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Agraval H, Kandhari K, Yadav UCS. MMPs as potential molecular targets in epithelial-to-mesenchymal transition driven COPD progression. Life Sci 2024; 352:122874. [PMID: 38942362 DOI: 10.1016/j.lfs.2024.122874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of mortality globally and the risk of developing lung cancer is six times greater in individuals with COPD who smoke compared to those who do not smoke. Matrix metalloproteinases (MMPs) play a crucial role in the pathophysiology of respiratory diseases by promoting inflammation and tissue degradation. Furthermore, MMPs are involved in key processes like epithelial-to-mesenchymal transition (EMT), metastasis, and invasion in lung cancer. While EMT has traditionally been associated with the progression of lung cancer, recent research highlights its active involvement in individuals with COPD. Current evidence underscores its role in orchestrating airway remodeling, fostering airway fibrosis, and contributing to the potential for malignant transformation in the complex pathophysiology of COPD. The precise regulatory roles of diverse MMPs in steering EMT during COPD progression needs to be elucidated. Additionally, the less-understood aspect involves how these MMPs bi-directionally activate or regulate various EMT-associated signaling cascades during COPD progression. This review article explores recent advancements in understanding MMPs' role in EMT during COPD progression and various pharmacological approaches to target MMPs. It also delves into the limitations of current MMP inhibitors and explores novel, advanced strategies for inhibiting MMPs, potentially offering new avenues for treating respiratory diseases.
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Affiliation(s)
- Hina Agraval
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Kushal Kandhari
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Umesh C S Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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2
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Torres-Sangiao E, Happonen L, Heusel M, Palm F, Gueto-Tettay C, Malmström L, Shannon O, Malmström J. Quantification of Adaptive Immune Responses Against Protein-Binding Interfaces in the Streptococcal M1 Protein. Mol Cell Proteomics 2024; 23:100753. [PMID: 38527648 PMCID: PMC11059317 DOI: 10.1016/j.mcpro.2024.100753] [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: 04/03/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024] Open
Abstract
Bacterial or viral antigens can contain subdominant protein regions that elicit weak antibody responses upon vaccination or infection although there is accumulating evidence that antibody responses against subdominant regions can enhance the protective immune response. One proposed mechanism for subdominant protein regions is the binding of host proteins that prevent antibody production against epitopes hidden within the protein binding interfaces. Here, we used affinity purification combined with quantitative mass spectrometry (AP-MS) to examine the level of competition between antigen-specific antibodies and host-pathogen protein interaction networks using the M1 protein from Streptococcus pyogenes as a model system. As most humans have circulating antibodies against the M1 protein, we first used AP-MS to show that the M1 protein interspecies protein network formed with human plasma proteins is largely conserved in naïve mice. Immunizing mice with the M1 protein generated a time-dependent increase of anti-M1 antibodies. AP-MS analysis comparing the composition of the M1-plasma protein network from naïve and immunized mice showed significant enrichment of 292 IgG peptides associated with 56 IgG chains in the immune mice. Despite the significant increase of bound IgGs, the levels of interacting plasma proteins were not significantly reduced in the immune mice. The results indicate that the antigen-specific polyclonal IgG against the M1 protein primarily targets epitopes outside the other plasma protein binding interfaces. In conclusion, this study demonstrates that AP-MS is a promising strategy to determine the relationship between antigen-specific antibodies and host-pathogen interaction networks that could be used to define subdominant protein regions of relevance for vaccine development.
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Affiliation(s)
- Eva Torres-Sangiao
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Escherichia coli Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Clinical Microbiology Lab, University Hospital Complex of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Lotta Happonen
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Morizt Heusel
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Evosep ApS, Odense, Denmark
| | - Frida Palm
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Carlos Gueto-Tettay
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lars Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Onna Shannon
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Faculty of Odontology, Section for Oral Biology and Pathology, Malmö University, Malmö, Sweden
| | - Johan Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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3
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Burgess JK, Weiss DJ, Westergren-Thorsson G, Wigen J, Dean CH, Mumby S, Bush A, Adcock IM. Extracellular Matrix as a Driver of Chronic Lung Diseases. Am J Respir Cell Mol Biol 2024; 70:239-246. [PMID: 38190723 DOI: 10.1165/rcmb.2023-0176ps] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
The extracellular matrix (ECM) is not just a three-dimensional scaffold that provides stable support for all cells in the lungs, but also an important component of chronic fibrotic airway, vascular, and interstitial diseases. It is a bioactive entity that is dynamically modulated during tissue homeostasis and disease, that controls structural and immune cell functions and drug responses, and that can release fragments that have biological activity and that can be used to monitor disease activity. There is a growing recognition of the importance of considering ECM changes in chronic airway, vascular, and interstitial diseases, including 1) compositional changes, 2) structural and organizational changes, and 3) mechanical changes and how these affect disease pathogenesis. As altered ECM biology is an important component of many lung diseases, disease models must incorporate this factor to fully recapitulate disease-driver pathways and to study potential novel therapeutic interventions. Although novel models are evolving that capture some or all of the elements of the altered ECM microenvironment in lung diseases, opportunities exist to more fully understand cell-ECM interactions that will help devise future therapeutic targets to restore function in chronic lung diseases. In this perspective article, we review evolving knowledge about the ECM's role in homeostasis and disease in the lung.
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Affiliation(s)
- Janette K Burgess
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD, and
- W.J. Kolff Institute for Biomedical Engineering and Materials Science, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Daniel J Weiss
- Department of Medicine, University of Vermont, Burlington, Vermont
| | | | - Jenny Wigen
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Charlotte H Dean
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Sharon Mumby
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
- Centre for Pediatrics and Child Health, Imperial College and Royal Brompton Hospital, London, United Kingdom
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
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4
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Coates-Park S, Rich JA, Stetler-Stevenson WG, Peeney D. The TIMP protein family: diverse roles in pathophysiology. Am J Physiol Cell Physiol 2024; 326:C917-C934. [PMID: 38284123 PMCID: PMC11193487 DOI: 10.1152/ajpcell.00699.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
The tissue inhibitors of matrix metalloproteinases (TIMPs) are a family of four matrisome proteins classically defined by their roles as the primary endogenous inhibitors of metalloproteinases (MPs). Their functions however are not limited to MP inhibition, with each family member harboring numerous MP-independent biological functions that play key roles in processes such as inflammation and apoptosis. Because of these multifaceted functions, TIMPs have been cited in diverse pathophysiological contexts. Herein, we provide a comprehensive overview of the MP-dependent and -independent roles of TIMPs across a range of pathological conditions. The potential therapeutic and biomarker applications of TIMPs in these disease contexts are also considered, highlighting the biomedical promise of this complex and often misunderstood protein family.
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Affiliation(s)
- Sasha Coates-Park
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States
| | - Joshua A Rich
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States
| | - William G Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States
| | - David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States
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5
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Major G, Simcock J, Kumar A, Kleffmann T, Woodfield TBF, Lim KS. Comprehensive Matrisome Profiling of Human Adipose Tissue for Soft Tissue Reconstruction. Adv Biol (Weinh) 2024; 8:e2300448. [PMID: 37953659 DOI: 10.1002/adbi.202300448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/14/2023] [Indexed: 11/14/2023]
Abstract
For effective translation of research from tissue engineering and regenerative medicine domains, the cell-instructive extracellular matrix (ECM) of specific tissues must be accurately realized. As adipose tissue is gaining traction as a biomaterial for soft tissue reconstruction, with highly variable clinical outcomes obtained, a quantitative investigation of the adipose tissue matrisome is overdue. In this study, the human adipose tissue matrisome is profiled using quantitative sequential windowed acquisition of all theoretical fragment ion spectra - mass spectrometry (SWATH-MS) proteomics across a cohort of 13 fat-grafting patients, to provide characterization of ECM proteins within the tissue, and to understand human population variation. There are considerable differences in the expression of matrisome proteins across the patient cohort, with age and lipoaspirate collection technique contributing to the greatest variation across the core matrisome. A high abundance of basement membrane proteins (collagen IV and heparan sulfate proteoglycan) is detected, as well as fibrillar collagens I and II, reflecting the hierarchical structure of the tissue. This study provides a comprehensive proteomic evaluation of the adipose tissue matrisome and contributes to an enhanced understanding of the influence of the matrisome in adipose-related pathologies by providing a healthy reference cohort and details an experimental pipeline that can be further exploited for future biomaterial development.
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Affiliation(s)
- Gretel Major
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
| | - Jeremy Simcock
- Department of Surgery, University of Otago, Christchurch, 8011, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, Research Infrastructure Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Research Infrastructure Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Tim B F Woodfield
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
| | - Khoon S Lim
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
- Light-Activated Biomaterials Group, School of Medical Science, University of Sydney, Sydney, NSW, 2006, Australia
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6
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Wang X, Zhang D, Zhu Y, Li D, Shen L, Wang Q, Gao Y, Li X, Yu M. Protein lysine acetylation played an important role in NH 3-induced AEC2 damage and pulmonary fibrosis in piglets. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168303. [PMID: 37939958 DOI: 10.1016/j.scitotenv.2023.168303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Gaseous ammonia (NH3), as a main air pollutant in pig farms and surrounding areas, directly affects animal and human health. The lung, as an important organ for gas exchange in the respiratory system, is damaged after NH3 exposure, but the underlying mechanism needs to be further explored. In this study, seven weeks old piglets were exposed to 50 ppm NH3 for 30 days, and displayed pulmonary fibrosis. Then, the toxicological mechanism of NH3-induced pulmonary fibrosis was explored from the aspects of whole genome wide protein expression and post-translational modification. Totally, 404 differentially expressed proteins (DEPs) and 136 differentially lysine acetylated proteins (DAPs) were identified. The expression or lysine acetylation levels of proteins involved in mitochondrial energy metabolism including fatty acid oxidation (CPT1A, ACADVL, ACADS, HADHA, and HADHB), TCA cycle (IDH2 and MDH2), and oxidative phosphorylation (NDUFB7, NDUFV1, ATP5PB, ATP5F1A, COX5A, and COX5B) were significantly changed after NH3 exposure, which suggested that NH3 disrupted mitochondrial energy metabolism in the lung of piglets. Next, we found that type 2 alveolar epithelial cells (AEC2) damaged after NH3 exposure in vivo and in vitro. Integrin-linked kinase (ILK) was enriched in focal adhesion pathway, and showed significantly up-regulated acetylation levels at K191 (FC = 2.99) and K209 sites (FC = 1.52) after NH3 exposure. We illustrated that ILK-K191 hyper-acetylation inhibited AEC2 proliferation and induced AEC2 apoptosis by down-regulating pAKT-S473 in vitro. In conclusion, for the first time, our study revealed that protein acetylation played an important role in the process of NH3-induced pulmonary fibrosis in piglets. Our findings provided valuable insights into toxicological harm of NH3 to human health.
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Affiliation(s)
- Xiaotong Wang
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Di Zhang
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaxue Zhu
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojie Li
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Shen
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiankun Wang
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun Gao
- College of Engineering, the Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoping Li
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Smart Animal Farming Technology, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mei Yu
- College of Animal Science and Technology, Center for Advanced Science in Animal Breeding and Health Breeding, Huazhong Agricultural University, Wuhan 430070, China
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7
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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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8
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Mattoo H, Bangari DS, Cummings S, Humulock Z, Habiel D, Xu EY, Pate N, Resnick R, Savova V, Qian G, Beil C, Rao E, Nestle FO, Bryce PJ, Subramaniam A. Molecular Features and Stages of Pulmonary Fibrosis Driven by Type 2 Inflammation. Am J Respir Cell Mol Biol 2023; 69:404-421. [PMID: 37369139 DOI: 10.1165/rcmb.2022-0301oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/27/2023] [Indexed: 06/29/2023] Open
Abstract
Systemic sclerosis (SSc) is a progressive, multiorgan disease with limited treatment options. Although a recent proof-of-concept study using romilkimab or SAR156597, a bispecific IL-4/IL-13 antibody, suggests a direct role of these cytokines in the pathophysiology of SSc, their contributions to the balance between inflammation and fibrosis are unclear. Here, we determine the roles of type 2 inflammation in fibrogenesis using FRA2-Tg (Fos-related antigen 2-overexpressing transgenic) mice, which develop spontaneous, age-dependent progressive lung fibrosis. We defined the molecular signatures of inflammation and fibrosis at three key stages in disease progression, corresponding to preonset, inflammatory dominant, and fibrosis dominant biology, and revealed an early increase in cytokine-cytokine receptor interactions and antigen-processing and presentation pathways followed by enhanced Th2- and M2 macrophage-driven type 2 responses. This type 2 inflammation progressed to extensive fibrotic pathology by 14-18 weeks of age, with these gene signatures overlapping significantly with those seen in the lungs of patients with SSc with interstitial lung disease (ILD). These changes were also evident in the histopathology, which showed perivascular and peribronchiolar inflammation with prominent eosinophilia and accumulation of profibrotic M2-like macrophages followed by rapid progression to fibrosis with thickened alveolar walls with multifocal fibrotic bands and signs of interstitial pneumonia. Critically, treatment with a bispecific antibody targeting IL-4 and IL-13 during the inflammatory phase abrogated the Th2 and M2 responses and led to near-complete abrogation of lung fibrosis. These data recapitulate important features of fibrotic progression in the lungs of patients with SSc-ILD and enhance our understanding of the progressive pathobiology of SSc. This study also further establishes FRA2-Tg mice as a valuable tool for testing future therapeutic agents in SSc-ILD.
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Affiliation(s)
| | | | - Sheila Cummings
- Discovery Pathology, Translational In Vivo Models Platform, and
| | | | - David Habiel
- Immunology and Inflammation Research Therapeutic Area
| | - Ethan Y Xu
- Precision Medicine and Computational Biology
- Aspen Neuroscience, San Diego, California
| | - Nathan Pate
- Discovery Pathology, Translational In Vivo Models Platform, and
| | | | | | - George Qian
- Immunology and Inflammation Research Therapeutic Area
| | | | - Ercole Rao
- Biologics Research, Sanofi, Frankfurt, Germany; and
| | | | - Paul J Bryce
- Immunology and Inflammation Research Therapeutic Area
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9
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Hewitt RJ, Puttur F, Gaboriau DCA, Fercoq F, Fresquet M, Traves WJ, Yates LL, Walker SA, Molyneaux PL, Kemp SV, Nicholson AG, Rice A, Roberts E, Lennon R, Carlin LM, Byrne AJ, Maher TM, Lloyd CM. Lung extracellular matrix modulates KRT5 + basal cell activity in pulmonary fibrosis. Nat Commun 2023; 14:6039. [PMID: 37758700 PMCID: PMC10533905 DOI: 10.1038/s41467-023-41621-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Aberrant expansion of KRT5+ basal cells in the distal lung accompanies progressive alveolar epithelial cell loss and tissue remodelling during fibrogenesis in idiopathic pulmonary fibrosis (IPF). The mechanisms determining activity of KRT5+ cells in IPF have not been delineated. Here, we reveal a potential mechanism by which KRT5+ cells migrate within the fibrotic lung, navigating regional differences in collagen topography. In vitro, KRT5+ cell migratory characteristics and expression of remodelling genes are modulated by extracellular matrix (ECM) composition and organisation. Mass spectrometry- based proteomics revealed compositional differences in ECM components secreted by primary human lung fibroblasts (HLF) from IPF patients compared to controls. Over-expression of ECM glycoprotein, Secreted Protein Acidic and Cysteine Rich (SPARC) in the IPF HLF matrix restricts KRT5+ cell migration in vitro. Together, our findings demonstrate how changes to the ECM in IPF directly influence KRT5+ cell behaviour and function contributing to remodelling events in the fibrotic niche.
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Affiliation(s)
- Richard J Hewitt
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Franz Puttur
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | | | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - William J Traves
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Laura L Yates
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Simone A Walker
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Philip L Molyneaux
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Samuel V Kemp
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, City Campus, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Andrew G Nicholson
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Alexandra Rice
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Edward Roberts
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Leo M Carlin
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Adam J Byrne
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Keck Medicine of USC, 1510 San Pablo Street, Los Angeles, CA, 90033, USA
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK.
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10
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Hewawasam RS, Blomberg R, Šerbedžija P, Magin CM. Chemical Modification of Human Decellularized Extracellular Matrix for Incorporation into Phototunable Hybrid-Hydrogel Models of Tissue Fibrosis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:15071-15083. [PMID: 36917510 PMCID: PMC11177228 DOI: 10.1021/acsami.2c18330] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Tissue fibrosis remains a serious health condition with high morbidity and mortality rates. There is a critical need to engineer model systems that better recapitulate the spatial and temporal changes in the fibrotic extracellular microenvironment and enable study of the cellular and molecular alterations that occur during pathogenesis. Here, we present a process for chemically modifying human decellularized extracellular matrix (dECM) and incorporating it into a dynamically tunable hybrid-hydrogel system containing a poly(ethylene glycol)-α methacrylate (PEGαMA) backbone. Following modification and characterization, an off-stoichiometry thiol-ene Michael addition reaction resulted in hybrid-hydrogels with mechanical properties that could be tuned to recapitulate many healthy tissue types. Next, photoinitiated, free-radical homopolymerization of excess α-methacrylates increased crosslinking density and hybrid-hydrogel elastic modulus to mimic a fibrotic microenvironment. The incorporation of dECM into the PEGαMA hydrogel decreased the elastic modulus and, relative to fully synthetic hydrogels, increased the swelling ratio, the average molecular weight between crosslinks, and the mesh size of hybrid-hydrogel networks. These changes were proportional to the amount of dECM incorporated into the network. Dynamic stiffening increased the elastic modulus and decreased the swelling ratio, average molecular weight between crosslinks, and the mesh size of hybrid-hydrogels, as expected. Stiffening also activated human fibroblasts, as measured by increases in average cellular aspect ratio (1.59 ± 0.02 to 2.98 ± 0.20) and expression of α-smooth muscle actin (αSMA). Fibroblasts expressing αSMA increased from 25.8 to 49.1% upon dynamic stiffening, demonstrating that hybrid-hydrogels containing human dECM support investigation of dynamic mechanosensing. These results improve our understanding of the biomolecular networks formed within hybrid-hydrogels: this fully human phototunable hybrid-hydrogel system will enable researchers to control and decouple the biochemical changes that occur during fibrotic pathogenesis from the resulting increases in stiffness to study the dynamic cell-matrix interactions that perpetuate fibrotic diseases.
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Affiliation(s)
- Rukshika S Hewawasam
- Department of Bioengineering, University of Colorado, Denver|Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
| | - Rachel Blomberg
- Department of Bioengineering, University of Colorado, Denver|Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
| | - Predrag Šerbedžija
- Department of Bioengineering, University of Colorado, Denver|Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
| | - Chelsea M Magin
- Department of Bioengineering, University of Colorado, Denver|Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Anschutz Medical Campus, 2115 Scranton Street, Suite 3010, Aurora, Colorado 80045-2559, United States
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11
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Christopoulou ME, Papakonstantinou E, Stolz D. Matrix Metalloproteinases in Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2023; 24:ijms24043786. [PMID: 36835197 PMCID: PMC9966421 DOI: 10.3390/ijms24043786] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are proteolytic enzymes that degrade proteins of the extracellular matrix and the basement membrane. Thus, these enzymes regulate airway remodeling, which is a major pathological feature of chronic obstructive pulmonary disease (COPD). Furthermore, proteolytic destruction in the lungs may lead to loss of elastin and the development of emphysema, which is associated with poor lung function in COPD patients. In this literature review, we describe and appraise evidence from the recent literature regarding the role of different MMPs in COPD, as well as how their activity is regulated by specific tissue inhibitors. Considering the importance of MMPs in COPD pathogenesis, we also discuss MMPs as potential targets for therapeutic intervention in COPD and present evidence from recent clinical trials in this regard.
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Affiliation(s)
- Maria-Elpida Christopoulou
- Department of Pneumology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Eleni Papakonstantinou
- Department of Pneumology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, 4031 Basel, Switzerland
| | - Daiana Stolz
- Department of Pneumology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, 4031 Basel, Switzerland
- Correspondence: ; Tel.: +49-(0)-761-270-37050
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12
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Chang M. Matrix metalloproteinase profiling and their roles in disease. RSC Adv 2023; 13:6304-6316. [PMID: 36825288 PMCID: PMC9942564 DOI: 10.1039/d2ra07005g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Matrix metalloproteinases (MMPs) play roles in remodelling of the extracellular matrix that occurs during morphogenesis, repair, and angiogenesis. Dysregulation of extracellular matrix remodelling can lead to cell proliferation, invasion, and tissue fibrosis. Identification of a specific MMP(s) in a disease has been challenging due to the presence of 24 closely-related human MMPs, each existing in three forms, of which only one is active and capable of catalysis. This review focuses on methods for MMP profiling, with particular emphasis on the batimastat affinity resin that binds only to the active forms of MMPs and related ADAMs (a disintegrin and metalloproteinases), which are then identified by mass spectrometry. Use of the batimastat affinity resin has identified targets for intervention in several human diseases.
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Affiliation(s)
- Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
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13
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Weiss DJ. What is the need and why is it time for innovative models for understanding lung repair and regeneration? Front Pharmacol 2023; 14:1130074. [PMID: 36860303 PMCID: PMC9968746 DOI: 10.3389/fphar.2023.1130074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
Advances in tissue engineering continue at a rapid pace and have provided novel methodologies and insights into normal cell and tissue homeostasis, disease pathogenesis, and new potential therapeutic strategies. The evolution of new techniques has particularly invigorated the field and span a range from novel organ and organoid technologies to increasingly sophisticated imaging modalities. This is particularly relevant for the field of lung biology and diseases as many lung diseases, including chronic obstructive pulmonary disease (COPD) and idiopathic fibrosis (IPF), among others, remain incurable with significant morbidity and mortality. Advances in lung regenerative medicine and engineering also offer new potential avenues for critical illnesses such as the acute respiratory distress syndrome (ARDS) which also continue to have significant morbidity and mortality. In this review, an overview of lung regenerative medicine with focus on current status of both structural and functional repair will be presented. This will serve as a platform for surveying innovative models and techniques for study, highlighting the need and timeliness for these approaches.
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14
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Renaud L, Waldrep KM, da Silveira WA, Pilewski JM, Feghali-Bostwick CA. First Characterization of the Transcriptome of Lung Fibroblasts of SSc Patients and Healthy Donors of African Ancestry. Int J Mol Sci 2023; 24:3645. [PMID: 36835058 PMCID: PMC9966000 DOI: 10.3390/ijms24043645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
Systemic sclerosis (SSc) is a connective tissue disorder that results in fibrosis of the skin and visceral organs. SSc-associated pulmonary fibrosis (SSc-PF) is the leading cause of death amongst SSc patients. Racial disparity is noted in SSc as African Americans (AA) have a higher frequency and severity of disease than European Americans (EA). Using RNAseq, we determined differentially expressed genes (DEGs; q < 0.1, log2FC > |0.6|) in primary pulmonary fibroblasts from SSc lungs (SScL) and normal lungs (NL) of AA and EA patients to characterize the unique transcriptomic signatures of AA-NL and AA-SScL fibroblasts using systems-level analysis. We identified 69 DEGs in "AA-NL vs. EA-NL" and 384 DEGs in "AA-SScL vs. EA-SScL" analyses, and a comparison of disease mechanisms revealed that only 7.5% of DEGs were commonly deregulated in AA and EA patients. Surprisingly, we also identified an SSc-like signature in AA-NL fibroblasts. Our data highlight differences in disease mechanisms between AA and EA SScL fibroblasts and suggest that AA-NL fibroblasts are in a "pre-fibrosis" state, poised to respond to potential fibrotic triggers. The DEGs and pathways identified in our study provide a wealth of novel targets to better understand disease mechanisms leading to racial disparity in SSc-PF and develop more effective and personalized therapies.
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Affiliation(s)
- Ludivine Renaud
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kristy M. Waldrep
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Willian A. da Silveira
- Department of Biological Sciences, School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent ST4 2DF, UK
| | - Joseph M. Pilewski
- Department of Medicine, Pulmonary, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carol A. Feghali-Bostwick
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
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15
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Hoffman ET, Uhl FE, Asarian L, Deng B, Becker C, Uriarte JJ, Downs I, Young B, Weiss DJ. Regional and disease specific human lung extracellular matrix composition. Biomaterials 2023; 293:121960. [PMID: 36580718 PMCID: PMC9868084 DOI: 10.1016/j.biomaterials.2022.121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Chronic lung diseases, such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), are characterized by regional extracellular matrix (ECM) remodeling which contributes to disease progression. Previous proteomic studies on whole decellularized lungs have provided detailed characterization on the impact of COPD and IPF on total lung ECM composition. However, such studies are unable to determine the differences in ECM composition between individual anatomical regions of the lung. Here, we employ a post-decellularization dissection method to compare the ECM composition of whole decellularized lungs (wECM) and specific anatomical lung regions, including alveolar-enriched ECM (aECM), airway ECM (airECM), and vasculature ECM (vECM), between non-diseased (ND), COPD, and IPF human lungs. We demonstrate, using mass spectrometry, that individual regions possess a unique ECM signature characterized primarily by differences in collagen composition and basement-membrane associated proteins, including ECM glycoproteins. We further demonstrate that both COPD and IPF lead to alterations in lung ECM composition in a region-specific manner, including enrichment of type-III collagen and fibulin in IPF aECM. Taken together, this study provides methodology for future studies, including isolation of region-specific lung biomaterials, as well as a dataset that may be applied for the identification of novel ECM targets for therapeutics.
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Affiliation(s)
- Evan T. Hoffman
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Franziska E. Uhl
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
| | - Loredana Asarian
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Bin Deng
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Chloe Becker
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Juan J. Uriarte
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Isaac Downs
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Brad Young
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Daniel J. Weiss
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
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16
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Wang Y, Zhang J, Zhang X, Zhang H, Cao X, Hu T, Lin J, Tang X, Chen X, Jiang Y, Yan X, Zhuang H, Luo P, Shen L. Study on the Mechanism of Arsenic-Induced Lung Injury Based on SWATH Proteomics Technology. Biol Trace Elem Res 2022:10.1007/s12011-022-03466-2. [PMID: 36333559 DOI: 10.1007/s12011-022-03466-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/07/2022]
Abstract
Chronic arsenic poisoning is a global health problem that affects millions of people, and studies have found that long-term ingestion of arsenic-containing compounds can lead to lung damage, but the exact mechanism is unknown. In this study, Sprague-Dawley (SD) rats were used as the research object, and the proteomic analysis method based on sequential window acquisition of all theoretical fragment ions (SWATH) was used to detect the changes in the expression levels of related proteins in the lung tissue of arsenic-exposed rats, and to explore the mechanism of arsenic compound-induced lung injury. The results showed that arsenic exposure resulted in the abnormal expression of collagen type III and proteins involved in metabolic, immune, and cellular processes, leading to the dysfunction of important pathways associated with these proteins, resulting in lung injury. It suggested that the underlying mechanism of arsenic-induced lung injury may be related to oxidative stress, immune injury, cell junction, and collagen type III. This result provides a new research idea for revealing the mechanism of lung injury caused by arsenic exposure.
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Affiliation(s)
- Yi Wang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Jun Zhang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xinglai Zhang
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Ting Hu
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Xiaolu Chen
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Yuxuan Jiang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xi Yan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Peng Luo
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China.
| | - Liming Shen
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, People's Republic of China.
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, People's Republic of China.
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17
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Pinezich MR, Tamargo MA, Fleischer S, Reimer JA, Hudock MR, Hozain AE, Kaslow SR, Tipograf Y, Soni RK, Gavaudan OP, Guenthart BA, Marboe CC, Bacchetta M, O'Neill JD, Dorrello NV, Vunjak-Novakovic G. Pathological remodeling of distal lung matrix in end-stage cystic fibrosis patients. J Cyst Fibros 2022; 21:1027-1035. [PMID: 35525782 PMCID: PMC10050894 DOI: 10.1016/j.jcf.2022.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/14/2022] [Accepted: 04/20/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Manifestations of cystic fibrosis, although well-characterized in the proximal airways, are understudied in the distal lung. Characterization of the cystic fibrosis lung 'matrisome' (matrix proteome) has not been previously described, and could help identify biomarkers and inform therapeutic strategies. METHODS We performed liquid chromatography-mass spectrometry, gene ontology analysis, and multi-modal imaging, including histology, immunofluorescence, and electron microscopy for a comprehensive evaluation of distal human lung extracellular matrix (matrix) structure and composition in end-stage cystic fibrosis. RESULTS Quantitative proteomic profiling identified sixty-eight (68) matrix constituents with significantly altered expression in end-stage cystic fibrosis. Over 90% of significantly different matrix peptides detected, including structural and basement membrane proteins, were expressed at lower levels in cystic fibrosis. However, the total abundance of matrix in cystic fibrosis lungs was not significantly different from control lungs, suggesting that cystic fibrosis leads to loss of diversity among lung matrix proteins rather than an absolute loss of matrix. Visualization of distal lung matrix via immunofluorescence and electron microscopy revealed pathological remodeling of distal lung tissue architecture and loss of alveolar basement membrane, consistent with significantly altered pathways identified by gene ontology analysis. CONCLUSIONS Dysregulation of matrix organization and aberrant wound healing pathways are associated with loss of matrix protein diversity and obliteration of distal lung tissue structure in end-stage cystic fibrosis. While many therapeutics aim to functionally restore defective cystic fibrosis transmembrane conductance regulator (CFTR), drugs that target dysregulated matrix pathways may serve as adjunct interventions to support lung recovery.
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Affiliation(s)
- Meghan R Pinezich
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jonathan A Reimer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria R Hudock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Ahmed E Hozain
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah R Kaslow
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Yuliya Tipograf
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Olimpia P Gavaudan
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Brandon A Guenthart
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Charles C Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew Bacchetta
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - John D O'Neill
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - N Valerio Dorrello
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; College of Dental Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Dooling LJ, Saini K, Anlaş AA, Discher DE. Tissue mechanics coevolves with fibrillar matrisomes in healthy and fibrotic tissues. Matrix Biol 2022; 111:153-188. [PMID: 35764212 PMCID: PMC9990088 DOI: 10.1016/j.matbio.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 12/12/2022]
Abstract
Fibrillar proteins are principal components of extracellular matrix (ECM) that confer mechanical properties to tissues. Fibrosis can result from wound repair in nearly every tissue in adults, and it associates with increased ECM density and crosslinking as well as increased tissue stiffness. Such fibrotic tissues are a major biomedical challenge, and an emerging view posits that the altered mechanical environment supports both synthetic and contractile myofibroblasts in a state of persistent activation. Here, we review the matrisome in several fibrotic diseases, as well as normal tissues, with a focus on physicochemical properties. Stiffness generally increases with the abundance of fibrillar collagens, the major constituent of ECM, with similar mathematical trends for fibrosis as well as adult tissues from soft brain to stiff bone and heart development. Changes in expression of other core matrisome and matrisome-associated proteins or proteoglycans contribute to tissue stiffening in fibrosis by organizing collagen, crosslinking ECM, and facilitating adhesion of myofibroblasts. Understanding how ECM composition and mechanics coevolve during fibrosis can lead to better models and help with antifibrotic therapies.
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Affiliation(s)
- Lawrence J Dooling
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Karanvir Saini
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Alişya A Anlaş
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA.
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19
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Peng Z, Konai MM, Avila-Cobian LF, Wang M, Mobashery S, Chang M. MMP-1 and ADAM10 as Targets for Therapeutic Intervention in Idiopathic Pulmonary Fibrosis. ACS Pharmacol Transl Sci 2022; 5:548-554. [DOI: 10.1021/acsptsci.2c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Zhihong Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mohini Mohan Konai
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Luis F. Avila-Cobian
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Man Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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20
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Christenson SA, Smith BM, Bafadhel M, Putcha N. Chronic obstructive pulmonary disease. Lancet 2022; 399:2227-2242. [PMID: 35533707 DOI: 10.1016/s0140-6736(22)00470-6] [Citation(s) in RCA: 254] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity, mortality, and health-care use worldwide. COPD is caused by exposure to inhaled noxious particles, notably tobacco smoke and pollutants. However, the broad range of factors that increase the risk of development and progression of COPD throughout the life course are increasingly being recognised. Innovations in omics and imaging techniques have provided greater insight into disease pathobiology, which might result in advances in COPD prevention, diagnosis, and treatment. Although few novel treatments have been approved for COPD in the past 5 years, advances have been made in targeting existing therapies to specific subpopulations using new biomarker-based strategies. Additionally, COVID-19 has undeniably affected individuals with COPD, who are not only at higher risk for severe disease manifestations than healthy individuals but also negatively affected by interruptions in health-care delivery and social isolation. This Seminar reviews COPD with an emphasis on recent advances in epidemiology, pathophysiology, imaging, diagnosis, and treatment.
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Affiliation(s)
- Stephanie A Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin M Smith
- Department of Medicine, Columbia University Medical Center, New York, NY, USA; Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Mona Bafadhel
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Department of Respiratory Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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21
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Tang F, Brune JE, Chang MY, Reeves SR, Altemeier WA, Frevert CW. Defining the Versican Interactome in Lung Health and Disease. Am J Physiol Cell Physiol 2022; 323:C249-C276. [PMID: 35649251 PMCID: PMC9291419 DOI: 10.1152/ajpcell.00162.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The extracellular matrix (ECM) imparts critical mechanical and biochemical information to cells in the lungs. Proteoglycans are essential constituents of the ECM and play a crucial role in controlling numerous biological processes, including regulating cellular phenotype and function. Versican, a chondroitin sulfate proteoglycan required for embryonic development, is almost absent from mature, healthy lungs and is re-expressed and accumulates in acute and chronic lung disease. Studies using genetically engineered mice show that the versican-enriched matrix can be pro- or anti-inflammatory depending on the cellular source or disease process studied. The mechanisms whereby versican develops a contextual ECM remain largely unknown. The primary goal of this review is to provide an overview of the interaction of versican with its many binding partners, the "versican interactome," and how through these interactions, versican is an integrator of complex extracellular information. Hopefully, the information provided in this review will be used to develop future studies to determine how versican and its binding partners can develop contextual ECMs that control select biological processes. While this review focuses on versican and the lungs, what is described can be extended to other proteoglycans, tissues, and organs.
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Affiliation(s)
- Fengying Tang
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Jourdan E Brune
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Mary Y Chang
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Stephen R Reeves
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - William A Altemeier
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,ivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Charles W Frevert
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States.,ivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
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22
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Yao Y, Li Z, Gao W. Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and NSCLC Progression:Evidence From Bioinformatics Analysis. Front Genet 2022; 13:855789. [PMID: 35480306 PMCID: PMC9038140 DOI: 10.3389/fgene.2022.855789] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/18/2022] [Indexed: 12/22/2022] Open
Abstract
Background: Lung cancer is the most common comorbidity of idiopathic pulmonary fibrosis. Thus there is an urgent need for the research of IPF and carcinogenesis Objective: The objective of this study was to explore hub genes which are common in pulmonary fibrosis and lung cancer progression through bioinformatic analysis. Methods: All the analysis was performed in R software. Differentially expressed genes (DEGs) were explored by comparing gene expression profiles between IPF tissues and healthy lung tissues from GSE24206, GSE53845, GSE101286 and GSE110147 datasets. Venn Diagram analysis was used to identify the overlapping genes, while GO and KEGG pathway enrichment analysis were used to explore the biological functions of the DEGs using clusterprofiler package. Hub genes were identified by analyzing protein-protein interaction networks using Cytoscape software. Nomogram was constructed using the rms package. Tumor immune dysfunction and exclusion (TIDE) and Genomics of Drug Sensitivity in Cancer (GDSC) analysis was used to quantify the immunotherapy and chemotherapy sensitivity of non-small cell lung cancer (NSCLC) patients. Results:COL1A1, COL3A1, MMP1, POSTN1 and TIMP3 were identified as the top five hub genes. The five hub genes were used to construct a diagnostic nomogram that was validated in another IPF dataset. Since the hub genes were also associated with lung cancer progression, we found that the nomogram also had diagnostic value in NSCLC patients. These five genes achieved a statistically difference of overall survival in NSCLC patients (p < 0.05). The expression of the five hub genes was mostly enriched in fibroblasts. Fibroblasts and the hub genes also showed significant ability to predict the susceptibility of NSCLC patients to chemotherapy and immunotherapy. Conclusion: We identified five hub genes as potential biomarkers of IPF and NSCLC progression. This finding may give insight into the underlying molecular mechanisms of IPF and lung cancer progression and provides potential targets for developing new therapeutic agents for IPF patients.
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23
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Staab-Weijnitz CA. Fighting the Fiber: Targeting Collagen in Lung Fibrosis. Am J Respir Cell Mol Biol 2021; 66:363-381. [PMID: 34861139 DOI: 10.1165/rcmb.2021-0342tr] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Organ fibrosis is characterized by epithelial injury and aberrant tissue repair, where activated effector cells, mostly fibroblasts and myofibroblasts, excessively deposit collagen into the extracellular matrix. Fibrosis frequently results in organ failure and has been estimated to contribute to at least one third of all global deaths. Also lung fibrosis, in particular idiopathic pulmonary fibrosis (IPF), is a fatal disease with rising incidence worldwide. As current treatment options targeting fibrogenesis are insufficient, there is an urgent need for novel therapeutic strategies. During the last decade, several studies have proposed to target intra- and extracellular components of the collagen biosynthesis, maturation, and degradation machinery. This includes intra- and extracellular targets directly acting on collagen gene products, but also such that anabolize essential building blocks of collagen, in particular glycine and proline biosynthetic enzymes. Collagen, however, is a ubiquitous molecule in the body and fulfils essential functions as a macromolecular scaffold, growth factor reservoir, and receptor binding site in virtually every tissue. This review summarizes recent advances and future directions in this field. Evidence for the proposed therapeutic targets and where they currently stand in terms of clinical drug development for treatment of fibrotic disease is provided. The drug targets are furthermore discussed in light of (1) specificity for collagen biosynthesis, maturation and degradation, and (2) specificity for disease-associated collagen. As therapeutic success and safety of these drugs may largely depend on targeted delivery, different strategies for specific delivery to the main effector cells and to the extracellular matrix are discussed.
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Affiliation(s)
- Claudia A Staab-Weijnitz
- Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Gesundheit und Umwelt, 9150, Comprehensive Pneumology Center/Institute of Lung Biology and Disease, Member of the German Center of Lung Research (DZL), München, Germany;
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24
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Li W, Zhang Y, Wang Y, Rong Z, Liu C, Miao H, Chen H, He Y, He W, Chen L. Candidate gene prioritization for chronic obstructive pulmonary disease using expression information in protein-protein interaction networks. BMC Pulm Med 2021; 21:280. [PMID: 34481483 PMCID: PMC8418003 DOI: 10.1186/s12890-021-01646-9] [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] [Received: 02/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Identifying or prioritizing genes for chronic obstructive pulmonary disease (COPD), one type of complex disease, is particularly important for its prevention and treatment. Methods In this paper, a novel method was proposed to Prioritize genes using Expression information in Protein–protein interaction networks with disease risks transferred between genes (abbreviated as PEP). A weighted COPD PPI network was constructed using expression information and then COPD candidate genes were prioritized based on their corresponding disease risk scores in descending order. Results Further analysis demonstrated that the PEP method was robust in prioritizing disease candidate genes, and superior to other existing prioritization methods exploiting either topological or functional information. Top-ranked COPD candidate genes and their significantly enriched functions were verified to be related to COPD. The top 200 candidate genes might be potential disease genes in the diagnosis and treatment of COPD. Conclusions The proposed method could provide new insights to the research of prioritizing candidate genes of COPD or other complex diseases with expression information from sequencing or microarray data. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01646-9.
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Affiliation(s)
- Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yihua Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Zherou Rong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Chenyu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Hui Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Hongwei Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Weiming He
- Institute of Opto-Electronics, Harbin Institute of Technology, Harbin, 150000, Heilongjiang, China.
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China.
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25
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Wan H, Huang X, Cong P, He M, Chen A, Wu T, Dai D, Li W, Gao X, Tian L, Liang H, Xiong L. Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary Fibrosis via Bioinformatics Analysis. Front Mol Biosci 2021; 8:711239. [PMID: 34476240 PMCID: PMC8406749 DOI: 10.3389/fmolb.2021.711239] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive disease whose etiology remains unknown. The purpose of this study was to explore hub genes and pathways related to IPF development and prognosis. Multiple gene expression datasets were downloaded from the Gene Expression Omnibus database. Weighted correlation network analysis (WGCNA) was performed and differentially expressed genes (DEGs) identified to investigate Hub modules and genes correlated with IPF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) network analysis were performed on selected key genes. In the PPI network and cytoHubba plugin, 11 hub genes were identified, including ASPN, CDH2, COL1A1, COL1A2, COL3A1, COL14A1, CTSK, MMP1, MMP7, POSTN, and SPP1. Correlation between hub genes was displayed and validated. Expression levels of hub genes were verified using quantitative real-time PCR (qRT-PCR). Dysregulated expression of these genes and their crosstalk might impact the development of IPF through modulating IPF-related biological processes and signaling pathways. Among these genes, expression levels of COL1A1, COL3A1, CTSK, MMP1, MMP7, POSTN, and SPP1 were positively correlated with IPF prognosis. The present study provides further insights into individualized treatment and prognosis for IPF.
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Affiliation(s)
- Hanxi Wan
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Xinwei Huang
- Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Peilin Cong
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Mengfan He
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Aiwen Chen
- Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Tingmei Wu
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Danqing Dai
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Wanrong Li
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Xiaofei Gao
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Li Tian
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, China
| | - Huazheng Liang
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, School of Medcine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China.,Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, China
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26
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Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
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Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
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27
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Li N, Liu M, Cao X, Li W, Li Y, Zhao Z. Identification of differentially expressed genes using microarray analysis and COL6A1 induction of bone metastasis in non-small cell lung cancer. Oncol Lett 2021; 22:693. [PMID: 34457048 PMCID: PMC8358737 DOI: 10.3892/ol.2021.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major cause of cancer-associated mortality worldwide, and bone metastasis is the most prevalent event observed in patients with advanced NSCLC. However, the pathogenesis of bone metastases has not been fully elucidated. In the present study, differentially expressed genes (DEGs) were identified by gene expression microarray analysis of NSCLC tissue samples with or without bone metastases. Subsequently, collagen type 6A1 (COL6A1) was chosen as the target gene through Ingenuity Pathway Analysis and reverse transcription-quantitative (RT-q) PCR validation of the top eight DEGs. COL6A1 was overexpressed or knocked down, and the proliferation and invasion of NSCLC cells was assessed using Cell Counting Kit-8, colony formation and Transwell invasion assays. Additionally, the osteogenic capacity of HOB and hES-MP 002.5 cells was assessed using RT-qPCR, western blotting, Alizarin Red and alkaline phosphatase staining. A total of 364 DEGs were identified in NSCLC tissues with bone metastases compared with NSCLC tissues without bone metastases, including 140 upregulated and 224 downregulated genes. Gene Ontology analysis results demonstrated that the upregulated and downregulated genes were primarily enriched in 'cellular process', 'metabolic process' and 'biological regulation'. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the upregulated genes were primarily enriched in 'cysteine and methionine metabolism', 'oxidative phosphorylation' and 'ribosome', whereas the downregulated genes were primarily enriched in the 'transcriptional misregulation in cancer', 'ribosome' and 'mitophagy-animal' pathways. COL6A1 was highly expressed in NSCLC tissue samples with bone metastases. Functionally, COL6A1 overexpression induced the proliferation and invasion of HARA cells, and its knockdown inhibited the proliferation and invasion of HARA-B4 cells. Finally, it was demonstrated that HOB and hES-MP 002.5 cells exhibited osteogenic capacity, and overexpression of COL6A1 in HARA cells increased the adhesion of these cells to the osteoblasts, whereas knockdown of COL6A1 in HARA-B4 cells reduced their adhesive ability. In conclusion, COL6A1 may serve as a potential diagnostic marker and therapeutic target for bone metastasis in NSCLC.
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Affiliation(s)
- Nan Li
- Department of Radiotherapy and Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Ming Liu
- Department of Radiotherapy and Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Xiaohui Cao
- Department of Radiotherapy and Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Wei Li
- Department of Radiotherapy and Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yunfang Li
- Department of Radiotherapy and Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
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28
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Tang Y, Chen Z, Fang Z, Zhao J, Zhou Y, Tang C. Multi-Omics study on biomarker and pathway discovery of chronic obstructive pulmonary disease. J Breath Res 2021; 15. [PMID: 34280912 DOI: 10.1088/1752-7163/ac15ea] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a common heterogeneous respiratory disease characterized by persistent and incompletely reversible airflow limitation. Due to the heterogeneity and phenotypes complexity of COPD, traditionally diagnostic methods can only give limited information on predicted results and treatment, which are not sufficient for accurate diagnosis and evaluation. With the development of omics technologies in recent years, genomics, proteomics, and metabolomics are widely used in the study of COPD, providing good tools for discovering biomarkers to diagnose and elucidate the complex mechanism of COPD. In this review, we summarized the biomarkers of COPD based on metabolomic, proteomic and transcriptomic studies that have been reported in recent years. Furthermore, protein-protein interactions and multi-omics integrated analysis were carried out to explore the important metabolites and proteins that involved in significant pathways in the progression of COPD for explanation the pathogenesis of COPD. Finally, the prospective and challenges in the study of COPD were proposed. It is expected that this review will provide some references for the development of diagnostic methods and elucidation of the pathogenesis of COPD.
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Affiliation(s)
- Yuqing Tang
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Zhengjun Chen
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Zhiling Fang
- Ningbo University Medical School, Ningbo University School of Medicine, Ningbo 315211, China, Ningbo, Zhejiang, 315211, CHINA
| | - Jinshun Zhao
- Ningbo University Medical School, Ningbo University School of Medicine, Ningbo 315211, China, Ningbo, Zhejiang, 315211, CHINA
| | - Yuping Zhou
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
| | - Chunlan Tang
- Ningbo University Medical School, The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China, Ningbo, Zhejiang, 315020, CHINA
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29
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Skerrett-Byrne DA, Bromfield EG, Murray HC, Jamaluddin MFB, Jarnicki AG, Fricker M, Essilfie AT, Jones B, Haw TJ, Hampsey D, Anderson AL, Nixon B, Scott RJ, Wark PAB, Dun MD, Hansbro PM. Time-resolved proteomic profiling of cigarette smoke-induced experimental chronic obstructive pulmonary disease. Respirology 2021; 26:960-973. [PMID: 34224176 DOI: 10.1111/resp.14111] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND OBJECTIVE Chronic obstructive pulmonary disease (COPD) is the third leading cause of illness and death worldwide. Current treatments aim to control symptoms with none able to reverse disease or stop its progression. We explored the major molecular changes in COPD pathogenesis. METHODS We employed quantitative label-based proteomics to map the changes in the lung tissue proteome of cigarette smoke-induced experimental COPD that is induced over 8 weeks and progresses over 12 weeks. RESULTS Quantification of 7324 proteins enabled the tracking of changes to the proteome. Alterations in protein expression profiles occurred in the induction phase, with 18 and 16 protein changes at 4- and 6-week time points, compared to age-matched controls, respectively. Strikingly, 269 proteins had altered expression after 8 weeks when the hallmark pathological features of human COPD emerge, but this dropped to 27 changes at 12 weeks with disease progression. Differentially expressed proteins were validated using other mouse and human COPD bronchial biopsy samples. Major changes in RNA biosynthesis (heterogeneous nuclear ribonucleoproteins C1/C2 [HNRNPC] and RNA-binding protein Musashi homologue 2 [MSI2]) and modulators of inflammatory responses (S100A1) were notable. Mitochondrial dysfunction and changes in oxidative stress proteins also occurred. CONCLUSION We provide a detailed proteomic profile, identifying proteins associated with the pathogenesis and disease progression of COPD establishing a platform to develop effective new treatment strategies.
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Affiliation(s)
- David A Skerrett-Byrne
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Elizabeth G Bromfield
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Heather C Murray
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - M Fairuz B Jamaluddin
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Andrew G Jarnicki
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Fricker
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Ama T Essilfie
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Bernadette Jones
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Tatt J Haw
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Daniel Hampsey
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Amanda L Anderson
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Brett Nixon
- Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Rodney J Scott
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia
| | - Matthew D Dun
- University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,University of Newcastle, Callaghan, New South Wales, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
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30
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Idiopathic pulmonary fibrosis and systemic sclerosis: pathogenic mechanisms and therapeutic interventions. Cell Mol Life Sci 2021; 78:5527-5542. [PMID: 34145462 PMCID: PMC8212897 DOI: 10.1007/s00018-021-03874-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 05/07/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
Fibrotic diseases take a very heavy toll in terms of morbidity and mortality equal to or even greater than that caused by metastatic cancer. In this review, we examine the pathogenesis of fibrotic diseases, mainly addressing triggers for induction, processes that lead to progression, therapies and therapeutic trials. For the most part, we have focused on two fibrotic diseases with lung involvement, idiopathic pulmonary fibrosis, in which the contribution of inflammatory mechanisms may be secondary to non-immune triggers, and systemic sclerosis in which the contribution of adaptive immunity may be predominant.
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31
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Ptasinski V, Stegmayr J, Belvisi MG, Wagner DE, Murray LA. Targeting Alveolar Repair in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 65:347-365. [PMID: 34129811 PMCID: PMC8525210 DOI: 10.1165/rcmb.2020-0476tr] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a fatal interstitial lung disease with limited therapeutic options. Current evidence suggests that IPF may be initiated by repeated epithelial injury in the distal lung followed by abnormal wound healing responses which occur due to intrinsic and extrinsic factors. Mechanisms contributing to chronic damage of the alveolar epithelium in IPF include dysregulated cellular processes such as apoptosis, senescence, abnormal activation of developmental pathways, aging, as well as genetic mutations. Therefore, targeting the regenerative capacity of the lung epithelium is an attractive approach in the development of novel therapies for IPF. Endogenous lung regeneration is a complex process involving coordinated cross-talk between multiple cell types and re-establishment of a normal extracellular matrix environment. This review will describe the current knowledge of reparative epithelial progenitor cells in the alveolar region of the lung and discuss potential novel therapeutic approaches for IPF focusing on endogenous alveolar repair. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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Affiliation(s)
- Victoria Ptasinski
- Lund University Faculty of Medicine, 59568, Lund, Sweden.,AstraZeneca R&D Gothenburg, 128698, Goteborg, Sweden
| | - John Stegmayr
- Lunds University Faculty of Medicine, 59568, Lund, Sweden
| | - Maria G Belvisi
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Darcy E Wagner
- Lunds Universitet, 5193, Experimental Medical Sciences, Lund, Sweden
| | - Lynne A Murray
- AstraZeneca PLC, 4625, Cambridge, United Kingdom of Great Britain and Northern Ireland;
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Evangelista-Leite D, Carreira ACO, Gilpin SE, Miglino MA. Protective Effects of Extracellular Matrix-Derived Hydrogels in Idiopathic Pulmonary Fibrosis. TISSUE ENGINEERING PART B-REVIEWS 2021; 28:517-530. [PMID: 33899554 DOI: 10.1089/ten.teb.2020.0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease with significant gas exchange impairment owing to exaggerated extracellular matrix (ECM) deposition and myofibroblast activation. IPF has no cure, and although nintedanib and pirfenidone are two approved medications for symptom management, the total treatment cost is exuberant and prohibitive to a global uninsured patient population. New therapeutic alternatives with moderate costs are needed to treat IPF. ECM hydrogels derived from decellularized lungs are cost-effective therapeutic candidates to treat pulmonary fibrosis because of their reported antioxidant properties. Oxidative stress contributes to IPF pathophysiology by damaging macromolecules, interfering with tissue remodeling, and contributing to myofibroblast activation. Thus, preventing oxidative stress has beneficial outcomes in IPF. For this purpose, this review describes ECM hydrogel's properties to regulate oxidative stress and tissue remodeling in IPF.
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Affiliation(s)
- Daniele Evangelista-Leite
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia O Carreira
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.,NUCEL (Cell and Molecular Therapy Center), University of São Paulo, São Paulo, Brazil
| | - Sarah E Gilpin
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USA
| | - Maria Angélica Miglino
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
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Hedström U, Öberg L, Vaarala O, Dellgren G, Silverborn M, Bjermer L, Westergren-Thorsson G, Hallgren O, Zhou X. Impaired Differentiation of Chronic Obstructive Pulmonary Disease Bronchial Epithelial Cells Grown on Bronchial Scaffolds. Am J Respir Cell Mol Biol 2021; 65:201-213. [PMID: 33882260 PMCID: PMC8399573 DOI: 10.1165/rcmb.2019-0395oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by airway inflammation, small airway remodeling, and emphysema. Airway remodeling in patients with COPD involves both the airway epithelium and the subepithelial extracellular matrix (ECM). However, it is currently unknown how epithelial remodeling in COPD airways depends on the relative influence from inherent defects in the epithelial cells and alterations in the ECM. To address this, we analyzed global gene expression in COPD human bronchial epithelial cells (HBEC) and normal HBEC after repopulation on decellularized bronchial scaffolds derived from patients with COPD or donors without COPD. COPD HBEC grown on bronchial scaffolds showed an impaired ability to initiate ciliated-cell differentiation, which was evident on all scaffolds regardless of their origin. In addition, although normal HBEC were less affected by the disease state of the bronchial scaffolds, COPD HBEC showed a gene expression pattern indicating increased proliferation and a retained basal-cell phenotype when grown on COPD bronchial scaffolds compared with normal bronchial scaffolds. By using mass spectrometry, we identified 13 matrisome proteins as being differentially abundant between COPD bronchial scaffolds and normal bronchial scaffolds. These observations are consistent with COPD pathology and suggest that both epithelial cells and the ECM contribute to epithelial-cell remodeling in COPD airways.
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Affiliation(s)
- Ulf Hedström
- Department of Bioscience COPD/IPF, and.,Division of Lung Biology, Department of Experimental Medical Science, and
| | - Lisa Öberg
- Department of Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Sweden
| | | | - Göran Dellgren
- Transplant Institute and.,Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Silverborn
- Transplant Institute and.,Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Leif Bjermer
- Division of Respiratory Medicine and Allergology, Department of Clinical Sciences, Lund University, Lund, Sweden; and
| | | | - Oskar Hallgren
- Division of Lung Biology, Department of Experimental Medical Science, and.,Division of Respiratory Medicine and Allergology, Department of Clinical Sciences, Lund University, Lund, Sweden; and
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Elowsson Rendin L, Löfdahl A, Kadefors M, Söderlund Z, Tykesson E, Rolandsson Enes S, Wigén J, Westergren-Thorsson G. Harnessing the ECM Microenvironment to Ameliorate Mesenchymal Stromal Cell-Based Therapy in Chronic Lung Diseases. Front Pharmacol 2021; 12:645558. [PMID: 34040521 PMCID: PMC8142268 DOI: 10.3389/fphar.2021.645558] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022] Open
Abstract
It is known that the cell environment such as biomechanical properties and extracellular matrix (ECM) composition dictate cell behaviour including migration, proliferation, and differentiation. Important constituents of the microenvironment, including ECM molecules such as proteoglycans and glycosaminoglycans (GAGs), determine events in both embryogenesis and repair of the adult lung. Mesenchymal stromal/stem cells (MSC) have been shown to have immunomodulatory properties and may be potent actors regulating tissue remodelling and regenerative cell responses upon lung injury. Using MSC in cell-based therapy holds promise for treatment of chronic lung diseases such as idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). However, so far clinical trials with MSCs in COPD have not had a significant impact on disease amelioration nor on IPF, where low cell survival rate and pulmonary retention time are major hurdles to overcome. Research shows that the microenvironment has a profound impact on transplanted MSCs. In our studies on acellular lung tissue slices (lung scaffolds) from IPF patients versus healthy individuals, we see a profound effect on cellular activity, where healthy cells cultured in diseased lung scaffolds adapt and produce proteins further promoting a diseased environment, whereas cells on healthy scaffolds sustain a healthy proteomic profile. Therefore, modulating the environmental context for cell-based therapy may be a potent way to improve treatment using MSCs. In this review, we will describe the importance of the microenvironment for cell-based therapy in chronic lung diseases, how MSC-ECM interactions can affect therapeutic output and describe current progress in the field of cell-based therapy.
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Affiliation(s)
- Linda Elowsson Rendin
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Anna Löfdahl
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Måns Kadefors
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Zackarias Söderlund
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Emil Tykesson
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Sara Rolandsson Enes
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Jenny Wigén
- Lung Biology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
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Chen Z, Huang J, Li M, Zhang L, Wan D, Lin S. High expression of MMP28 indicates unfavorable prognosis in pancreatic cancer. Medicine (Baltimore) 2021; 100:e25320. [PMID: 33761734 PMCID: PMC9282082 DOI: 10.1097/md.0000000000025320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
To investigate the expression pattern and diagnostic performance of matrix metalloproteinase 28 (MMP28) in pancreatic cancer (PC).The RNA-seq data of PC and normal pancreas tissue were acquired from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression. Clinical information of PC that included prognostic data was obtained from TCGA. Later, Fisher exact test was applied for comparison of different clinicopathological features between high and low expression of MMP28 in PC. Afterwards, Kaplan-Meier survival analysis and Cox analysis (univariate and multivariate analysis) were used to explore the prognostic performance of MMP28 in PC cohort. Finally, gene set enrichment analysis (GSEA) revealed the potential signaling pathways related to high expression of MMP28 in PC.Upregulation of MMP28 was identified in PC tissue compared to normal pancreas tissue (P < .001). Overexpression of MMP28 was related to histological grade (P < .001), M classification (P = .014), and survival status (P = .028). Kaplan-Meier survival analysis revealed that high level of MMP28 implied unfavorable prognosis in PC (P = .002). Multivariate analysis confirmed that MMP28 was an independent risk factor in PC (hazard rate = 1.308, P = .018). Our GSEA analysis found that signaling pathways including glycolysis, p53 pathway, notch signaling, estrogen response late, cholesterol homeostasis, estrogen response early, mitotic spindle, and transforming growth factor beta signaling were enriched in the group with higher MMP28 expression.High expression of MMP28 could be identified in PC, which also served as an independent risk element for PC.
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Affiliation(s)
- Zhitao Chen
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine
- School of Medicine, Zhejiang University
- Key Laboratory of Combined Multi-organ Transplantation, Hangzhou
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences
- Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Jiacheng Huang
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine
- School of Medicine, Zhejiang University
- Key Laboratory of Combined Multi-organ Transplantation, Hangzhou
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences
- Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Mengxia Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine
- School of Medicine, Zhejiang University
- Key Laboratory of Combined Multi-organ Transplantation, Hangzhou
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences
- Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Lele Zhang
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine
- School of Medicine, Zhejiang University
- Key Laboratory of Combined Multi-organ Transplantation, Hangzhou
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences
- Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Dalong Wan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine
| | - Shengzhang Lin
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College
- School of Medicine, Zhejiang University
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Bagher M, Rosmark O, Elowsson Rendin L, Nybom A, Wasserstrom S, Müller C, Zhou XH, Dellgren G, Hallgren O, Bjermer L, Larsson-Callerfelt AK, Westergren-Thorsson G. Crosstalk between Mast Cells and Lung Fibroblasts Is Modified by Alveolar Extracellular Matrix and Influences Epithelial Migration. Int J Mol Sci 2021; 22:ijms22020506. [PMID: 33419174 PMCID: PMC7825515 DOI: 10.3390/ijms22020506] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mast cells play an important role in asthma, however, the interactions between mast cells, fibroblasts and epithelial cells in idiopathic pulmonary fibrosis (IPF) are less known. The objectives were to investigate the effect of mast cells on fibroblast activity and migration of epithelial cells. Lung fibroblasts from IPF patients and healthy individuals were co-cultured with LAD2 mast cells or stimulated with the proteases tryptase and chymase. Human lung fibroblasts and mast cells were cultured on cell culture plastic plates or decellularized human lung tissue (scaffolds) to create a more physiological milieu by providing an alveolar extracellular matrix. Released mediators were analyzed and evaluated for effects on epithelial cell migration. Tryptase increased vascular endothelial growth factor (VEGF) release from fibroblasts, whereas co-culture with mast cells increased IL-6 and hepatocyte growth factor (HGF). Culture in scaffolds increased the release of VEGF compared to culture on plastic. Migration of epithelial cells was reduced by IL-6, while HGF and conditioned media from scaffold cultures promoted migration. In conclusion, mast cells and tryptase increased fibroblast release of mediators that influenced epithelial migration. These data indicate a role of mast cells and tryptase in the interplay between fibroblasts, epithelial cells and the alveolar extracellular matrix in health and lung disease.
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Affiliation(s)
- Mariam Bagher
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund University, 221 85 Lund, Sweden; (O.H.); (L.B.)
| | - Oskar Rosmark
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
| | - Linda Elowsson Rendin
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
| | - Annika Nybom
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
| | | | - Catharina Müller
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
| | - Xiao-Hong Zhou
- Bioscience Department, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, 431 53 Mölndal, Sweden;
| | - Göran Dellgren
- Department of Cardiothoracic Surgery and Transplant Institute, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden;
| | - Oskar Hallgren
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund University, 221 85 Lund, Sweden; (O.H.); (L.B.)
| | - Leif Bjermer
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund University, 221 85 Lund, Sweden; (O.H.); (L.B.)
| | - Anna-Karin Larsson-Callerfelt
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
- Correspondence: ; Tel.: +46-46-222-8580 or +46-733-525420
| | - Gunilla Westergren-Thorsson
- Unit of Lung Biology, Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden; (M.B.); (O.R.); (L.E.R.); (A.N.); (C.M.); (G.W.-T.)
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Khan T, Dasgupta S, Ghosh N, Chaudhury K. Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers. Mol Omics 2021; 17:43-58. [PMID: 33073811 DOI: 10.1039/d0mo00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a debilitating chronic progressive and fibrosing lung disease that culminates in the destruction of alveolar integrity and dismal prognosis. Its etiology is unknown and pathophysiology remains unclear. While great advances have been made in elucidating the pathogenesis mechanism, considerable gaps related to information on pathogenetic pathways and key protein targets involved in the clinical course of the disease exist. These issues need to be addressed for better clinical management of this highly challenging disease. Omics approach has revolutionized the entire area of disease understanding and holds promise in its translation to clinical biomarker discovery. This review outlines the contribution of proteomics towards identification of important biomarkers in IPF in terms of their clinical utility, i.e. prognosis, differential diagnosis, disease progression and treatment monitoring. The major dysregulated pathways associated with IPF are also discussed. Based on numerous proteomics studies on human and animal models, it is proposed that IPF pathogenesis involves complex interactions of several pathways such as oxidative stress, endoplasmic reticulum stress, unfolded protein response, coagulation system, inflammation, abnormal wounding, fibroblast proliferation, fibrogenesis and deposition of extracellular matrix. These pathways and their key path-changing mediators need further validation in large well-planned multi-centric trials at various geographical locations for successful development of clinical biomarkers of this confounding disease.
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Affiliation(s)
- Tila Khan
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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Liu Y, Qi Y. Vildagliptin, a CD26/DPP4 inhibitor, ameliorates bleomycin-induced pulmonary fibrosis via regulating the extracellular matrix. Int Immunopharmacol 2020; 87:106774. [PMID: 32731178 DOI: 10.1016/j.intimp.2020.106774] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/10/2020] [Accepted: 07/02/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis is a debilitating lung disease. CD26/DPP4 plays promotive roles in pulmonary damage and fibrosis. This study aimed to explore the roles of vildagliptin in bleomycin-induced pulmonary fibrosis, and to address its ameliorative effect on the extracellular matrix (ECM). METHODS Idiopathic pulmonary fibrosis mice models were induced by intratracheal injection of bleomycin. DPP4 activity was evaluated, and the fibrosis was investigated by Hematoxylin-eosin, Masson's trichrome staining and hydroxyproline assay. Expression of extracellular matrix proteins including α-SMA, collagen IV, collagen I, FN and TGF-β were analyzed by immunochemistry and western blot. Percentages of the numbers of monocytes, leukocytes, basophils and lymphocytes were classified, and inflammatory factors in plasma as well as lung tissues were examined by enzyme-linked immunosorbent assay and western blot. The influences of vildagliptin on TGF-β1-induced cell proliferation, differentiation and inflammatory factors in MRC-5 cells were detected. RESULTS Vildagliptin effectively attenuated inflammation and fibrosis in bleomycin-induced pulmonary tissue via inhibiting the activity of CD26/DPP4. extracellular matrix proteins were suppressed by vildagliptin. Thus, lung tissue fibrosis was efficiently alleviated by vildagliptin. CONCLUSION As an inhibitor of CD26/DPP4, Vildagliptin could be a promising therapeutic candidate for idiopathic pulmonary fibrosis.
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Affiliation(s)
- Yang Liu
- Medical College of Pingdingshan University, Chongwen Road, Xinhua District, Pingdingshan City, Henan 467000, China
| | - Yongchao Qi
- Department of Cardiothoracic Surgery (907 Inpatient Ward), Nanjing First Hospital Nanjing Medical University, Nanjing 210000, China.
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Herrera JA, Mallikarjun V, Rosini S, Montero MA, Lawless C, Warwood S, O’Cualain R, Knight D, Schwartz MA, Swift J. Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. Clin Proteomics 2020; 17:24. [PMID: 32565759 PMCID: PMC7302139 DOI: 10.1186/s12014-020-09287-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Haematoxylin and eosin (H&E)-which respectively stain nuclei blue and other cellular and stromal material pink-are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing and H&E staining of tissues provides challenges with standard sample preparation methods for mass spectrometry, resulting in low protein yield. Here we describe a microproteomics technique to analyse H&E-stained, formalin-fixed paraffin-embedded (FFPE) tissues. METHODS Herein, we utilize heat extraction, physical disruption, and in column digestion for the analysis of H&E stained FFPE tissues. Micro-dissected morphologically normal human lung alveoli (0.082 mm3) and human lung blood vessels (0.094 mm3) from FFPE-fixed H&E-stained sections from Idiopathic Pulmonary Fibrosis (IPF) specimens (n = 3 IPF specimens) were then subject to a qualitative and then quantitative proteomics approach using BayesENproteomics. In addition, we tested the sensitivity of this method by processing and analysing a range of micro-dissected human lung blood vessel tissue volumes. RESULTS This approach yields 1252 uniquely expressed proteins (at a protein identification threshold of 3 unique peptides) with 892 differentially expressed proteins between these regions. In accord with prior knowledge, our methodology approach confirms that human lung blood vessels are enriched with smoothelin, CNN1, ITGA7, MYH11, TAGLN, and PTGIS; whereas morphologically normal human lung alveoli are enriched with cytokeratin-7, -8, -18, -19, 14, and -17. In addition, we identify a total of 137 extracellular matrix (ECM) proteins and immunohistologically validate that laminin subunit beta-1 localizes to morphologically normal human lung alveoli and tenascin localizes to human lung blood vessels. Lastly, we show that this micro-proteomics technique can be applied to tissue volumes as low as 0.0125 mm3. CONCLUSION Herein we show that our multistep sample preparation methodology of LCM-MS can identify distinct, characteristic proteomic compositions of anatomical features within complex fixed and stained tissues.
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Affiliation(s)
- Jeremy A. Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Venkatesh Mallikarjun
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Silvia Rosini
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Maria Angeles Montero
- Histopathology Department, Manchester University NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester, M23 9LT UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Stacey Warwood
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Ronan O’Cualain
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - David Knight
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Joe Swift
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
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Wan XL, Zhou ZL, Wang P, Zhou XM, Xie MY, Mei J, Weng J, Xi HT, Chen C, Wang ZY, Wang ZB. Small molecule proteomics quantifies differences between normal and fibrotic pulmonary extracellular matrices. Chin Med J (Engl) 2020; 133:1192-1202. [PMID: 32433051 PMCID: PMC7249707 DOI: 10.1097/cm9.0000000000000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pulmonary fibrosis is a respiratory disease caused by the proliferation of fibroblasts and accumulation of the extracellular matrix (ECM). It is known that the lung ECM is mainly composed of a three-dimensional fiber mesh filled with various high-molecular-weight proteins. However, the small-molecular-weight proteins in the lung ECM and their differences between normal and fibrotic lung ECM are largely unknown. METHODS Healthy adult male Sprague-Dawley rats (Rattus norvegicus) weighing about 150 to 200 g were randomly divided into three groups using random number table: A, B, and C and each group contained five rats. The rats in Group A were administered a single intragastric (i.g.) dose of 500 μL of saline as control, and those in Groups B and C were administered a single i.g. dose of paraquat (PQ) dissolved in 500 μL of saline (20 mg/kg). After 2 weeks, the lungs of rats in Group B were harvested for histological observation, preparation of de-cellularized lung scaffolds, and proteomic analysis for small-molecular-weight proteins, and similar procedures were performed on Group C and A after 4 weeks. The differentially expressed small-molecular-weight proteins (DESMPs) between different groups and the subcellular locations were analyzed. RESULTS Of the 1626 small-molecular-weight proteins identified, 1047 were quantifiable. There were 97 up-regulated and 45 down-regulated proteins in B vs. A, 274 up-regulated and 31 down-regulated proteins in C vs. A, and 237 up-regulated and 28 down-regulated proteins identified in C vs. B. Both the up-regulated and down-regulated proteins in the three comparisons were mainly distributed in single-organism processes and cellular processes within biological process, cell and organelle within cellular component, and binding within molecular function. Further, more up-regulated than down-regulated proteins were identified in most sub-cellular locations. The interactions of DESMPs identified in extracellular location in all comparisons showed that serum albumin (Alb) harbored the highest degree of node (25), followed by prolyl 4-hydroxylase beta polypeptide (12), integrin β1 (10), apolipoprotein A1 (9), and fibrinogen gamma chain (9). CONCLUSIONS Numerous PQ-induced DESMPs were identified in de-cellularized lungs of rats by high throughput proteomics analysis. The DESMPs between the control and treatment groups showed diversity in molecular functions, biological processes, and pathways. In addition, the interactions of extracellular DESMPs suggested that the extracellular proteins Alb, Itgb1, Apoa1, P4hb, and Fgg in ECM could be potentially used as biomarker candidates for pulmonary fibrosis. These results provided useful information and new insights regarding pulmonary fibrosis.
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Affiliation(s)
- Xin-Long Wan
- Platform for Radiation Protection and Emergency Preparedness of Southern Zhejiang, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Liang Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Peng Wang
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiao-Ming Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Meng-Ying Xie
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jin Mei
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jie Weng
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hai-Tao Xi
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chan Chen
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Zhi-Yi Wang
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Bin Wang
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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41
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Ricard-Blum S, Miele AE. Omic approaches to decipher the molecular mechanisms of fibrosis, and design new anti-fibrotic strategies. Semin Cell Dev Biol 2020; 101:161-169. [DOI: 10.1016/j.semcdb.2019.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
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42
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Liu B, Leng L, Sun X, Wang Y, Ma J, Zhu Y. ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence. PeerJ 2020; 8:e9066. [PMID: 32377454 PMCID: PMC7195829 DOI: 10.7717/peerj.9066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/05/2020] [Indexed: 01/28/2023] Open
Abstract
Extracellular matrix (ECM) proteins play an essential role in various biological processes in multicellular organisms, and their abnormal regulation can lead to many diseases. For large-scale ECM protein identification, especially through proteomic-based techniques, a theoretical reference database of ECM proteins is required. In this study, based on the experimentally verified ECM datasets and by the integration of protein domain features and a machine learning model, we developed ECMPride, a flexible and scalable tool for predicting ECM proteins. ECMPride achieved excellent performance in predicting ECM proteins, with appropriate balanced accuracy and sensitivity, and the performance of ECMPride was shown to be superior to the previously developed tool. A new theoretical dataset of human ECM components was also established by applying ECMPride to all human entries in the SwissProt database, containing a significant number of putative ECM proteins as well as the abundant biological annotations. This dataset might serve as a valuable reference resource for ECM protein identification.
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Affiliation(s)
- Binghui Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Ling Leng
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xuer Sun
- Tissue Engineering Lab, Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Yunfang Wang
- Tissue Engineering Lab, Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China.,Basic Medical School, Anhui Medical University, Anhui, China
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43
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Conditional deletion of Nedd4-2 in lung epithelial cells causes progressive pulmonary fibrosis in adult mice. Nat Commun 2020; 11:2012. [PMID: 32332792 PMCID: PMC7181726 DOI: 10.1038/s41467-020-15743-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease characterized by patchy scarring of the distal lung with limited therapeutic options and poor prognosis. Here, we show that conditional deletion of the ubiquitin ligase Nedd4-2 (Nedd4l) in lung epithelial cells in adult mice produces chronic lung disease sharing key features with IPF including progressive fibrosis and bronchiolization with increased expression of Muc5b in peripheral airways, honeycombing and characteristic alterations in the lung proteome. NEDD4-2 is implicated in the regulation of the epithelial Na+ channel critical for proper airway surface hydration and mucus clearance and the regulation of TGFβ signaling, which promotes fibrotic remodeling. Our data support a role of mucociliary dysfunction and aberrant epithelial pro-fibrotic response in the multifactorial disease pathogenesis. Further, treatment with the anti-fibrotic drug pirfenidone reduced pulmonary fibrosis in this model. This model may therefore aid studies of the pathogenesis and therapy of IPF. Idiopathic pulmonary fibrosis (IPF) is a devastating disease with poor prognosis. Here, the authors show that deficiency of the E3 ubiqutin-protein ligase Nedd4-2 in airway epithelial cells causes IPF-like disease in adult mice. This model may aid studies of the pathogenesis and therapy of IPF.
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Comparison of Normal and Metaplastic Epithelium in Patients with Stable versus Persistently Symptomatic Severe Asthma Using Laser-Capture Microdissection and Data-Independent Acquisition-Mass Spectrometry. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 189:2358-2365. [PMID: 31761031 DOI: 10.1016/j.ajpath.2019.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023]
Abstract
A proportion of patients with severe asthma (SA) show poor responses to traditional asthma medications; however, it remains unknown why some patients remain persistently symptomatic. Our objective was to explore the use of laser-capture microdissection of specific epithelial structures combined with quantitative data-independent acquisition mass spectrometry to elucidate differences in protein composition in patients with SA with varying symptom control. Unbiased label-free quantitative proteome analyses were performed on laser-capture-microdissected areas of specific epithelial structures from patients with SA with varying degrees of symptom control. A total of 1993 stable SA and 1652 symptomatic SA proteins in normal epithelium and 1458 stable SA and 1647 symptomatic SA proteins in metaplastic epithelium were quantified. When comparing proteome profiles based on symptom control, 33 proteins in patients with stable SA (≥twofold change; P ≤ 0.05) and 13 proteins in patients with persistently symptomatic SA (≥twofold change; P ≤ 0.05) were enriched significantly. When comparing proteome profiles based on epithelial status, 21 proteins in normal epithelium (≥twofold change; P ≤ 0.05) and 6 proteins in metaplastic epithelium (≥twofold change; P ≤ 0.05) were enriched significantly. New treatment strategies are needed for patients with severe asthma and exploratory studies of unbiased nature such as this may help when searching for new mechanisms and potential targets involved in the disease pathology.
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45
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Exploring the extracellular matrix in health and disease using proteomics. Essays Biochem 2019; 63:417-432. [DOI: 10.1042/ebc20190001] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins that constitutes the scaffold of multicellular organisms. In addition to providing architectural and mechanical support to the surrounding cells, it conveys biochemical signals that regulate cellular processes including proliferation and survival, fate determination, and cell migration. Defects in ECM protein assembly, decreased ECM protein production or, on the contrary, excessive ECM accumulation, have been linked to many pathologies including cardiovascular and skeletal diseases, cancers, and fibrosis. The ECM thus represents a potential reservoir of prognostic biomarkers and therapeutic targets. However, our understanding of the global protein composition of the ECM and how it changes during pathological processes has remained limited until recently.
In this mini-review, we provide an overview of the latest methodological advances in sample preparation and mass spectrometry-based proteomics that have permitted the profiling of the ECM of now dozens of normal and diseased tissues, including tumors and fibrotic lesions.
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46
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Sample Fractionation Techniques for CSF Peptide Spectral Library Generation. Methods Mol Biol 2019. [PMID: 31432407 DOI: 10.1007/978-1-4939-9706-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Data-independent acquisition (DIA) is becoming more prominent as a method for comprehensive proteomic analysis of clinical samples due to its ability to acquire essentially all fragment ion spectra in a single LC-ESI-MS/MS experiment. Since the direct correlation between a precursor and its fragment ions is lost when acquiring all ions in a defined m/z range, one data analysis strategy is using so-called peptide spectral libraries. These are usually generated by measuring similar biological samples in data-dependent (DDA) mode. The peptide spectral library content is a major limitation for the successful identification from DIA data. This is because a fragment ion spectrum from the sample can only be matched, and thus identified, when it is present in the peptide spectral library. In order to enhance peptide spectral library size, the sample for generating the peptide spectral library can be subjected to extended separation strategies prior to DDA. These strategies are of special relevance for biological samples containing a few very high-abundant proteins, such as CSF, as they enlarge the identification of low-abundant proteins. In instances of CSF separation, suitable methods include the 1D SDS-PAGE of proteins and high-pH reversed-phase peptide fractionation. Both methods are based on different protein/peptide characteristics, are complementary with one another, and are inexpensive and easy to establish. Ideally, DDA spectra from samples generated with both methods combine to achieve a comprehensive spectral library.
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47
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Elowsson Rendin L, Löfdahl A, Åhrman E, Müller C, Notermans T, Michaliková B, Rosmark O, Zhou XH, Dellgren G, Silverborn M, Bjermer L, Malmström A, Larsson-Callerfelt AK, Isaksson H, Malmström J, Westergren-Thorsson G. Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2019; 20:ijms20164013. [PMID: 31426504 PMCID: PMC6719040 DOI: 10.3390/ijms20164013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
In idiopathic pulmonary fibrosis (IPF) structural properties of the extracellular matrix (ECM) are altered and influence cellular responses through cell-matrix interactions. Scaffolds (decellularized tissue) derived from subpleural healthy and IPF lungs were examined regarding biomechanical properties and ECM composition of proteins (the matrisome). Scaffolds were repopulated with healthy fibroblasts cultured under static stretch with heavy isotope amino acids (SILAC), to examine newly synthesized proteins over time. IPF scaffolds were characterized by increased tissue density, stiffness, ultimate force, and differential expressions of matrisome proteins compared to healthy scaffolds. Collagens, proteoglycans, and ECM glycoproteins were increased in IPF scaffolds, however while specific basement membrane (BM) proteins such as laminins and collagen IV were decreased, nidogen-2 was also increased. Findings were confirmed with histology, clearly showing a disorganized BM. Fibroblasts produced scaffold-specific proteins mimicking preexisting scaffold composition, where 11 out of 20 BM proteins were differentially expressed, along with increased periostin and proteoglycans production. We demonstrate how matrisome changes affect fibroblast activity using novel approaches to study temporal differences, where IPF scaffolds support a disorganized BM and upregulation of disease-associated proteins. These matrix-directed cellular responses emphasize the IPF matrisome and specifically the BM components as important factors for disease progression.
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Affiliation(s)
- Linda Elowsson Rendin
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden.
| | - Anna Löfdahl
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden
| | - Emma Åhrman
- Division of Infection Medicine Proteomics, Department Clinical Sciences, Lund University, Lund 221 84, Sweden
| | - Catharina Müller
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden
| | - Thomas Notermans
- Department of Biomedical engineering, Lund University, Lund 221 84, Sweden
| | - Barbora Michaliková
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden
| | - Oskar Rosmark
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden
| | - Xiao-Hong Zhou
- Bioscience Department, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Mölndal 431 53, Sweden
| | - Göran Dellgren
- Department of Cardiothoracic Surgery and Transplant Institute, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Martin Silverborn
- Department of Cardiothoracic Surgery and Transplant Institute, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Leif Bjermer
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund University, Lund 221 85, Sweden
| | - Anders Malmström
- Lung Biology, Department of Experimental Medical Sciences, Lund University, BMC C12, Lund 221 84, Sweden
| | | | - Hanna Isaksson
- Department of Biomedical engineering, Lund University, Lund 221 84, Sweden
| | - Johan Malmström
- Division of Infection Medicine Proteomics, Department Clinical Sciences, Lund University, Lund 221 84, Sweden
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48
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Moodley YP, Corte TJ, Oliver BG, Glaspole IN, Livk A, Ito J, Peters K, Lipscombe R, Casey T, Tan DBA. Analysis by proteomics reveals unique circulatory proteins in idiopathic pulmonary fibrosis. Respirology 2019; 24:1111-1114. [PMID: 31393655 DOI: 10.1111/resp.13668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 04/13/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease that has a poor 3-year median survival rate with unclear pathophysiology. Radiological features include bibasal, subpleural fibrosis and honeycombing while its pathology is characterized by fibroblastic foci and honeycombing. Proteomic analysis of circulating molecules in plasma may identify factors that characterize IPF and may assist in the diagnosis, prognostication and determination of pathogenic pathways in this condition. METHODS Two independent quantitative proteomic techniques were used, isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM), to identify differentially expressed plasma proteins in a group of IPF patients in comparison to healthy controls with normal lung function matched for age and gender. RESULTS Five proteins were identified to be differentially expressed in IPF compared to healthy controls (upregulation of platelet basic protein and downregulation of actin, cytoplasmic 2, antithrombin-III, extracellular matrix protein-1 and fibronectin). CONCLUSION This study further validates the combinational use of non-targeted discovery proteomics (iTRAQ) with targeted quantitation by mass spectrometry (MRM) of soluble biomarkers to identify potentially important molecules and pathways for pulmonary diseases such as IPF.
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Affiliation(s)
- Yuben P Moodley
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia.,National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia
| | - Tamera J Corte
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,School of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Brian G Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Ian N Glaspole
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Allergy and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia.,Faculty of Medicine, Monash University, Melbourne, VIC, Australia
| | | | - Jason Ito
- Proteomics International, Perth, WA, Australia
| | | | | | - Tammy Casey
- Proteomics International, Perth, WA, Australia
| | - Dino B A Tan
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia
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Wigén J, Elowsson-Rendin L, Karlsson L, Tykesson E, Westergren-Thorsson G. Glycosaminoglycans: A Link Between Development and Regeneration in the Lung. Stem Cells Dev 2019; 28:823-832. [PMID: 31062651 DOI: 10.1089/scd.2019.0009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
What can we learn from embryogenesis to increase our understanding of how regeneration of damaged adult lung tissue could be induced in serious lung diseases such as chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and asthma? The local tissue niche determines events in both embryogenesis and repair of the adult lung. Important constituents of the niche are extracellular matrix (ECM) molecules, including proteoglycans and glycosaminoglycans (GAGs). GAGs, strategically located in the pericellular and extracellular space, bind developmentally active growth factors (GFs) and morphogens such as fibroblast growth factors (FGFs), transforming growth factor-β (TGF-β), and bone morphogenetic proteins (BMPs) aside from cytokines. These interactions affect activities in many cells, including stem cells, important in development and tissue regeneration. Moreover, it is becoming clear that the "inherent code," such as sulfation of disaccharides of GAGs, is a strong determinant of cellular outcome. Sulfation patterns, deacetylations, and epimerizations of GAG chains function as tuning forks in gradient formation of morphogens, growth factors, and cytokines. Learning to tune these fine instruments, that is, interactions between GFs, chemokines, and cytokines with the specific disaccharide code of GAGs in the adult lung, could become the key to unlock inherent regenerative forces to override pathological remodeling. This review aims to provide an overview of the role GAGs play during development and similar events in regenerative efforts in the adult lung.
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Affiliation(s)
- Jenny Wigén
- Experimental Medical Sciences, Lung Biology, Lund, Sweden
| | | | - Lisa Karlsson
- Experimental Medical Sciences, Lung Biology, Lund, Sweden
| | - Emil Tykesson
- Experimental Medical Sciences, Lung Biology, Lund, Sweden
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50
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Abstract
A critical step in proteomics analysis is the optimal extraction and processing of protein material to ensure the highest sensitivity in downstream detection. Achieving this requires a sample-handling technology that exhibits unbiased protein manipulation, flexibility in reagent use, and virtually lossless processing. Addressing these needs, the single-pot, solid-phase-enhanced sample-preparation (SP3) technology is a paramagnetic bead-based approach for rapid, robust, and efficient processing of protein samples for proteomic analysis. SP3 uses a hydrophilic interaction mechanism for exchange or removal of components that are commonly used to facilitate cell or tissue lysis, protein solubilization, and enzymatic digestion (e.g., detergents, chaotropes, salts, buffers, acids, and solvents) before downstream proteomic analysis. The SP3 protocol consists of nonselective protein binding and rinsing steps that are enabled through the use of ethanol-driven solvation capture on the surface of hydrophilic beads, and elution of purified material in aqueous conditions. In contrast to alternative approaches, SP3 combines compatibility with a substantial collection of solution additives with virtually lossless and unbiased recovery of proteins independent of input quantity, all in a simplified single-tube protocol. The SP3 protocol is simple and efficient, and can be easily completed by a standard user in ~30 min, including reagent preparation. As a result of these properties, SP3 has successfully been used to facilitate examination of a broad range of sample types spanning simple and complex protein mixtures in large and very small amounts, across numerous organisms. This work describes the steps and extensive considerations involved in performing SP3 in bottom-up proteomics, using a simplified protein cleanup scenario for illustration.
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