1
|
Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024; 23:2908-2918. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [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] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
Collapse
Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| |
Collapse
|
2
|
Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Mol Cell Proteomics 2023; 22:100528. [PMID: 36918099 PMCID: PMC10152135 DOI: 10.1016/j.mcpro.2023.100528] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
Collapse
Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
| |
Collapse
|
3
|
Mitten EK, Baffy G. Mechanotransduction in the pathogenesis of non-alcoholic fatty liver disease. J Hepatol 2022; 77:1642-1656. [PMID: 36063966 DOI: 10.1016/j.jhep.2022.08.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022]
Abstract
Mechanobiology is a domain of interdisciplinary research that aims to explore the impact of physical force, applied externally or internally, on cell and tissue function, including development, growth, and differentiation. Mechanotransduction is a term that describes how cells sense physical forces (such as compression, stretch, and shear stress), convert them into biochemical signals, and mount adaptive responses integrated by the nucleus. There is accumulating evidence that mechanical forces extensively inform the biological behaviour of liver cells in health and disease. Recent research has elucidated many cellular and molecular mechanisms involved in this process including the pleiotropic control and diverse effects of the paralogous transcription co-activators YAP/TAZ, which play a prominent role in mechanotransduction. The liver sinusoids represent a unique microenvironment in which cells are exposed to mechanical cues originating in the cytoskeleton and at interfaces with adjacent cells, the extracellular matrix, and vascular or interstitial fluids. In non-alcoholic fatty liver disease (NAFLD), hepatocellular lipid accumulation and ballooning, activation of inflammatory responses, dysfunction of liver sinusoidal endothelial cells, and transdifferentiation of hepatic stellate cells into a pro-contractile and pro-fibrotic phenotype have been associated with aberrant cycles of mechanosensing and mechanoresponses. The downstream consequences of disrupted mechanical homeostasis likely contribute to the progression of NAFLD and promote the development of portal hypertension, cirrhosis, and hepatocellular carcinoma. Identification of molecular targets involved in pathogenic mechanotransduction will allow for the development of novel strategies to prevent the progression of liver disease in NAFLD.
Collapse
Affiliation(s)
- Emilie K Mitten
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - György Baffy
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Section of Gastroenterology, Department of Medicine, VA Boston Healthcare System, Boston MA, USA.
| |
Collapse
|
4
|
Multimerin-1 and cancer: a review. Biosci Rep 2022; 42:230760. [PMID: 35132992 PMCID: PMC8881648 DOI: 10.1042/bsr20211248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Multimerin-1 (MMRN1) is a platelet protein with a role in haemostasis and coagulation. It is also present in endothelial cells (ECs) and the extracellular matrix (ECM), where it may be involved in cell adhesion, but its molecular functions and protein–protein interactions in these cellular locations have not been studied in detail yet. In recent years, MMRN1 has been identified as a differentially expressed gene (DEG) in various cancers and it has been proposed as a possible cancer biomarker. Some evidence suggest that MMRN1 expression is regulated by methylation, protein interactions, and non-coding RNAs (ncRNAs) in different cancers. This raises the questions if a functional role of MMRN1 is being targeted during cancer development, and if MMRN1’s differential expression pattern correlates with cancer progression. As a result, it is timely to review the current state of what is known about MMRN1 to help inform future research into MMRN1’s molecular mechanisms in cancer.
Collapse
|
5
|
Padhi A, Danielsson BE, Alabduljabbar DS, Wang J, Conway DE, Kapania RK, Nain AS. Cell Fragment Formation, Migration, and Force Exertion on Extracellular Mimicking Fiber Nanonets. Adv Biol (Weinh) 2021; 5:e2000592. [PMID: 33759402 DOI: 10.1002/adbi.202000592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/01/2021] [Indexed: 12/16/2022]
Abstract
Cell fragments devoid of the nucleus play an essential role in intercellular communication. Mostly studied on flat 2D substrates, their origins and behavior in native fibrous environments remain unknown. Here, cytoplasmic fragments' spontaneous formation and behavior in suspended extracellular matrices mimicking fiber architectures (parallel, crosshatch, and hexagonal) are described. After cleaving from the parent cell body, the fragments of diverse shapes on fibers migrate faster compared to 2D. Furthermore, while fragments in 2D are mostly circular, a higher number of rectangular and blob-like shapes are formed on fibers, and, interestingly, each shape is capable of forming protrusive structures. Absent in 2D, fibers' fragments display oscillatory migratory behavior with dramatic shape changes, sometimes remarkably sustained over long durations (>20 h). Immunostaining reveals paxillin distribution along fragment body-fiber length, while Forster Resonance Energy Transfer imaging of vinculin reveals mechanical loading of fragment adhesions comparable to whole cell adhesions. Using nanonet force microscopy, the forces exerted by fragments are estimated, and peculiarly small area fragments can exert forces similar to larger fragments in a Rho-associated kinase dependent manner. Overall, fragment dynamics on 2D substrates are insufficient to describe the mechanosensitivity of fragments to fibers, and the architecture of fiber networks can generate entirely new behaviors.
Collapse
Affiliation(s)
- Abinash Padhi
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Brooke E Danielsson
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
| | - Deema S Alabduljabbar
- Department of Biomedical Engineering, University of California, Davis, CA, 95616, USA
| | - Ji Wang
- Department of Engineering Science and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Daniel E Conway
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
| | - Rakesh K Kapania
- Kevin T. Crofton Department of Aerospace and Ocean Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amrinder S Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Prediction of Extracellular Matrix Proteins by Fusing Multiple Feature Information, Elastic Net, and Random Forest Algorithm. MATHEMATICS 2020. [DOI: 10.3390/math8020169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Extracellular matrix (ECM) proteins play an important role in a series of biological processes of cells. The study of ECM proteins is helpful to further comprehend their biological functions. We propose ECMP-RF (extracellular matrix proteins prediction by random forest) to predict ECM proteins. Firstly, the features of the protein sequence are extracted by combining encoding based on grouped weight, pseudo amino-acid composition, pseudo position-specific scoring matrix, a local descriptor, and an autocorrelation descriptor. Secondly, the synthetic minority oversampling technique (SMOTE) algorithm is employed to process the class imbalance data, and the elastic net (EN) is used to reduce the dimension of the feature vectors. Finally, the random forest (RF) classifier is used to predict the ECM proteins. Leave-one-out cross-validation shows that the balanced accuracy of the training and testing datasets is 97.3% and 97.9%, respectively. Compared with other state-of-the-art methods, ECMP-RF is significantly better than other predictors.
Collapse
|
8
|
|
9
|
Wierer M, Prestel M, Schiller HB, Yan G, Schaab C, Azghandi S, Werner J, Kessler T, Malik R, Murgia M, Aherrahrou Z, Schunkert H, Dichgans M, Mann M. Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression. Mol Cell Proteomics 2017; 17:321-334. [PMID: 29208753 PMCID: PMC5795394 DOI: 10.1074/mcp.ra117.000315] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/20/2017] [Indexed: 12/29/2022] Open
Abstract
Atherosclerosis leads to vascular lesions that involve major rearrangements of the vascular proteome, especially of the extracellular matrix (ECM). Using single aortas from ApoE knock out mice, we quantified formation of plaques by single-run, high-resolution mass spectrometry (MS)-based proteomics. To probe localization on a proteome-wide scale we employed quantitative detergent solubility profiling. This compartment- and time-resolved resource of atherogenesis comprised 5117 proteins, 182 of which changed their expression status in response to vessel maturation and atherosclerotic plaque development. In the insoluble ECM proteome, 65 proteins significantly changed, including relevant collagens, matrix metalloproteinases and macrophage derived proteins. Among novel factors in atherosclerosis, we identified matrilin-2, the collagen IV crosslinking enzyme peroxidasin as well as the poorly characterized MAM-domain containing 2 (Mamdc2) protein as being up-regulated in the ECM during atherogenesis. Intriguingly, three subunits of the osteoclast specific V-ATPase complex were strongly increased in mature plaques with an enrichment in macrophages thus implying an active de-mineralization function.
Collapse
Affiliation(s)
- Michael Wierer
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Prestel
- §Institute for Stroke and Dementia Research, Klinikum der Universität München, München, Germany
| | - Herbert B Schiller
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.,¶Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Guangyao Yan
- §Institute for Stroke and Dementia Research, Klinikum der Universität München, München, Germany
| | - Christoph Schaab
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Sepiede Azghandi
- §Institute for Stroke and Dementia Research, Klinikum der Universität München, München, Germany
| | - Julia Werner
- ‖Klinik für Herz- und Kreislauferkrankungen, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Thorsten Kessler
- ‖Klinik für Herz- und Kreislauferkrankungen, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Rainer Malik
- §Institute for Stroke and Dementia Research, Klinikum der Universität München, München, Germany
| | - Marta Murgia
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.,**Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Zouhair Aherrahrou
- ‡‡Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany.,§§Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), e.V., Partner Site Hamburg/Kiel/Lübeck, Lübeck Germany
| | - Heribert Schunkert
- ‖Klinik für Herz- und Kreislauferkrankungen, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,¶¶DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Martin Dichgans
- §Institute for Stroke and Dementia Research, Klinikum der Universität München, München, Germany;
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany;
| |
Collapse
|
10
|
Analysis of Soluble Molecular Fibronectin-Fibrin Complexes and EDA-Fibronectin Concentration in Plasma of Patients with Atherosclerosis. Inflammation 2017; 39:1059-68. [PMID: 27022744 PMCID: PMC4883272 DOI: 10.1007/s10753-016-0336-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Atherosclerosis, a chronic vascular disease, leads to molecular events bound with interplaying processes of inflammation and coagulation. In the present study, fibronectin (FN), FN containing extra domain A (EDA-FN), frequency of occurrence, and relative amounts of soluble plasma FN-fibrin complexes were analyzed in 80 plasma samples of patients suspected of coronary artery disease based on clinical evaluation and changes in arteries found by computed tomographic coronary angiography. The study showed that in the plasma of the patients’ group with high risk of coronary artery disease EDA-FN concentration was significantly higher (3.5 ± 2.5 mg/L; P < 0.025) and the molecular FN-fibrin complexes of 1000 kDa and higher occurred more often than in the groups of patients with mild risk of coronary artery disease and the normal age-matched. The increased level of EDA-FN and occurrence of FN-fibrin complexes could have a potential diagnostic value in the diagnosis and management of patients with coronary artery disease.
Collapse
|
11
|
Guo Z, Zhang T, Fang K, Liu P, Li M, Gu N. The effect of porosity and stiffness of glutaraldehyde cross-linked egg white scaffold simulating aged extracellular matrix on distribution and aggregation of ovarian cancer cells. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.05.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
12
|
Nair GB, Matela A, Kurbanov D, Raghu G. Newer developments in idiopathic pulmonary fibrosis in the era of anti-fibrotic medications. Expert Rev Respir Med 2016; 10:699-711. [PMID: 27094006 DOI: 10.1080/17476348.2016.1177461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease with a fatal prognosis. Over the last decade, the concepts in pathobiology of pulmonary fibrosis have shifted from a model of chronic inflammation to dysregulated fibroproliferative repair in genetically predisposed patients. Although new breakthrough treatments are now available that slow the progression of the disease, several newer anti-inflammatory and anti-fibrotic drugs are under investigation. Patients with IPF often have coexistent conditions; prompt detection and interventions of which may improve the overall outcome of patients with IPF. Here, we summarize the present understanding of pathogenesis of IPF and treatment options for IPF in the current landscape of new anti-fibrotic treatment options.
Collapse
Affiliation(s)
- Girish B Nair
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA.,b Department of Medicine , SUNY Stony Brook School of Medicine , NY , USA
| | - Ajsza Matela
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA
| | - Daniel Kurbanov
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA
| | - Ganesh Raghu
- c Department of Medicine & Lab Medicine (Adjunct), Division of Pulmonary & Critical Care Medicine , University of Washington , Seattle , WA , USA
| |
Collapse
|
13
|
Cromar GL, Zhao A, Xiong X, Swapna LS, Loughran N, Song H, Parkinson J. PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw013. [PMID: 26980519 PMCID: PMC4792532 DOI: 10.1093/database/baw013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022]
Abstract
PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya. In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary heatmaps and detailed level views of domain conservation; (iii) an interactive, network-based visualization tool for exploration of domain architectures and their conservation; (iv) ability to browse based on protein functional categories (GOSlim); (v) improvements to the web interface to enhance drill down capability from the heatmap view; and (vi) improved coverage including 164 eukaryotes and 12 reference species. In addition, we provide improved support for downloading data and images in a variety of formats. Among the existing tools available for phylogenetic profiles, PhyloPro provides several innovative domain-based features including a novel domain adjacency visualization tool. These are designed to allow the user to identify and compare proteins with similar domain architectures across species and thus develop hypotheses about the evolution of lineage-specific trajectories. Database URL: http://www.compsysbio.org/phylopro/.
Collapse
Affiliation(s)
- Graham L Cromar
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Anthony Zhao
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Xuejian Xiong
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Lakshmipuram S Swapna
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Noeleen Loughran
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Hongyan Song
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and Departments of Biochemistry, Computer Science and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
14
|
Abstract
Biomaterials have played an increasingly prominent role in the success of biomedical devices and in the development of tissue engineering, which seeks to unlock the regenerative potential innate to human tissues/organs in a state of deterioration and to restore or reestablish normal bodily function. Advances in our understanding of regenerative biomaterials and their roles in new tissue formation can potentially open a new frontier in the fast-growing field of regenerative medicine. Taking inspiration from the role and multi-component construction of native extracellular matrices (ECMs) for cell accommodation, the synthetic biomaterials produced today routinely incorporate biologically active components to define an artificial in vivo milieu with complex and dynamic interactions that foster and regulate stem cells, similar to the events occurring in a natural cellular microenvironment. The range and degree of biomaterial sophistication have also dramatically increased as more knowledge has accumulated through materials science, matrix biology and tissue engineering. However, achieving clinical translation and commercial success requires regenerative biomaterials to be not only efficacious and safe but also cost-effective and convenient for use and production. Utilizing biomaterials of human origin as building blocks for therapeutic purposes has provided a facilitated approach that closely mimics the critical aspects of natural tissue with regard to its physical and chemical properties for the orchestration of wound healing and tissue regeneration. In addition to directly using tissue transfers and transplants for repair, new applications of human-derived biomaterials are now focusing on the use of naturally occurring biomacromolecules, decellularized ECM scaffolds and autologous preparations rich in growth factors/non-expanded stem cells to either target acceleration/magnification of the body's own repair capacity or use nature's paradigms to create new tissues for restoration. In particular, there is increasing interest in separating ECMs into simplified functional domains and/or biopolymeric assemblies so that these components/constituents can be discretely exploited and manipulated for the production of bioscaffolds and new biomimetic biomaterials. Here, following an overview of tissue auto-/allo-transplantation, we discuss the recent trends and advances as well as the challenges and future directions in the evolution and application of human-derived biomaterials for reconstructive surgery and tissue engineering. In particular, we focus on an exploration of the structural, mechanical, biochemical and biological information present in native human tissue for bioengineering applications and to provide inspiration for the design of future biomaterials.
Collapse
|
15
|
Guo Z, Zhang T, Fang K, Dou J, Zhou N, Ma X, Gu N. The effects of macroporosity and stiffness of poly[(methyl vinyl ether)-alt-(maleic acid)] cross-linked egg white simulations of an aged extracellular matrix on the proliferation of ovarian cancer cells. RSC Adv 2016. [DOI: 10.1039/c6ra05134k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effects of macroporosity and stiffness of P(MVE-alt-MA) cross-linked EW simulations of an aged ECM on the proliferation of cancer cells.
Collapse
Affiliation(s)
- Zhenchao Guo
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| | - Tianzhu Zhang
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| | - Kun Fang
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| | - Jun Dou
- Medical School
- Southeast University
- Nanjing 210009
- China
| | - Naizhen Zhou
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| | - Xiaoe Ma
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| | - Ning Gu
- State Key Laboratory of Bioelectronics
- Jiangsu Key Laboratory for Biomaterials and Devices
- School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology
- Southeast University
- Nanjing 210096
| |
Collapse
|
16
|
Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M. Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair. Mol Syst Biol 2015; 11:819. [PMID: 26174933 PMCID: PMC4547847 DOI: 10.15252/msb.20156123] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The extracellular matrix (ECM) is a key regulator of tissue morphogenesis and repair. However, its composition and architecture are not well characterized. Here, we monitor remodeling of the extracellular niche in tissue repair in the bleomycin-induced lung injury mouse model. Mass spectrometry quantified 8,366 proteins from total tissue and bronchoalveolar lavage fluid (BALF) over the course of 8 weeks, surveying tissue composition from the onset of inflammation and fibrosis to its full recovery. Combined analysis of proteome, secretome, and transcriptome highlighted post-transcriptional events during tissue fibrogenesis and defined the composition of airway epithelial lining fluid. To comprehensively characterize the ECM, we developed a quantitative detergent solubility profiling (QDSP) method, which identified Emilin-2 and collagen-XXVIII as novel constituents of the provisional repair matrix. QDSP revealed which secreted proteins interact with the ECM, and showed drastically altered association of morphogens to the insoluble matrix upon injury. Thus, our proteomic systems biology study assigns proteins to tissue compartments and uncovers their dynamic regulation upon lung injury and repair, potentially contributing to the development of anti-fibrotic strategies.
Collapse
Affiliation(s)
- Herbert B Schiller
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Isis E Fernandez
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Christoph Schaab
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Richard A Scheltema
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
17
|
Klamer S, Voermans C. The role of novel and known extracellular matrix and adhesion molecules in the homeostatic and regenerative bone marrow microenvironment. Cell Adh Migr 2015; 8:563-77. [PMID: 25482635 PMCID: PMC4594522 DOI: 10.4161/19336918.2014.968501] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Maintenance of haematopoietic stem cells and differentiation of committed progenitors occurs in highly specialized niches. The interactions of haematopoietic stem and progenitor cells (HSPCs) with cells, growth factors and extracellular matrix (ECM) components of the bone marrow (BM) microenvironment control homeostasis of HSPCs. We only start to understand the complexity of the haematopoietic niche(s) that comprises endosteal, arterial, sinusoidal, mesenchymal and neuronal components. These distinct niches produce a broad range of soluble factors and adhesion molecules that modulate HSPC fate during normal hematopoiesis and BM regeneration. Adhesive interactions between HSPCs and the microenvironment will influence their localization and differentiation potential. In this review we highlight the current understanding of the functional role of ECM- and adhesion (regulating) molecules in the haematopoietic niche during homeostatic and regenerative hematopoiesis. This knowledge may lead to the improvement of current cellular therapies and more efficient development of future cellular products.
Collapse
Affiliation(s)
- Sofieke Klamer
- a Department of Hematopoiesis; Sanquin Research; Landsteiner Laboratory; Academic Medical Centre ; University of Amsterdam ; Amsterdam , The Netherlands
| | | |
Collapse
|
18
|
Yang R, Zhang C, Gao R, Zhang L. An ensemble method with hybrid features to identify extracellular matrix proteins. PLoS One 2015; 10:e0117804. [PMID: 25680094 PMCID: PMC4334504 DOI: 10.1371/journal.pone.0117804] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/02/2015] [Indexed: 12/29/2022] Open
Abstract
The extracellular matrix (ECM) is a dynamic composite of secreted proteins that play important roles in numerous biological processes such as tissue morphogenesis, differentiation and homeostasis. Furthermore, various diseases are caused by the dysfunction of ECM proteins. Therefore, identifying these important ECM proteins may assist in understanding related biological processes and drug development. In view of the serious imbalance in the training dataset, a Random Forest-based ensemble method with hybrid features is developed in this paper to identify ECM proteins. Hybrid features are employed by incorporating sequence composition, physicochemical properties, evolutionary and structural information. The Information Gain Ratio and Incremental Feature Selection (IGR-IFS) methods are adopted to select the optimal features. Finally, the resulting predictor termed IECMP (Identify ECM Proteins) achieves an balanced accuracy of 86.4% using the 10-fold cross-validation on the training dataset, which is much higher than results obtained by other methods (ECMPRED: 71.0%, ECMPP: 77.8%). Moreover, when tested on a common independent dataset, our method also achieves significantly improved performance over ECMPP and ECMPRED. These results indicate that IECMP is an effective method for ECM protein prediction, which has a more balanced prediction capability for positive and negative samples. It is anticipated that the proposed method will provide significant information to fully decipher the molecular mechanisms of ECM-related biological processes and discover candidate drug targets. For public access, we develop a user-friendly web server for ECM protein identification that is freely accessible at http://iecmp.weka.cc.
Collapse
Affiliation(s)
- Runtao Yang
- School of Control Science and Engineering, Shandong University, Jinan, China
| | - Chengjin Zhang
- School of Control Science and Engineering, Shandong University, Jinan, China
- School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, China
- * E-mail: (CJZ); (RG)
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, China
- * E-mail: (CJZ); (RG)
| | - Lina Zhang
- School of Control Science and Engineering, Shandong University, Jinan, China
| |
Collapse
|
19
|
Launay G, Salza R, Multedo D, Thierry-Mieg N, Ricard-Blum S. MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. Nucleic Acids Res 2014; 43:D321-7. [PMID: 25378329 PMCID: PMC4383919 DOI: 10.1093/nar/gku1091] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. It is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB content has been updated by curation and by importing extracellular interaction data from other IMEx databases. Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks. Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data). Any molecule of the network may be selected and its partners added to the network at any time. Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.
Collapse
Affiliation(s)
- G Launay
- UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France
| | - R Salza
- UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France
| | - D Multedo
- UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France
| | - N Thierry-Mieg
- TIMC- IMAG/BCM, UMR 5525 CNRS - Université Grenoble 1, Faculté de Médecine, 38706 La Tronche Cedex, France
| | - S Ricard-Blum
- UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France
| |
Collapse
|
20
|
Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, Parkinson J. New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biol Evol 2014; 6:2897-917. [PMID: 25323955 PMCID: PMC4224354 DOI: 10.1093/gbe/evu228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins.
Collapse
Affiliation(s)
- Graham Cromar
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Ka-Chun Wong
- Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada
| | - Noeleen Loughran
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tuan On
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Hongyan Song
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xuejian Xiong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada
| |
Collapse
|
21
|
Duscher D, Maan ZN, Wong VW, Rennert RC, Januszyk M, Rodrigues M, Hu M, Whitmore AJ, Whittam AJ, Longaker MT, Gurtner GC. Mechanotransduction and fibrosis. J Biomech 2014; 47:1997-2005. [PMID: 24709567 DOI: 10.1016/j.jbiomech.2014.03.031] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 01/06/2023]
Abstract
Scarring and tissue fibrosis represent a significant source of morbidity in the United States. Despite considerable research focused on elucidating the mechanisms underlying cutaneous scar formation, effective clinical therapies are still in the early stages of development. A thorough understanding of the various signaling pathways involved is essential to formulate strategies to combat fibrosis and scarring. While initial efforts focused primarily on the biochemical mechanisms involved in scar formation, more recent research has revealed a central role for mechanical forces in modulating these pathways. Mechanotransduction, which refers to the mechanisms by which mechanical forces are converted to biochemical stimuli, has been closely linked to inflammation and fibrosis and is believed to play a critical role in scarring. This review provides an overview of our current understanding of the mechanisms underlying scar formation, with an emphasis on the relationship between mechanotransduction pathways and their therapeutic implications.
Collapse
Affiliation(s)
- Dominik Duscher
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Zeshaan N Maan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Victor W Wong
- Department of Plastic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert C Rennert
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Melanie Rodrigues
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Hu
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Arnetha J Whitmore
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexander J Whittam
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Geoffrey C Gurtner
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
22
|
Abstract
PURPOSE OF REVIEW Extracellular matrix (ECM) has both structural and regulatory roles. This update reviews the representative recent developments in diverse aspects of ECM biology relevant to inflammation, tissue destruction, fibrosis, and regeneration. RECENT FINDINGS Biological regulation by ECM is emerging as a major research area, driven by several new directions. Sensing of mechanical cues provided by ECM was found to be crucial in regulating cell differentiation. Transforming growth factor-β (TGF-β) is a pivotal agent in fibrosis and inflammation. A combination of structural biology and cell biology provided novel insights on the mechanisms of its activation by cellular traction and ECM. Improved understanding of how fibrillin microfibrils and associated proteins regulated TGF-β sequestration and activation was achieved by analysis of inherited connective tissue disorders having TGF-β dysregulation as an underlying pathologic mechanism. Insights on microRNA-mediated ECM regulation suggest a key role for miR-29, for which potential therapeutic roles are emerging. Advances in understanding the ECM turnover by proteinases provided novel insights on cell regulation and identified useful disease biomarkers. SUMMARY As a crucial modulator of cell behavior, ECM has exceptionally strong relevance and translational implications for human disease, opening novel opportunities for mechanistic understanding of disease pathogenesis as well as treatment.
Collapse
|
23
|
Byron A, Humphries JD, Humphries MJ. Defining the extracellular matrix using proteomics. Int J Exp Pathol 2013; 94:75-92. [PMID: 23419153 DOI: 10.1111/iep.12011] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 09/13/2012] [Accepted: 11/16/2012] [Indexed: 12/11/2022] Open
Abstract
The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology.
Collapse
Affiliation(s)
- Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | | | | |
Collapse
|