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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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Kononikhin AS, Brzhozovskiy AG, Ryabokon AM, Fedorchenko K, Zakharova NV, Spasskii AI, Popov IA, Ilyin VK, Solovyova ZO, Pastushkova LK, Polyakov AV, Varfolomeev SD, Larina IM, Nikolaev EN. Proteome Profiling of the Exhaled Breath Condensate after Long-Term Spaceflights. Int J Mol Sci 2019; 20:E4518. [PMID: 31547269 PMCID: PMC6770753 DOI: 10.3390/ijms20184518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/22/2019] [Accepted: 09/10/2019] [Indexed: 11/21/2022] Open
Abstract
Comprehensive studies of the effects of prolonged exposure to space conditions and the overload experienced during landing on physiological and biochemical changes in the human body are extremely important in the context of planning long-distance space flights, which can be associated with constant overloads and various risk factors for significant physiological changes. Exhaled breath condensate (EBC) can be considered as a valuable subject for monitoring physiological changes and is more suitable for long-term storage than traditional monitoring subjects such as blood and urine. Herein, the EBC proteome changes due to the effects of spaceflight factors are analyzed. Thirteen EBC samples were collected from five Russian cosmonauts (i) one month before flight (background), (ii) immediately upon landing modules in the field (R0) after 169-199 days spaceflights, and (iii) on the seventh day after landing (R+7). Semi-quantitative label-free EBC proteomic analysis resulted in 164 proteins, the highest number of which was detected in EBC after landing (R0). Pathways enrichment analysis using the GO database reveals a large group of proteins which take part in keratinization processes (CASP14, DSG1, DSP, JUP, and so on). Nine proteins (including KRT2, KRT9, KRT1, KRT10, KRT14, DCD, KRT6C, KRT6A, and KRT5) were detected in all three groups. A two-sample Welch's t-test identified a significant change in KRT2 and KRT9 levels after landing. Enrichment analysis using the KEGG database revealed the significant participation of detected proteins in pathogenic E. coli infection (ACTG1, TUBA1C, TUBA4A, TUBB, TUBB8, and YWHAZ), which may indicate microbiota changes associated with being in space. This assumption is confirmed by microbial composition analysis. In general, the results suggest that EBC can be used for noninvasive monitoring of health status and respiratory tract pathologies during spaceflights, and that the obtained data are important for the development of medicine for use in extreme situations. Data are available from ProteomeXchange using the identifier PXD014191.
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Affiliation(s)
- Alexey S Kononikhin
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia.
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Alexander G Brzhozovskiy
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna M Ryabokon
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kristina Fedorchenko
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia.
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Natalia V Zakharova
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander I Spasskii
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vyacheslav K Ilyin
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Zoya O Solovyova
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Lyudmila Kh Pastushkova
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey V Polyakov
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey D Varfolomeev
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Larina
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia.
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia.
| | - Evgeny N Nikolaev
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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Cagnone M, Salvini R, Bardoni A, Fumagalli M, Iadarola P, Viglio S. Searching for biomarkers of chronic obstructive pulmonary disease using proteomics: The current state. Electrophoresis 2018; 40:151-164. [PMID: 30216498 DOI: 10.1002/elps.201800305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 12/24/2022]
Abstract
Detection of proteins which may be potential biomarkers of disorders represents a big step forward in understanding the molecular mechanisms that underlie pathological processes. In this context proteomics plays the important role of opening a path for the identification of molecular signatures that can potentially assist in early diagnosis of several clinical disturbances. Aim of this report is to provide an overview of the wide variety of proteomic strategies that have been applied to the investigation of chronic obstructive pulmonary disease (COPD), a severe disorder that causes an irreversible damage to the lungs and for which there is no cure yet. The results in this area published over the past decade show that proteomics indeed has the ability of monitoring alterations in expression profiles of proteins from fluids/tissues of patients affected by COPD and healthy controls. However, these data also suggest that proteomics, while being an attractive tool for the identification of novel pathological mediators of COPD, remains a technique mainly generated and developed in research laboratories. Great efforts dedicated to the validation of these biological signatures will result in the proof of their clinical utility.
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Affiliation(s)
- Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L.Spallanzani", Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L.Spallanzani", Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
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Fedorchenko KY, Ryabokon’ AM, Kononikhin AS, Mitrofanov SI, Mikhant’eva EA, Spasskii AI, Sukhodolov IR, Popov IA, Polyakov AV, Larina IM, Nikolaev EN, Varfolomeev SD. The effect of space flight on the protein composition of the exhaled breath condensate of cosmonauts. Russ Chem Bull 2017. [DOI: 10.1007/s11172-016-1645-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kononikhin AS, Starodubtseva NL, Pastushkova LK, Kashirina DN, Fedorchenko KY, Brhozovsky AG, Popov IA, Larina IM, Nikolaev EN. Spaceflight induced changes in the human proteome. Expert Rev Proteomics 2016; 14:15-29. [PMID: 27817217 DOI: 10.1080/14789450.2017.1258307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts. Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors' research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments. Expert commentary: Overall, the authors believe that the present background, methodology and equipment improvements will enhance spaceflight safety and support accumulation of new knowledge on how organisms adapt to extreme conditions.
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Affiliation(s)
- Alexey S Kononikhin
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia.,b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Natalia L Starodubtseva
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Lyudmila Kh Pastushkova
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Daria N Kashirina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | | | - Alexander G Brhozovsky
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Igor A Popov
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Irina M Larina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Evgeny N Nikolaev
- d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia.,e Emanuel Institute for Biochemical Physics , Russian Academy of Sciences , Moscow , Russia.,f Skolkovo Institute of Science and Technology, Space Cluster , Skolkovo , Russia
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