proteins. Urinary tract infections (UTIs) are one of the world’s most widespread infectious diseases, with an estimated number of 150 million cases per year. Neutrophils play an important role in the defense of human patients against microbes causing UTIs. Molecules produced by neutrophils that migrate into the urinary tract can kill the invading microbes and resolve an infection, often without a need to treat patients with an antibiotic. Our work shows strong support for a mechanism called the formation of neutrophil extracellular traps (NETs), previously described for other infections and autoimmune conditions, which are involved in killing pathogens that have invaded the urinary tract. We show evidence of extracellular chromatin-containing structures using immunofluorescence microscopy and identified proteins that bind to the chromatin DNA and have functions to damage and kill bacterial cells or stop their growth.
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Affiliation(s)
- Yanbao Yu
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Keehwan Kwon
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Tamara Tsitrin
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Shiferaw Bekele
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Patricia Sikorski
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Karen E. Nelson
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Rembert Pieper
- The J. Craig Venter Institute, Rockville, MD, United States of America
- * E-mail:
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Meijer M, Rijkers GT, van Overveld FJ. Neutrophils and emerging targets for treatment in chronic obstructive pulmonary disease. Expert Rev Clin Immunol 2014; 9:1055-68. [PMID: 24168412 DOI: 10.1586/1744666x.2013.851347] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by a decreased airflow due to airway narrowing that, once it occurs, is not fully reversible. The disease usually is progressive and associated with an enhanced inflammatory response in the lungs after exposure to noxious particles or gases. After removal of the noxious particles, the inflammation can continue in a self-sustaining manner. It has been established that improper activation of neutrophils lies at the core of the pathology. This paper provides an overview of the mechanisms by which neutrophils can induce the pulmonary damage of COPD. As the pathogenesis of COPD is slowly being unraveled, new points of intervention are discovered, some of which with promising results.
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Affiliation(s)
- Mariska Meijer
- Department of Science, University College Roosevelt, Lange Noordstraat 1, 4113 CB Middelburg, The Netherlands
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Shahriary A, Mehrani H, Ghanei M, Parvin S. Comparative proteome analysis of peripheral neutrophils from sulfur mustard-exposed and COPD patients. J Immunotoxicol 2014; 12:132-9. [DOI: 10.3109/1547691x.2014.914110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Vijverberg SJH, Hilvering B, Raaijmakers JAM, Lammers JWJ, Maitland-van der Zee AH, Koenderman L. Clinical utility of asthma biomarkers: from bench to bedside. Biologics 2013; 7:199-210. [PMID: 24009412 PMCID: PMC3762671 DOI: 10.2147/btt.s29976] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Asthma is a chronic disease characterized by airway inflammation, bronchial hyperresponsiveness, and recurrent episodes of reversible airway obstruction. The disease is very heterogeneous in onset, course, and response to treatment, and seems to encompass a broad collection of heterogeneous disease subtypes with different underlying pathophysiological mechanisms. There is a strong need for easily interpreted clinical biomarkers to assess the nature and severity of the disease. Currently available biomarkers for clinical practice - for example markers in bronchial lavage, bronchial biopsies, sputum, or fraction of exhaled nitric oxide (FeNO) - are limited due to invasiveness or lack of specificity. The assessment of markers in peripheral blood might be a good alternative to study airway inflammation more specifically, compared to FeNO, and in a less invasive manner, compared to bronchoalveolar lavage, biopsies, or sputum induction. In addition, promising novel biomarkers are discovered in the field of breath metabolomics (eg, volatile organic compounds) and (pharmaco)genomics. Biomarker research in asthma is increasingly shifting from the assessment of the value of single biomarkers to multidimensional approaches in which the clinical value of a combination of various markers is studied. This could eventually lead to the development of a clinically applicable algorithm composed of various markers and clinical features to phenotype asthma and improve diagnosis and asthma management.
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Affiliation(s)
- Susanne JH Vijverberg
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Bart Hilvering
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jan AM Raaijmakers
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Jan-Willem J Lammers
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Anke-Hilse Maitland-van der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Leo Koenderman
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
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Vijverberg SJH, Koenderman L, van Erp FC, van der Ent CK, Postma DS, Brinkman P, Sterk PJ, Raaijmakers JAM, Maitland-van der Zee AH. Inflammatory phenotypes underlying uncontrolled childhood asthma despite inhaled corticosteroid treatment: rationale and design of the PACMAN2 study. BMC Pediatr 2013; 13:94. [PMID: 23768206 PMCID: PMC3691827 DOI: 10.1186/1471-2431-13-94] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 06/10/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The diagnosis of childhood asthma covers a broad spectrum of pathological mechanisms that can lead to similarly presenting clinical symptoms, but may nonetheless require different treatment approaches. Distinct underlying inflammatory patterns are thought to influence responsiveness to standard asthma medication. METHODS/DESIGN The purpose of the PACMAN2 study is to identify inflammatory phenotypes that can discriminate uncontrolled childhood asthma from controlled childhood asthma by measures in peripheral blood and exhaled air. PACMAN2 is a nested, case-control follow-up study to the ongoing pharmacy-based "Pharmacogenetics of Asthma medication in Children: Medication with Anti-inflammatory effects" (PACMAN) study. The original PACMAN cohort consists of children aged 4-12 years with reported use of asthma medication. The PACMAN2 study will be conducted within the larger PACMAN cohort, and will focus on detailed phenotyping of a subset of the PACMAN children. The selected participants will be invited to a follow-up visit in a clinical setting at least six months after their baseline visit based on their adherence to usage of inhaled corticosteroids, their asthma symptoms in the past year, and their age (≥ 8 years). During the follow-up visit, current and long-term asthma symptoms, medication use, environmental factors, medication adherence and levels of exhaled nitric oxide will be reassessed. The following measures will also be examined: pulmonary function, exhaled volatile organic compounds, as well as inflammatory markers in peripheral blood and blood plasma. Comparative analysis and cluster-analyses will be used to identify markers that differentiate children with uncontrolled asthma despite their use of inhaled corticosteroids (ICS) (cases) from children whose asthma is controlled by the use of ICS (controls). DISCUSSION Asthmatic children with distinct inflammatory phenotypes may respond differently to anti-inflammatory therapy. Therefore, by identifying inflammatory phenotypes in children with the PACMAN2 study, we may greatly impact future personalised treatment strategies, uncover new leads for therapeutic targets and improve the design of future clinical studies in the assessment of the efficacy of novel therapeutics.
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Affiliation(s)
- Susanne JH Vijverberg
- Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3508 TB, the Netherlands
- Department of Respiratory Medicine, University Medical Centre Utrecht, Heidelberglaan 100, Utrecht 3584 CX, the Netherlands
| | - Leo Koenderman
- Department of Respiratory Medicine, University Medical Centre Utrecht, Heidelberglaan 100, Utrecht 3584 CX, the Netherlands
| | - Francine C van Erp
- Department of Paediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, Utrecht 3584 EA, the Netherlands
| | - Cornelis K van der Ent
- Department of Paediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, Utrecht 3584 EA, the Netherlands
| | - Dirkje S Postma
- Department of Pulmonology, Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, the Netherlands
| | - Paul Brinkman
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Jan AM Raaijmakers
- Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3508 TB, the Netherlands
| | - Anke-Hilse Maitland-van der Zee
- Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3508 TB, the Netherlands
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The Completed Self: An Immunological View of the Human-Microbiome Superorganism and Risk of Chronic Diseases. ENTROPY 2012. [DOI: 10.3390/e14112036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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