1
|
Cheng J, Ji D, Yin Y, Wang S, Song K, Pan Q, Zhang Q, Yang L. Proteomic profiling of serum small extracellular vesicles reveals immune signatures of children with pneumonia. Transl Pediatr 2022; 11:891-908. [PMID: 35800266 PMCID: PMC9253949 DOI: 10.21037/tp-22-134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pneumonia is the leading cause of death in young children globally. However, the underlying pathological mechanism of pediatric pneumonia remains unclear. In infection disease contexts, small extracellular vesicles (sEVs) have been shown to be a useful source of markers for pathogenesis and immune response. We hypothesized that functional molecules such as protein harbored by sEVs would provide mechanistic insights into the immune response in children with pneumonia. METHODS We isolated sEVs from serum collected from children with and without pneumonia, performed proteomic analysis of the sEVs with label-free mass spectrometry, and then conducted functional enrichment analysis of proteomic data. RESULTS We identified fifteen differentially expressed proteins and ten unique proteins in children with pneumonia as compared to healthy children. In the pneumonia group, immune-related processes and pathways were positively enriched as upregulated proteins were involved in neutrophil activation, complement regulation, defense against bacteria, humoral immune response and regulation of immune effector processes However, pathways associated with tissue development and extracellular matrix remodeling were negatively enriched, as downregulated proteins were linked to extracellular matrix structure and cell adhesions. CONCLUSIONS Our findings provided insights into host responses to pathogen infection, which has contributed to understanding the pathogenesis of children with pneumonia. Furthermore, our studies suggested that serum sEVs proteins could be considered a potential source of biomarkers for diagnosing pediatric pneumonia.
Collapse
Affiliation(s)
- Juan Cheng
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongrui Ji
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Yong Yin
- Department of Pulmonary Disease, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shidong Wang
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Kai Song
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China
| | - Qiuhui Pan
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinghua Zhang
- Wayen Biotechnologies (Shanghai), Inc., Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai, China
| | - Lin Yang
- Department of Clinical Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
2
|
D’Amato M, Iadarola P, Viglio S. Proteomic Analysis of Human Sputum for the Diagnosis of Lung Disorders: Where Are We Today? Int J Mol Sci 2022; 23:ijms23105692. [PMID: 35628501 PMCID: PMC9144372 DOI: 10.3390/ijms23105692] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
The identification of markers of inflammatory activity at the early stages of pulmonary diseases which share common characteristics that prevent their clear differentiation is of great significance to avoid misdiagnosis, and to understand the intrinsic molecular mechanism of the disorder. The combination of electrophoretic/chromatographic methods with mass spectrometry is currently a promising approach for the identification of candidate biomarkers of a disease. Since the fluid phase of sputum is a rich source of proteins which could provide an early diagnosis of specific lung disorders, it is frequently used in these studies. This report focuses on the state-of-the-art of the application, over the last ten years (2011-2021), of sputum proteomics in the investigation of severe lung disorders such as COPD; asthma; cystic fibrosis; lung cancer and those caused by COVID-19 infection. Analysis of the complete set of proteins found in sputum of patients affected by these disorders has allowed the identification of proteins whose levels change in response to the organism's condition. Understanding proteome dynamism may help in associating these proteins with alterations in the physiology or progression of diseases investigated.
Collapse
Affiliation(s)
- Maura D’Amato
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
| | - Paolo Iadarola
- Department of Biology and Biotechnologies “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
- Correspondence:
| | - Simona Viglio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
| |
Collapse
|
3
|
Gomez N, James V, Onion D, Fairclough LC. Extracellular vesicles and chronic obstructive pulmonary disease (COPD): a systematic review. Respir Res 2022; 23:82. [PMID: 35382831 PMCID: PMC8985325 DOI: 10.1186/s12931-022-01984-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/12/2022] [Indexed: 12/15/2022] Open
Abstract
Background Chronic Obstructive Pulmonary Disease (COPD) is a common inflammatory disease of the airways characterized by irreversible airflow limitation, ranking the third highest cause of death worldwide. Extracellular vesicles (EVs) are important intercellular communication mediators released by cells into their extracellular environment with the capacity to transfer biological signals. EVs involved in COPD hold great potential to understand disease pathogenesis and identify important biomarkers. This systematic review aims to examine all available research on EVs in the pathogenesis and diagnosis of COPD to identify existing knowledge and support further research within the field. Methods Publications were searched using PubMed and EMBASE with the search terms (Exosomes or extracellular vesicles or microvesicles or microparticles or ectosomes) AND (chronic obstructive pulmonary disease or COPD or emphysema or bronchitis). Results Initial search yielded 512 papers of which 142 were manually selected for review and 43 were eligible for analyses. The studies were divided into groups according to the role of EVs in pathogenesis, EV origin and cargo, their role in COPD exacerbations and their diagnostic utility. EVs were found to be involved in the mechanism of pathogenesis of COPD, derived from various cell types, as well as containing modified levels of miRNAs. EVs also varied according to the pathophysiological status of disease, therefore presenting a possible method for COPD diagnosis and progress monitoring. Conclusion The current findings show the limited but good quality research looking at the role of EVs in COPD, demonstrating the need for more studies to better define and provide further insight into the functional characteristics of EV in COPD pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-01984-0.
Collapse
Affiliation(s)
- Nancy Gomez
- School of Life Sciences, The University of Nottingham, Life Sciences Building, Nottingham, NG7 2RD, UK
| | - Victoria James
- School of Veterinary Medicine and Science, The University of Nottingham, Nottingham, NG7 2UH, UK
| | - David Onion
- School of Life Sciences, The University of Nottingham, Life Sciences Building, Nottingham, NG7 2RD, UK
| | - Lucy C Fairclough
- School of Life Sciences, The University of Nottingham, Life Sciences Building, Nottingham, NG7 2RD, UK.
| |
Collapse
|
4
|
Lättekivi F, Guljavina I, Midekessa G, Viil J, Heath PR, Bæk R, Jørgensen MM, Andronowska A, Kingo K, Fazeli A. Profiling Blood Serum Extracellular Vesicles in Plaque Psoriasis and Psoriatic Arthritis Patients Reveals Potential Disease Biomarkers. Int J Mol Sci 2022; 23:ijms23074005. [PMID: 35409365 PMCID: PMC9000144 DOI: 10.3390/ijms23074005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Psoriasis vulgaris (PsV) and psoriatic arthritis (PsA) are inflammatory diseases with unresolved pathophysiological aspects. Extracellular vesicles (EVs) play an important role in intercellular communication. We compared the miRNA contents and surface proteome of the EVs in the blood serum of PsV and PsA patients to healthy controls. Size-exclusion chromatography was used to isolate EVs from the blood serum of 12 PsV patients, 12 PsA patients and 12 healthy control subjects. EV samples were characterized and RNA sequencing was used to identify differentially enriched EV-bound miRNAs. We found 212 differentially enriched EV-bound miRNAs present in both PsV and PsA groups—a total of 13 miRNAs at FDR ≤ 0.05. The predicted target genes of these miRNAs were significantly related to lesser known but potentially disease-relevant pathways. The EV array revealed that PsV patient EV samples were significantly enriched with CD9 EV-marker compared to controls. Analysis of EV-bound miRNAs suggests that signaling via EVs in the blood serum could play a role in the pathophysiological processes of PsV and PsA. EVs may be able to fill the void in clinically applicable diagnostic and prognostic biomarkers for PsV and PsA.
Collapse
Affiliation(s)
- Freddy Lättekivi
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia; (F.L.); (I.G.); (G.M.)
| | - Irina Guljavina
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia; (F.L.); (I.G.); (G.M.)
| | - Getnet Midekessa
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia; (F.L.); (I.G.); (G.M.)
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
| | - Janeli Viil
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia;
| | - Paul R. Heath
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK;
| | - Rikke Bæk
- Department of Clinical Immunology, Aalborg University Hospital, Urbansgade 32-36, 9000 Aalborg, Denmark; (R.B.); (M.M.J.)
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital, Urbansgade 32-36, 9000 Aalborg, Denmark; (R.B.); (M.M.J.)
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9220 Aalborg, Denmark
| | - Aneta Andronowska
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima St. 10, 10-748 Olsztyn, Poland;
| | - Kulli Kingo
- Clinic of Dermatology, Institute of Clinical Medicine, University of Tartu, Raja 31, 50417 Tartu, Estonia;
- Clinic of Dermatology, Tartu University Hospital, Raja 31, 50417 Tartu, Estonia
| | - Alireza Fazeli
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia; (F.L.); (I.G.); (G.M.)
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
- Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield S10 2SF, UK
- Correspondence: ; Tel.: +372-737-4425
| |
Collapse
|
5
|
Rai A, Fang H, Claridge B, Simpson RJ, Greening DW. Proteomic dissection of large extracellular vesicle surfaceome unravels interactive surface platform. J Extracell Vesicles 2021; 10:e12164. [PMID: 34817906 PMCID: PMC8612312 DOI: 10.1002/jev2.12164] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/20/2021] [Accepted: 10/13/2021] [Indexed: 12/17/2022] Open
Abstract
The extracellular vesicle (EV) surface proteome (surfaceome) acts as a fundamental signalling gateway by bridging intra- and extracellular signalling networks, dictates EVs' capacity to communicate and interact with their environment, and is a source of potential disease biomarkers and therapeutic targets. However, our understanding of surface protein composition of large EVs (L-EVs, 100-800 nm, mean 310 nm, ATP5F1A, ATP5F1B, DHX9, GOT2, HSPA5, HSPD1, MDH2, STOML2), a major EV-subtype that are distinct from small EVs (S-EVs, 30-150 nm, mean 110 nm, CD44, CD63, CD81, CD82, CD9, PDCD6IP, SDCBP, TSG101) remains limited. Using a membrane impermeant derivative of biotin to capture surface proteins coupled to mass spectrometry analysis, we show that out of 4143 proteins identified in density-gradient purified L-EVs (1.07-1.11 g/mL, from multiple cancer cell lines), 961 proteins are surface accessible. The surface molecular diversity of L-EVs include (i) bona fide plasma membrane anchored proteins (cluster of differentiation, transporters, receptors and GPI anchored proteins implicated in cell-cell and cell-ECM interactions); and (ii) membrane surface-associated proteins (that are released by divalent ion chelator EDTA) implicated in actin cytoskeleton regulation, junction organization, glycolysis and platelet activation. Ligand-receptor analysis of L-EV surfaceome (e.g., ITGAV/ITGB1) uncovered interactome spanning 172 experimentally verified cognate binding partners (e.g., ANGPTL3, PLG, and VTN) with highest tissue enrichment for liver. Assessment of biotin inaccessible L-EV proteome revealed enrichment for proteins belonging to COPI/II-coated ER/Golgi-derived vesicles and mitochondria. Additionally, despite common surface proteins identified in L-EVs and S-EVs, our data reveals surfaceome heterogeneity between the two EV-subtype. Collectively, our study provides critical insights into diverse proteins operating at the interactive platform of L-EVs and molecular leads for future studies seeking to decipher L-EV heterogeneity and function.
Collapse
Affiliation(s)
- Alin Rai
- Molecular ProteomicsBaker Heart and Diabetes InstituteMelbourneVictoria3004Australia
- Central Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoria3052Australia
| | - Haoyun Fang
- Molecular ProteomicsBaker Heart and Diabetes InstituteMelbourneVictoria3004Australia
| | - Bethany Claridge
- Molecular ProteomicsBaker Heart and Diabetes InstituteMelbourneVictoria3004Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoria3086Australia
| | - Richard J. Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoria3086Australia
| | - David W Greening
- Molecular ProteomicsBaker Heart and Diabetes InstituteMelbourneVictoria3004Australia
- Central Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoria3052Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoria3086Australia
| |
Collapse
|
6
|
Hermann S, Brandes F, Kirchner B, Buschmann D, Borrmann M, Klein M, Kotschote S, Bonin M, Reithmair M, Kaufmann I, Schelling G, Pfaffl MW. Diagnostic potential of circulating cell-free microRNAs for community-acquired pneumonia and pneumonia-related sepsis. J Cell Mol Med 2020; 24:12054-12064. [PMID: 32916773 PMCID: PMC7578906 DOI: 10.1111/jcmm.15837] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-free microRNAs (miRNAs) are transferred in disease state including inflammatory lung diseases and are often packed into extracellular vesicles (EVs). To assess their suitability as biomarkers for community-acquired pneumonia (CAP) and severe secondary complications such as sepsis, we studied patients with CAP (n = 30), sepsis (n = 65) and healthy volunteers (n = 47) subdivided into a training (n = 67) and a validation (n = 75) cohort. After precipitating crude EVs from sera, associated small RNA was profiled by next-generation sequencing (NGS) and evaluated in multivariate analyses. A subset of the thereby identified biomarker candidates was validated both technically and additionally by reverse transcription quantitative real-time PCR (RT-qPCR). Differential gene expression (DGE) analysis revealed 29 differentially expressed miRNAs in CAP patients when compared to volunteers, and 25 miRNAs in patients with CAP, compared to those with sepsis. Sparse partial-least discriminant analysis separated groups based on 12 miRNAs. Three miRNAs proved as a significant biomarker signature. While expression levels of miR-1246 showed significant changes with an increase in overall disease severity from volunteers to CAP and to sepsis, miR-193a-5p and miR-542-3p differentiated patients with an infectious disease (CAP or sepsis) from volunteers. Cell-free miRNAs are potentially novel biomarkers for CAP and may help to identify patients at risk for progress to sepsis, facilitating early intervention and treatment.
Collapse
Affiliation(s)
- Stefanie Hermann
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Melanie Borrmann
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Matthias Klein
- Department of Neurology, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | | | | | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ines Kaufmann
- Department of Anesthesia, Klinikum Neuperlach, Munich City Hospitals, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| |
Collapse
|
7
|
Fong KM, Welte T. World Lung Day: what, why, and where to? Am J Physiol Lung Cell Mol Physiol 2020; 319:L527-L533. [PMID: 32783632 DOI: 10.1152/ajplung.00364.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Kwun M Fong
- Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia.,University of Queensland Thoracic Research Centre, Brisbane, Queensland, Australia
| | - Tobias Welte
- Department of Pulmonary and Infectious Diseases at Hannover University School of Medicine, Member of the German Center of Lung Research, Hannover, Germany
| | -
- The Forum of International Respiratory Societies, Lausanne, Switzerland
| |
Collapse
|