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Ross RB, Gadwa J, Yu J, Darragh LB, Knitz MW, Nguyen D, Olimpo NA, Abdelazeem KN, Nguyen A, Corbo S, Van Court B, Beynor J, Neupert B, Saviola AJ, D'Alessandro A, Karam SD. PPARα Agonism Enhances Immune Response to Radiotherapy While Dietary Oleic Acid Results in Counteraction. Clin Cancer Res 2024; 30:1916-1933. [PMID: 38363297 PMCID: PMC11061609 DOI: 10.1158/1078-0432.ccr-23-3433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 02/17/2024]
Abstract
PURPOSE Head and neck cancer (HNC) improvements are stagnant, even with advances in immunotherapy. Our previous clinical trial data show that altered fatty acid (FA) metabolism correlates with outcome. We hypothesized that pharmacologic and dietary modulation of FA catabolism will affect therapeutic efficacy. EXPERIMENTAL DESIGN We performed in vivo and in vitro experiments using PPARα agonism with fenofibrate (FF) or high oleic acid diets (OAD) with radiotherapy, generating metabolomic, proteomic, stable isotope tracing, extracellular flux analysis, and flow-cytometric data to investigate these alterations. RESULTS FF improved antitumor efficacy of high dose per fraction radiotherapy in HNC murine models, whereas the OAD reversed this effect. FF-treated mice on the control diet had evidence of increased FA catabolism. Stable isotope tracing showed less glycolytic utilization by ex vivo CD8+ T cells. Improved efficacy correlated with intratumoral alterations in eicosanoid metabolism and downregulated mTOR and CD36. CONCLUSIONS Metabolic intervention with increased FA catabolism improves the efficacy of HNC therapy and enhances antitumoral immune response.
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Affiliation(s)
- Richard Blake Ross
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Jacob Gadwa
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Justin Yu
- Department of Otolaryngology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Laurel B. Darragh
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Michael W. Knitz
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Diemmy Nguyen
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Nicholas A. Olimpo
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Khalid N.M. Abdelazeem
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
- Radiation Biology Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Alexander Nguyen
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Sophia Corbo
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Benjamin Van Court
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Jessica Beynor
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Brooke Neupert
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado Anschutz Medical Center, Aurora, Colorado
- Department of Immunology, University of Colorado Anschutz Medical Center, Aurora, Colorado
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Cruz LC, Habibovic A, Dempsey B, Massafera MP, Janssen-Heininger YMW, Lin MCJ, Hoffman ET, Weiss DJ, Huang SK, van der Vliet A, Meotti FC. Identification of tyrosine brominated extracellular matrix proteins in normal and fibrotic lung tissues. Redox Biol 2024; 71:103102. [PMID: 38430684 PMCID: PMC10912723 DOI: 10.1016/j.redox.2024.103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Peroxidasin (PXDN) is a secreted heme peroxidase that catalyzes the oxidative crosslinking of collagen IV within the extracellular matrix (ECM) via intermediate hypobromous acid (HOBr) synthesis from hydrogen peroxide and bromide, but recent findings have also suggested alternative ECM protein modifications by PXDN, including incorporation of bromide into tyrosine residues. In this work, we sought to identify the major target proteins for tyrosine bromination by HOBr or by PXDN-mediated oxidation in ECM from mouse teratocarcinoma PFHR9 cells. We detected 61 bromotyrosine (BrY)-containing peptides representing 23 proteins in HOBr-modified ECM from PFHR9 cells, among which laminins displayed the most prominent bromotyrosine incorporation. Moreover, we also found that laminin α1, laminin β1, and tubulointerstitial nephritis antigen-like (TINAGL1) contained BrY in untreated PFHR9 cells, which depended on PXDN. We extended these analyses to lung tissues from both healthy mice and mice with experimental lung fibrosis, and in lung tissues obtained from human subjects. Analysis of ECM-enriched mouse lung tissue extracts showed that 83 ECM proteins were elevated in bleomycin-induced fibrosis, which included various collagens and laminins, and PXDN. Similarly, mRNA and protein expression of PXDN and laminin α/β1 were enhanced in fibrotic mouse lung tissues, and also in mouse bone-marrow-derived macrophages or human fibroblasts stimulated with transforming growth factor β1, a profibrotic growth factor. We identified 11 BrY-containing ECM proteins, including collagen IV α2, collagen VI α1, TINAGL1, and various laminins, in both healthy and mouse fibrotic lung tissues, although the relative extent of tyrosine bromination of laminins was not significantly increased during fibrosis. Finally, we also identified 7 BrY-containing ECM proteins in human lung tissues, again including collagen IV α2, collagen VI α1, and TINAGL1. Altogether, this work demonstrates the presence of several bromotyrosine-modified ECM proteins, likely involving PXDN, even in normal lung tissues, suggesting a potential biological function for these modifications.
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Affiliation(s)
- Litiele Cezar Cruz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil; Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, VT, USA
| | - Aida Habibovic
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, VT, USA
| | - Bianca Dempsey
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil
| | - Mariana P Massafera
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil
| | | | - Miao-Chong Joy Lin
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, VT, USA
| | - Evan T Hoffman
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Daniel J Weiss
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Steven K Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, VT, USA.
| | - Flavia C Meotti
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil.
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Noro J, Vilaça-Faria H, Reis RL, Pirraco RP. Extracellular matrix-derived materials for tissue engineering and regenerative medicine: A journey from isolation to characterization and application. Bioact Mater 2024; 34:494-519. [PMID: 38298755 PMCID: PMC10827697 DOI: 10.1016/j.bioactmat.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Biomaterial choice is an essential step during the development tissue engineering and regenerative medicine (TERM) applications. The selected biomaterial must present properties allowing the physiological-like recapitulation of several processes that lead to the reestablishment of homeostatic tissue or organ function. Biomaterials derived from the extracellular matrix (ECM) present many such properties and their use in the field has been steadily increasing. Considering this growing importance, it becomes imperative to provide a comprehensive overview of ECM biomaterials, encompassing their sourcing, processing, and integration into TERM applications. This review compiles the main strategies used to isolate and process ECM-derived biomaterials as well as different techniques used for its characterization, namely biochemical and chemical, physical, morphological, and biological. Lastly, some of their applications in the TERM field are explored and discussed.
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Affiliation(s)
- Jennifer Noro
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Helena Vilaça-Faria
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rogério P. Pirraco
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Darula Z, McCabe MC, Barrett A, Schmitt LR, Maslanka MD, Saviola AJ, Orgel J, Burlingame A, Staab-Weijnitz CA, Stenmark K, Weaver V, Chalkley RJ, Hansen KC. Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry. bioRxiv 2024:2024.03.31.587441. [PMID: 38585857 PMCID: PMC10996605 DOI: 10.1101/2024.03.31.587441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Collagen cross-links created by the lysyl oxidase and lysyl hydroxylase families of enzymes are a significant contributing factor to the biomechanical strength and rigidity of tissues, which in turn influence cell signaling and ultimately cell phenotype. In the clinic, the proteolytically liberated N-terminal cross-linked peptide of collagen I (NTX) is used as a biomarker of bone and connective tissue turnover, which is altered in several disease processes. Despite the clinical utility of these collagen breakdown products, the majority of the cross-linked peptide species have not been identified in proteomic datasets. Here we evaluate several parameters for the preparation and identification of these peptides from the collagen I-rich Achilles tendon. Our refined approach involving chemical digestion for protein solubilization coupled with mass spectrometry allows for the identification of the NTX cross-links in a range of modification states. Based on the specificity of the enzymatic cross-linking reaction we utilized follow-up variable modification searches to facilitate identification with a wider range of analytical workflows. We then applied a spectral library approach to identify differences in collagen cross-links in bovine pulmonary hypertension. The presented method offers unique opportunities to understand extracellular matrix remodeling events in development, aging, wound healing, and fibrotic disease that modulate collagen architecture through lysyl-hydroxylase and lysyl-oxidase enzymes.
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Diedrich AM, Daneshgar A, Tang P, Klein O, Mohr A, Onwuegbuchulam OA, von Rueden S, Menck K, Bleckmann A, Juratli MA, Becker F, Sauer IM, Hillebrandt KH, Pascher A, Struecker B. Proteomic analysis of decellularized mice liver and kidney extracellular matrices. J Biol Eng 2024; 18:17. [PMID: 38389090 PMCID: PMC10885605 DOI: 10.1186/s13036-024-00413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The extracellular matrix (ECM) is a three-dimensional network of proteins that encases and supports cells within a tissue and promotes physiological and pathological cellular differentiation and functionality. Understanding the complex composition of the ECM is essential to decrypt physiological processes as well as pathogenesis. In this context, the method of decellularization is a useful technique to eliminate cellular components from tissues while preserving the majority of the structural and functional integrity of the ECM. RESULTS In this study, we employed a bottom-up proteomic approach to elucidate the intricate network of proteins in the decellularized extracellular matrices of murine liver and kidney tissues. This approach involved the use of a novel, perfusion-based decellularization protocol to generate acellular whole organ scaffolds. Proteomic analysis of decellularized mice liver and kidney ECM scaffolds revealed tissue-specific differences in matrisome composition, while we found a predominantly stable composition of the core matrisome, consisting of collagens, glycoproteins, and proteoglycans. Liver matrisome analysis revealed unique proteins such as collagen type VI alpha-6, fibrillin-2 or biglycan. In the kidney, specific ECM-regulators such as cathepsin z were detected. CONCLUSION The identification of distinct proteomic signatures provides insights into how different matrisome compositions might influence the biological properties of distinct tissues. This experimental workflow will help to further elucidate the proteomic landscape of decellularized extracellular matrix scaffolds of mice in order to decipher complex cell-matrix interactions and their contribution to a tissue-specific microenvironment.
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Affiliation(s)
- Anna-Maria Diedrich
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Assal Daneshgar
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Peter Tang
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
| | - Oliver Klein
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, Core Facility Imaging Mass Spectrometry, 13353, Berlin, Germany
| | - Annika Mohr
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Olachi A Onwuegbuchulam
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Sabine von Rueden
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
| | - Kerstin Menck
- Department of Medicine A for Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Annalen Bleckmann
- Department of Medicine A for Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Mazen A Juratli
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Felix Becker
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Igor M Sauer
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
| | - Karl H Hillebrandt
- Department of Surgery, Charité Mitte | Campus Virchow-Klinikum, Charité -Universitaetsmedizin Berlin, Campus, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitaetsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Andreas Pascher
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany
| | - Benjamin Struecker
- Department of General, Visceral, and Transplant Surgery, University Hospital Muenster, 48149, Muenster, Germany.
- West German Cancer Center, University Hospital Muenster, 48149, Muenster, Germany.
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Jacobson KR, Saleh AM, Lipp SN, Tian C, Watson AR, Luetkemeyer CM, Ocken AR, Spencer SL, Kinzer-Ursem TL, Calve S. Extracellular matrix protein composition dynamically changes during murine forelimb development. iScience 2024; 27:108838. [PMID: 38303699 PMCID: PMC10831947 DOI: 10.1016/j.isci.2024.108838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome was assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system. This resource will guide future research investigating the role of the matrisome during complex tissue development.
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Affiliation(s)
- Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah N. Lipp
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- The Indiana University Medical Scientist/Engineer Training Program, Indiana University, Indianapolis, IN 46202, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Research Center for Molecular Medicine (CEMM) of the Austrian Academy of Sciences, Vienna, Austria
| | - Audrey R. Watson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Callan M. Luetkemeyer
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alexander R. Ocken
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Tamara L. Kinzer-Ursem
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah Calve
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lorentzen LG, Yeung K, Eldrup N, Eiberg JP, Sillesen HH, Davies MJ. Proteomic analysis of the extracellular matrix of human atherosclerotic plaques shows marked changes between plaque types. Matrix Biol Plus 2024; 21:100141. [PMID: 38292008 PMCID: PMC10825564 DOI: 10.1016/j.mbplus.2024.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/01/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Cardiovascular disease is the leading cause of death, with atherosclerosis the major underlying cause. While often asymptomatic for decades, atherosclerotic plaque destabilization and rupture can arise suddenly and cause acute arterial occlusion or peripheral embolization resulting in myocardial infarction, stroke and lower limb ischaemia. As extracellular matrix (ECM) remodelling is associated with plaque instability, we hypothesized that the ECM composition would differ between plaques. We analyzed atherosclerotic plaques obtained from 21 patients who underwent carotid surgery following recent symptomatic carotid artery stenosis. Plaques were solubilized using a new efficient, single-step approach. Solubilized proteins were digested to peptides, and analyzed by liquid chromatography-mass spectrometry using data-independent acquisition. Identification and quantification of 4498 plaque proteins was achieved, including 354 ECM proteins, with unprecedented coverage and high reproducibility. Multidimensional scaling analysis and hierarchical clustering indicate two distinct clusters, which correlate with macroscopic plaque morphology (soft/unstable versus hard/stable), ultrasound classification (echolucent versus echogenic) and the presence of hemorrhage/ulceration. We identified 714 proteins with differential abundances between these groups. Soft/unstable plaques were enriched in proteins involved in inflammation, ECM remodelling, and protein degradation (e.g. matrix metalloproteinases, cathepsins). In contrast, hard/stable plaques contained higher levels of ECM structural proteins (e.g. collagens, versican, nidogens, biglycan, lumican, proteoglycan 4, mineralization proteins). These data indicate that a single-step proteomics method can provide unique mechanistic insights into ECM remodelling and inflammatory mechanisms within plaques that correlate with clinical parameters, and help rationalize plaque destabilization. These data also provide an approach towards identifying biomarkers for individualized risk profiling of atherosclerosis.
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Affiliation(s)
- Lasse G. Lorentzen
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Karin Yeung
- Department of Vascular Surgery, Heart Centre, University Hospital Copenhagen - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nikolaj Eldrup
- Department of Vascular Surgery, Heart Centre, University Hospital Copenhagen - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jonas P. Eiberg
- Department of Vascular Surgery, Heart Centre, University Hospital Copenhagen - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Copenhagen Academy for Medical Education and Simulation (CAMES), Capital Region of Denmark, Copenhagen, Denmark
| | - Henrik H. Sillesen
- Department of Vascular Surgery, Heart Centre, University Hospital Copenhagen - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
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Sano T, Ochiai T, Nagayama T, Nakamura A, Kubota N, Kadowaki T, Wakabayashi T, Iwatsubo T. Genetic Reduction of Insulin Signaling Mitigates Amyloid-β Deposition by Promoting Expression of Extracellular Matrix Proteins in the Brain. J Neurosci 2023; 43:7226-7241. [PMID: 37699718 PMCID: PMC10601373 DOI: 10.1523/jneurosci.0071-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023] Open
Abstract
The insulin/IGF-1 signaling (IIS) regulates a wide range of biological processes, including aging and lifespan, and has also been implicated in the pathogenesis of Alzheimer's disease (AD). We and others have reported that reduced signaling by genetic ablation of the molecules involved in IIS (e.g., insulin receptor substrate 2 [IRS-2]) markedly mitigates amyloid plaque formation in the brains of mouse models of AD, although the molecular underpinnings of the amelioration remain unsolved. Here, we revealed, by a transcriptomic analysis of the male murine cerebral cortices, that the expression of genes encoding extracellular matrix (ECM) was significantly upregulated by the loss of IRS-2. Insulin signaling activity negatively regulated the phosphorylation of Smad2 and Smad3 in the brain, and suppressed TGF-β/Smad-dependent expression of a subset of ECM genes in brain-derived cells. The ECM proteins inhibited Aβ fibril formation in vitro, and IRS-2 deficiency suppressed the aggregation process of Aβ in the brains of male APP transgenic mice as revealed by injection of aggregation seeds in vivo Our results propose a novel mechanism in AD pathophysiology whereby IIS modifies Aβ aggregation and amyloid pathology by altering the expression of ECM genes in the brain.SIGNIFICANCE STATEMENT The insulin/IGF-1 signaling (IIS) has been recognized as a regulator of aging, a leading risk factor for the onset of Alzheimer's disease (AD). In AD mouse models, genetic deletion of key IIS molecules markedly reduces the amyloid plaque formation in the brain, although the molecular underpinnings of this amelioration remain elusive. We found that the deficiency of insulin receptor substrate 2 leads to an increase in the expression of various extracellular matrices (ECMs) in the brain, potentially through TGF-β/Smad signaling. Furthermore, some of those ECMs exhibited the potential to inhibit amyloid plaque accumulation by disrupting the formation of Aβ fibrils. This study presents a novel mechanism by which IIS regulates Aβ accumulation, which may involve altered brain ECM expression.
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Affiliation(s)
- Toshiharu Sano
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Toshitaka Ochiai
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- Pharmacology Department, Drug Research Center, Kaken Pharmaceutical Company, LTD, Kyoto, 607-8042, Japan
| | - Takeru Nagayama
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ayaka Nakamura
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Naoto Kubota
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Clinical Nutrition Therapy, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- Toranomon Hospital, Tokyo, 105-8470, Japan
| | - Tomoko Wakabayashi
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Innovative Dementia Prevention, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
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10
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McCabe MC, Okamura DM, Erickson CB, Perry BW, Brewer CM, Nguyen ED, Saviola AJ, Majesky MW, Hansen KC. ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus. bioRxiv 2023:2023.10.11.561940. [PMID: 37873317 PMCID: PMC10592745 DOI: 10.1101/2023.10.11.561940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genus Acomys represent the first example of full skin autotomy in mammals. Acomys cahirinus has evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed between Mus musculus and A. cahirinus , yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches in A. cahirinus and M. musculus from weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility between Mus and Acomys. Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, in Acomys, whereas little or no increase in CD206 was detected in Mus. Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity of Acomys and identify a number of potential targets for future pro-regenerative therapies.
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11
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Avila-Martinez N, Gansevoort M, Verbakel J, Jayaprakash H, Araujo IM, Vitorino M, Tiscornia G, van Kuppevelt TH, Daamen WF. Matrisomal components involved in regenerative wound healing in axolotl and Acomys: implications for biomaterial development. Biomater Sci 2023; 11:6060-6081. [PMID: 37525590 DOI: 10.1039/d3bm00835e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Achieving regeneration in humans has been a long-standing goal of many researchers. Whereas amphibians like the axolotl (Ambystoma mexicanum) are capable of regenerating whole organs and even limbs, most mammals heal their wounds via fibrotic scarring. Recently, the African spiny mouse (Acomys sp.) has been shown to be injury resistant and capable of regenerating several tissue types. A major focal point of research with Acomys has been the identification of drivers of regeneration. In this search, the matrisome components related to the extracellular matrix (ECM) are often overlooked. In this review, we compare Acomys and axolotl skin wound healing and blastema-mediated regeneration by examining their wound healing responses and comparing the expression pattern of matrisome genes, including glycosaminoglycan (GAG) related genes. The goal of this review is to identify matrisome genes that are upregulated during regeneration and could be potential candidates for inclusion in pro-regenerative biomaterials. Research papers describing transcriptomic or proteomic coverage of either skin regeneration or blastema formation in Acomys and axolotl were selected. Matrisome and GAG related genes were extracted from each dataset and the resulting lists of genes were compared. In our analysis, we found several genes that were consistently upregulated, suggesting possible involvement in regenerative processes. Most of the components have been implicated in regulation of cell behavior, extracellular matrix remodeling and wound healing. Incorporation of such pro-regenerative factors into biomaterials may help to shift pro-fibrotic processes to regenerative responses in treated wounds.
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Affiliation(s)
- Nancy Avila-Martinez
- Department of Medical BioSciences, Radboud Research Institute, Radboud university medical center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Merel Gansevoort
- Department of Medical BioSciences, Radboud Research Institute, Radboud university medical center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Juul Verbakel
- Department of Medical BioSciences, Radboud Research Institute, Radboud university medical center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Haarshaadri Jayaprakash
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139, Faro, Portugal
| | - Ines Maria Araujo
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139, Faro, Portugal
| | - Marta Vitorino
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139, Faro, Portugal
| | - Gustavo Tiscornia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Eugin Barcelona, Balmes, 236, 08006 Barcelona, Spain
| | - Toin H van Kuppevelt
- Department of Medical BioSciences, Radboud Research Institute, Radboud university medical center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Willeke F Daamen
- Department of Medical BioSciences, Radboud Research Institute, Radboud university medical center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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12
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. Mass Spectrom Rev 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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13
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Duran P, Sesillo FB, Cook M, Burnett L, Menefee SA, Do E, French S, Zazueta-Damian G, Dzieciatkowska M, Saviola AJ, Shah MM, Sanvictores C, Osborn KG, Hansen KC, Shtrahman M, Christman KL, Alperin M. Proregenerative extracellular matrix hydrogel mitigates pathological alterations of pelvic skeletal muscles after birth injury. Sci Transl Med 2023; 15:eabj3138. [PMID: 37531414 PMCID: PMC10460616 DOI: 10.1126/scitranslmed.abj3138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
Pelvic floor disorders, including pelvic organ prolapse and urinary and fecal incontinence, affect millions of women globally and represent a major public health concern. Pelvic floor muscle (PFM) dysfunction has been identified as one of the leading risk factors for the development of these morbid conditions. Childbirth, specifically vaginal delivery, has been recognized as the most important potentially modifiable risk factor for PFM injury; however, the precise mechanisms of PFM dysfunction after parturition remain elusive. In this study, we demonstrated that PFMs exhibit atrophy and fibrosis in parous women with symptomatic pelvic organ prolapse. These pathological alterations were recapitulated in a preclinical rat model of simulated birth injury (SBI). The transcriptional signature of PFMs after injury demonstrated an impairment in muscle anabolism, persistent expression of genes that promote extracellular matrix (ECM) deposition, and a sustained inflammatory response. We also evaluated the administration of acellular injectable skeletal muscle ECM hydrogel for the prevention of these pathological alterations. Treatment of PFMs with the ECM hydrogel either at the time of birth injury or 4 weeks after injury mitigated PFM atrophy and fibrosis. By evaluating gene expression, we demonstrated that these changes are mainly driven by the hydrogel-induced enhancement of endogenous myogenesis, ECM remodeling, and modulation of the immune response. This work furthers our understanding of PFM birth injury and demonstrates proof of concept for future investigations of proregenerative biomaterial approaches for the treatment of injured pelvic soft tissues.
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Affiliation(s)
- Pamela Duran
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Francesca Boscolo Sesillo
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark Cook
- Department of Integrative, Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lindsey Burnett
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Shawn A. Menefee
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Kaiser Permanente, San Diego, CA 92110, USA
| | - Emmy Do
- Department of Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Saya French
- Department of Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Gisselle Zazueta-Damian
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Kaiser Permanente, San Diego, CA 92110, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Manali M. Shah
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Clyde Sanvictores
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kent G. Osborn
- Center for Veterinary Sciences and Comparative Medicine, Division of Comparative Pathology and Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Matthew Shtrahman
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Karen L. Christman
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Marianna Alperin
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California San Diego, La Jolla, CA 92093, USA
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14
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Han DS, Erickson C, Hansen KC, Kirkbride-Romeo L, He Z, Rodell CB, Soranno DE. Mesenchymal Stem Cells Delivered Locally to Ischemia-Reperfused Kidneys via Injectable Hyaluronic Acid Hydrogels Decrease Extracellular Matrix Remodeling 1 Month after Injury in Male Mice. Cells 2023; 12:1771. [PMID: 37443806 PMCID: PMC10340256 DOI: 10.3390/cells12131771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The translation of stem cell therapies has been hindered by low cell survival and retention rates. Injectable hydrogels enable the site-specific delivery of therapeutic cargo, including cells, to overcome these challenges. We hypothesized that delivery of mesenchymal stem cells (MSC) via shear-thinning and injectable hyaluronic acid (HA) hydrogels would mitigate renal damage following ischemia-reperfusion acute kidney injury. Acute kidney injury (AKI) was induced in mice by bilateral or unilateral ischemia-reperfusion kidney injury. Three days later, mice were treated with MSCs either suspended in media injected intravenously via the tail vein, or injected under the capsule of the left kidney, or MSCs suspended in HA injected under the capsule of the left kidney. Serial measurements of serum and urine biomarkers of renal function and injury, as well as transcutaneous glomerular filtration rate (tGFR) were performed. In vivo optical imaging showed that MSCs localized to both kidneys in a sustained manner after bilateral ischemia and remained within the ipsilateral treated kidney after unilateral ischemic AKI. One month after injury, MSC/HA treatment significantly reduced urinary NGAL compared to controls; it did not significantly reduce markers of fibrosis compared to untreated controls. An analysis of kidney proteomes revealed decreased extracellular matrix remodeling and high overlap with sham proteomes in MSC/HA-treated animals. Hydrogel-assisted MSC delivery shows promise as a therapeutic treatment following acute kidney injury.
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Affiliation(s)
- Daniel S. Han
- Pediatric Urology, Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Christopher Erickson
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045, USA
| | | | - Zhibin He
- Department of Pediatrics, University of Colorado, Aurora, CO 80045, USA
| | - Christopher B. Rodell
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
| | - Danielle E. Soranno
- Division of Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Bioengineering, Purdue University, West Lafayette, IN 47907, USA
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15
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Maples MM, Schneider MC, Bryant SJ. Impact of Inter- and Intra-Donor Variability by Age on the Gel-to-Tissue Transition in MMP-Sensitive PEG Hydrogels for Cartilage Regeneration. ACS Appl Bio Mater 2023. [PMID: 37367934 DOI: 10.1021/acsabm.3c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Matrix metalloproteinase (MMP)-sensitive hydrogels are promising for cartilage tissue engineering due to cell-mediated control over hydrogel degradation. However, any variability in MMP, tissue inhibitors of matrix metalloproteinase (TIMP), and/or extracellular matrix (ECM) production among donors will impact neotissue formation in the hydrogels. The goal for this study was to investigate the impact of inter- and intra-donor variability on the hydrogel-to-tissue transition. Transforming growth factor β3 was tethered into the hydrogel to maintain the chondrogenic phenotype and support neocartilage production, allowing the use of chemically defined medium. Bovine chondrocytes were isolated from two donor groups, skeletally immature juvenile and skeletally mature adult donors (inter-donor variability) and three donors within each group (intra-donor group variability). While the hydrogel supported neocartilaginous growth by all donors, donor age impacted MMP, TIMP, and ECM synthesis rates. Of the MMPs and TIMPs studied, MMP-1 and TIMP-1 were the most abundantly produced by all donors. Adult chondrocytes secreted higher levels of MMPs, which was accompanied by higher production of TIMPs. Juvenile chondrocytes exhibited more rapid ECM growth. By day 29, juvenile chondrocytes had surpassed the gel-to-tissue transition. On the contrary, the adult donors had a percolated polymer network indicating that despite higher levels of MMPs the gel-to-transition had not yet been achieved. The intra-donor group variability of MMP, TIMP, and ECM production was higher in adult chondrocytes but did not impact the extent of the gel-to-tissue transition. In summary, age-dependent inter-donor variations in MMPs and TIMPs significantly impact the timing of the gel-to-tissue transition in MMP-sensitive hydrogels.
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Affiliation(s)
- Mollie M Maples
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Margaret C Schneider
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Stephanie J Bryant
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309-0596, United States
- Materials Science and Engineering Program, University of Colorado, Boulder, Colorado 80309-0596, United States
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309-0596, United States
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16
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Brown RD, Hunter KS, Li M, Frid MG, Harral J, Krafsur GM, Holt TN, Williams J, Zhang H, Riddle SR, Edwards MG, Kumar S, Hu CJ, Graham BB, Walker LA, Garry FB, Buttrick PM, Lahm T, Kheyfets VO, Hansen KC, Stenmark KR. Functional and molecular determinants of right ventricular response to severe pulmonary hypertension in a large animal model. Am J Physiol Heart Circ Physiol 2023; 324:H804-H820. [PMID: 36961489 PMCID: PMC10190846 DOI: 10.1152/ajpheart.00614.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/01/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Right ventricular (RV) failure is the major determinant of outcome in pulmonary hypertension (PH). Calves exposed to 2-wk hypoxia develop severe PH and unlike rodents, hypoxia-induced PH in this species can lead to right heart failure. We, therefore, sought to examine the molecular and structural changes in the RV in calves with hypoxia-induced PH, hypothesizing that we could identify mechanisms underlying compensated physiological function in the face of developing severe PH. Calves were exposed to 14 days of environmental hypoxia (equivalent to 4,570 m/15,000 ft elevation, n = 29) or ambient normoxia (1,525 m/5,000 ft, n = 25). Cardiopulmonary function was evaluated by right heart catheterization and pressure volume loops. Molecular and cellular determinants of RV remodeling were analyzed by cDNA microarrays, RealTime PCR, proteomics, and immunochemistry. Hypoxic exposure induced robust PH, with increased RV contractile performance and preserved cardiac output, yet evidence of dysregulated RV-pulmonary artery mechanical coupling as seen in advanced disease. Analysis of gene expression revealed cellular processes associated with structural remodeling, cell signaling, and survival. We further identified specific clusters of gene expression associated with 1) hypertrophic gene expression and prosurvival mechanotransduction through YAP-TAZ signaling, 2) extracellular matrix (ECM) remodeling, 3) inflammatory cell activation, and 4) angiogenesis. A potential transcriptomic signature of cardiac fibroblasts in RV remodeling was detected, enriched in functions related to cell movement, tissue differentiation, and angiogenesis. Proteomic and immunohistochemical analysis confirmed RV myocyte hypertrophy, together with localization of ECM remodeling, inflammatory cell activation, and endothelial cell proliferation within the RV interstitium. In conclusion, hypoxia and hemodynamic load initiate coordinated processes of protective and compensatory RV remodeling to withstand the progression of PH.NEW & NOTEWORTHY Using a large animal model and employing a comprehensive approach integrating hemodynamic, transcriptomic, proteomic, and immunohistochemical analyses, we examined the early (2 wk) effects of severe PH on the RV. We observed that RV remodeling during PH progression represents a continuum of transcriptionally driven processes whereby cardiac myocytes, fibroblasts, endothelial cells, and proremodeling macrophages act to coordinately maintain physiological homeostasis and protect myocyte survival during chronic, severe, and progressive pressure overload.
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Affiliation(s)
- R Dale Brown
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Kendall S Hunter
- Department of Bioengineering, University of Coloradoo Denver, Denver, Colorado, United States
| | - Min Li
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Maria G Frid
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Julie Harral
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Greta M Krafsur
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Timothy N Holt
- Department of Clinical Sciences, College of Veterinary Medicine and Biological Sciences, Colorado State University, Fort Collins, Colorado, United States
| | - Jason Williams
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Denver, Colorado, United States
| | - Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Suzette R Riddle
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | | | - Sushil Kumar
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Cheng-Jun Hu
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Brian B Graham
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, California, United States
| | - Lori A Walker
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Franklyn B Garry
- Department of Clinical Sciences, College of Veterinary Medicine and Biological Sciences, Colorado State University, Fort Collins, Colorado, United States
| | - Peter M Buttrick
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Tim Lahm
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, University of Colorado Denver, Denver, Colorado, United States
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Vitaly O Kheyfets
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
- Department of Biomedical Informatics, University of Colorado Denver, Denver, Colorado, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Denver, Colorado, United States
| | - Kurt R Stenmark
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
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17
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Chen W, Zhang W, Zhang N, Chen S, Huang T, You H. Pipeline for precise insoluble matrisome coverage in tissue extracellular matrices. Front Bioeng Biotechnol 2023; 11:1135936. [PMID: 37284237 PMCID: PMC10239929 DOI: 10.3389/fbioe.2023.1135936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
The extracellular matrix (ECM) is assembled by hundreds of proteins orchestrating tissue patterning and surrounding cell fates via the mechanical-biochemical feedback loop. Aberrant ECM protein production or assembly usually creates pathological niches eliciting lesions that mainly involve fibrogenesis and carcinogenesis. Yet, our current knowledge about the pathophysiological ECM compositions and alterations in healthy or diseased tissues is limited since the methodology for precise insoluble matrisome coverage in the ECM is a "bottleneck." Our current study proposes an enhanced sodium dodecyl sulfonate (E-SDS) workflow for thorough tissue decellularization and an intact pipeline for the accurate identification and quantification of highly insoluble ECM matrisome proteins. We tested this pipeline in nine mouse organs and highlighted the full landscape of insoluble matrisome proteins in the decellularized ECM (dECM) scaffolds. Typical experimental validations and mass spectrometry (MS) analysis confirmed very little contamination of cellular debris remaining in the dECM scaffolds. Our current study will provide a low-cost, simple, reliable, and effective pipeline for tissue insoluble matrisome analysis in the quest to comprehend ECM discovery proteomic studies.
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Affiliation(s)
- Wei Chen
- Beijing Clinical Research Institute, Beijing, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wen Zhang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Ning Zhang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Shuyan Chen
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Tao Huang
- Beijing Clinical Research Institute, Beijing, China
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong You
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
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18
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Puttock EH, Tyler EJ, Manni M, Maniati E, Butterworth C, Burger Ramos M, Peerani E, Hirani P, Gauthier V, Liu Y, Maniscalco G, Rajeeve V, Cutillas P, Trevisan C, Pozzobon M, Lockley M, Rastrick J, Läubli H, White A, Pearce OMT. Extracellular matrix educates an immunoregulatory tumor macrophage phenotype found in ovarian cancer metastasis. Nat Commun 2023; 14:2514. [PMID: 37188691 DOI: 10.1038/s41467-023-38093-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Recent studies have shown that the tumor extracellular matrix (ECM) associates with immunosuppression, and that targeting the ECM can improve immune infiltration and responsiveness to immunotherapy. A question that remains unresolved is whether the ECM directly educates the immune phenotypes seen in tumors. Here, we identify a tumor-associated macrophage (TAM) population associated with poor prognosis, interruption of the cancer immunity cycle, and tumor ECM composition. To investigate whether the ECM was capable of generating this TAM phenotype, we developed a decellularized tissue model that retains the native ECM architecture and composition. Macrophages cultured on decellularized ovarian metastasis shared transcriptional profiles with the TAMs found in human tissue. ECM-educated macrophages have a tissue-remodeling and immunoregulatory phenotype, inducing altered T cell marker expression and proliferation. We conclude that the tumor ECM directly educates this macrophage population found in cancer tissues. Therefore, current and emerging cancer therapies that target the tumor ECM may be tailored to improve macrophage phenotype and their downstream regulation of immunity.
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Affiliation(s)
- E H Puttock
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - E J Tyler
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - M Manni
- Department of Biomedicine and Division of Medical Oncology, University Hospital Basel, Hebelstrasse 20, 4031, Basel, Switzerland
| | - E Maniati
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - C Butterworth
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - M Burger Ramos
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - E Peerani
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - P Hirani
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - V Gauthier
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - Y Liu
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - G Maniscalco
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - V Rajeeve
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - P Cutillas
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - C Trevisan
- Department of Women and Children Health, University of Padova and Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy
| | - M Pozzobon
- Department of Women and Children Health, University of Padova and Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy
| | - M Lockley
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK
| | - J Rastrick
- UCB Pharma Ltd, 208 Bath Road, Slough, Berkshire, SL1 3WE, UK
| | - H Läubli
- Department of Biomedicine and Division of Medical Oncology, University Hospital Basel, Hebelstrasse 20, 4031, Basel, Switzerland
| | - A White
- UCB Pharma Ltd, 208 Bath Road, Slough, Berkshire, SL1 3WE, UK
| | - O M T Pearce
- Queen Mary University of London, Barts Cancer Institute, John Vane Science Centre, London, EC1M 6BQ, UK.
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19
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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: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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20
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Abstract
The extracellular matrix (ECM) is a critical non-cellular component of multicellular organisms containing a variety of proteins, glycoproteins, and proteoglycans which have been implicated in a wide variety of essential biological processes, including development, wound healing, and aging. Due to low solubility, many ECM proteins have been underrepresented in previous proteomic datasets. Using an optimized three-step decellularization and ECM extraction method involving chaotrope extraction and digestion via hydroxylamine hydrochloride, we have generated coverage of the matrisome across 25 organs. We observe that the top 100 most abundant proteins from the ECM fractions of all tissues are generally present in all tissues, indicating that tissue matrices are principally composed of a shared set of ECM proteins. However, these proteins vary up to 4000-fold between tissues, resulting in highly unique matrix profiles even with the same primary set of proteins. A data reduction approach was used to reveal related networks of expressed ECM proteins across varying tissues, including basement membrane and collagen subtypes.
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Affiliation(s)
- Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
- Cancer Center Proteomics Core, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
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21
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van Tienderen GS, Conboy J, Muntz I, Willemse J, Tieleman J, Monfils K, Schurink IJ, Demmers JAA, Doukas M, Koenderink GH, van der Laan LJW, Verstegen MMA. Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer. Biomater Adv 2023; 146:213289. [PMID: 36724550 DOI: 10.1016/j.bioadv.2023.213289] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Tumor initiation and progression are critically dependent on interaction of cancer cells with their cellular and extracellular microenvironment. Alterations in the composition, integrity, and mechanical properties of the extracellular matrix (ECM) dictate tumor processes including cell proliferation, migration, and invasion. Also in primary liver cancer, consisting of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), the dysregulation of the extracellular environment by liver fibrosis and tumor desmoplasia is pertinent. Yet, the exact changes occurring in liver cancer ECM remain uncharacterized and underlying tumor-promoting mechanisms remain largely unknown. Herein, an integrative molecular and mechanical approach is used to extensively characterize the ECM of HCC and CCA tumors by utilizing an optimized decellularization technique. We identified a myriad of proteins in both tumor and adjacent liver tissue, uncovering distinct malignancy-related ECM signatures. The resolution of this approach unveiled additional ECM-related proteins compared to large liver cancer transcriptomic datasets. The differences in ECM protein composition resulted in divergent mechanical properties on a macro- and micro-scale that are tumor-type specific. Furthermore, the decellularized tumor ECM was employed to create a tumor-specific hydrogel that supports patient-derived tumor organoids, which provides a new avenue for personalized medicine applications. Taken together, this study contributes to a better understanding of alterations to composition, stiffness, and collagen alignment of the tumor ECM that occur during liver cancer development.
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22
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Rende U, Ahn SB, Adhikari S, Moh ESX, Pollock CA, Saad S, Guller A. Deciphering the Kidney Matrisome: Identification and Quantification of Renal Extracellular Matrix Proteins in Healthy Mice. Int J Mol Sci 2023; 24:ijms24032827. [PMID: 36769148 PMCID: PMC9917693 DOI: 10.3390/ijms24032827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Precise characterization of a tissue's extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules' activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome.
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Affiliation(s)
- Umut Rende
- ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Seong Beom Ahn
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Edward S. X. Moh
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol A. Pollock
- Department of Medicine, Kolling Institute of Medical Research, University of Sydney, St. Leonards, NSW 2065, Australia
| | - Sonia Saad
- Department of Medicine, Kolling Institute of Medical Research, University of Sydney, St. Leonards, NSW 2065, Australia
| | - Anna Guller
- ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
- Correspondence:
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23
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Alfonso AB, Pomerleau V, Nicolás VR, Raisch J, Jurkovic CM, Boisvert FM, Perreault N. Comprehensive Profiling of Early Neoplastic Gastric Microenvironment Modifications and Biodynamics in Impaired BMP-Signaling FoxL1 +-Telocytes. Biomedicines 2022; 11:biomedicines11010019. [PMID: 36672527 PMCID: PMC9856000 DOI: 10.3390/biomedicines11010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
FoxL1+telocytes (TCFoxL1+) are novel gastrointestinal subepithelial cells that form a communication axis between the mesenchyme and epithelium. TCFoxL1+ are strategically positioned to be key contributors to the microenvironment through production and secretion of growth factors and extracellular matrix (ECM) proteins. In recent years, the alteration of the bone morphogenetic protein (BMP) signaling in TCFoxL1+ was demonstrated to trigger a toxic microenvironment with ECM remodeling that leads to the development of pre-neoplastic gastric lesions. However, a comprehensive analysis of variations in the ECM composition and its associated proteins in gastric neoplasia linked to TCFoxL1+ dysregulation has never been performed. This study provides a better understanding of how TCFoxL1+ defective BMP signaling participates in the gastric pre-neoplastic microenvironment. Using a proteomic approach, we determined the changes in the complete matrisome of BmpR1a△FoxL1+ and control mice, both in total antrum as well as in isolated mesenchyme-enriched antrum fractions. Comparative proteomic analysis revealed that the deconstruction of the gastric antrum led to a more comprehensive analysis of the ECM fraction of gastric tissues microenvironment. These results show that TCFoxL1+ are key members of the mesenchymal cell population and actively participate in the establishment of the matrisomic fraction of the microenvironment, thus influencing epithelial cell behavior.
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24
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Sarohi V, Chakraborty S, Basak T. Exploring the cardiac ECM during fibrosis: A new era with next-gen proteomics. Front Mol Biosci 2022; 9:1030226. [PMID: 36483540 PMCID: PMC9722982 DOI: 10.3389/fmolb.2022.1030226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 10/24/2023] Open
Abstract
Extracellular matrix (ECM) plays a critical role in maintaining elasticity in cardiac tissues. Elasticity is required in the heart for properly pumping blood to the whole body. Dysregulated ECM remodeling causes fibrosis in the cardiac tissues. Cardiac fibrosis leads to stiffness in the heart tissues, resulting in heart failure. During cardiac fibrosis, ECM proteins get excessively deposited in the cardiac tissues. In the ECM, cardiac fibroblast proliferates into myofibroblast upon various kinds of stimulations. Fibroblast activation (myofibroblast) contributes majorly toward cardiac fibrosis. Other than cardiac fibroblasts, cardiomyocytes, epithelial/endothelial cells, and immune system cells can also contribute to cardiac fibrosis. Alteration in the expression of the ECM core and ECM-modifier proteins causes different types of cardiac fibrosis. These different components of ECM culminated into different pathways inducing transdifferentiation of cardiac fibroblast into myofibroblast. In this review, we summarize the role of different ECM components during cardiac fibrosis progression leading to heart failure. Furthermore, we highlight the importance of applying mass-spectrometry-based proteomics to understand the key changes occurring in the ECM during fibrotic progression. Next-gen proteomics studies will broaden the potential to identify key targets to combat cardiac fibrosis in order to achieve precise medicine-development in the future.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Sanchari Chakraborty
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
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25
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Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y(T, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Res 2022; 51:D1519-D1530. [PMID: 36399478 PMCID: PMC9825471 DOI: 10.1093/nar/gkac1009] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based proteomics has become the method of choice to profile the composition of the ECM, or the matrisome, of tissues. To assist non-specialists with the reuse of ECM proteomic datasets, we released MatrisomeDB (https://matrisomedb.org) in 2020. Here, we report the expansion of the database to include 25 new curated studies on the ECM of 24 new tissues in addition to datasets on tissues previously included, more than doubling the size of the original database and achieving near-complete coverage of the in-silico predicted matrisome. We further enhanced data visualization by maps of peptides and post-translational-modifications detected onto domain-based representations and 3D structures of ECM proteins. We also referenced external resources to facilitate the design of targeted mass spectrometry assays. Last, we implemented an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.
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Affiliation(s)
- Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Clarissa D Gomez
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Nandini Kapoor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - James M Considine
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher Grams
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yu (Tom) Gao
- Correspondence may also be addressed to Dr. Yu (Tom) Gao. Tel: +1 312 996 8087;
| | - Alexandra Naba
- To whom correspondence should be addressed. Tel: +1 312 355 5417;
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26
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Clift CL, Saunders J, Drake RR, Angel PM. Perspectives on pediatric congenital aortic valve stenosis: Extracellular matrix proteins, post translational modifications, and proteomic strategies. Front Cardiovasc Med 2022; 9:1024049. [PMID: 36439995 PMCID: PMC9685993 DOI: 10.3389/fcvm.2022.1024049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
In heart valve biology, organization of the extracellular matrix structure is directly correlated to valve function. This is especially true in cases of pediatric congenital aortic valve stenosis (pCAVS), in which extracellular matrix (ECM) dysregulation is a hallmark of the disease, eventually leading to left ventricular hypertrophy and heart failure. Therapeutic strategies are limited, especially in pediatric cases in which mechanical and tissue engineered valve replacements may not be a suitable option. By identifying mechanisms of translational and post-translational dysregulation of ECM in CAVS, potential drug targets can be identified, and better bioengineered solutions can be developed. In this review, we summarize current knowledge regarding ECM proteins and their post translational modifications (PTMs) during aortic valve development and disease and contributing factors to ECM dysregulation in CAVS. Additionally, we aim to draw parallels between other fibrotic disease and contributions to ECM post-translational modifications. Finally, we explore the current treatment options in pediatrics and identify how the field of proteomics has advanced in recent years, highlighting novel characterization methods of ECM and PTMs that may be used to identify potential therapeutic strategies relevant to pCAVS.
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Affiliation(s)
- Cassandra L. Clift
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
- Division of Cardiovascular Medicine, Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Janet Saunders
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
- *Correspondence: Peggi M. Angel,
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27
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Li Y, Yuan H, Cheng M, Zhu X, Yang K, Zhang W, Sui Z, Zhang C, Zhang L, Zhang Y. Solid-phase alkylation: a low-loss and anti-interference sample preparation strategy for low-input proteome profiling. Sci Bull (Beijing) 2022; 67:1628-1631. [PMID: 36546039 DOI: 10.1016/j.scib.2022.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Affiliation(s)
- Yilan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Mengchun Cheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xudong Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunyu Zhang
- The Second Affiliated Hospital of Dalian Medical University, Dalian 116021, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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28
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Dempsey B, Cruz LC, Mineiro MF, da Silva RP, Meotti FC. Uric Acid Reacts with Peroxidasin, Decreases Collagen IV Crosslink, Impairs Human Endothelial Cell Migration and Adhesion. Antioxidants (Basel) 2022; 11:antiox11061117. [PMID: 35740014 PMCID: PMC9220231 DOI: 10.3390/antiox11061117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023] Open
Abstract
Uric acid is considered the main substrate for peroxidases in plasma. The oxidation of uric acid by human peroxidases generates urate free radical and urate hydroperoxide, which might affect endothelial function and explain, at least in part, the harmful effects of uric acid on the vascular system. Peroxidasin (PXDN), the most recent heme-peroxidase described in humans, catalyzes the formation of hypobromous acid, which mediates collagen IV crosslinks in the extracellular matrix. This enzyme has gained increasing scientific interest since it is associated with cardiovascular disease, cancer, and renal fibrosis. The main objective here was to investigate whether uric acid would react with PXDN and compromise the function of the enzyme in human endothelial cells. Urate decreased Amplex Red oxidation and brominating activity in the extracellular matrix (ECM) from HEK293/PXDN overexpressing cells and in the secretome of HUVECs. Parallelly, urate was oxidized to 5-hydroxyisourate. It also decreased collagen IV crosslink in isolated ECM from PFHR9 cells. Urate, the PXDN inhibitor phloroglucinol, and the PXDN knockdown impaired migration and adhesion of HUVECs. These results demonstrated that uric acid can affect extracellular matrix formation by competing for PXDN. The oxidation of uric acid by PXDN is likely a relevant mechanism in the endothelial dysfunction related to this metabolite.
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Thant L, Kaku M, Kakihara Y, Mizukoshi M, Kitami M, Arai M, Kitami K, Kobayashi D, Yoshida Y, Maeda T, Saito I, Uoshima K, Saeki M. Extracellular Matrix-Oriented Proteomic Analysis of Periodontal Ligament Under Mechanical Stress. Front Physiol 2022; 13:899699. [PMID: 35669581 PMCID: PMC9163570 DOI: 10.3389/fphys.2022.899699] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
The periodontal ligament (PDL) is a specialized connective tissue that provides structural support to the tooth and is crucial for oral functions. The mechanical properties of the PDL are mainly derived from the tissue-specific composition and structural characteristics of the extracellular matrix (ECM). The ECM also plays key roles in determining cell fate in the cellular microenvironment thus crucial in the PDL tissue homeostasis. In the present study, we determined the comprehensive ECM profile of mouse molar PDL using laser microdissection and mass spectrometry-based proteomic analysis with ECM-oriented data curation. Additionally, we evaluated changes in the ECM proteome under mechanical loading using a mouse orthodontic tooth movement (OTM) model and analyzed potential regulatory networks using a bioinformatics approach. Proteomic changes were evaluated in reference to the novel second harmonic generation (SHG)-based fiber characterization. Our ECM-oriented proteomics approach succeeded in illustrating the comprehensive ECM profile of the mouse molar PDL. We revealed the presence of type II collagen in PDL, possibly associated with the load-bearing function upon occlusal force. Mechanical loading induced unique architectural changes in collagen fibers along with dynamic compositional changes in the matrisome profile, particularly involving ECM glycoproteins and matrisome-associated proteins. We identified several unique matrisome proteins which responded to the different modes of mechanical loading in PDL. Notably, the proportion of type VI collagen significantly increased at the mesial side, contributing to collagen fibrogenesis. On the other hand, type XII collagen increased at the PDL-cementum boundary of the distal side. Furthermore, a multifaceted bioinformatics approach illustrated the potential molecular cues, including PDGF signaling, that maintain ECM homeostasis under mechanical loading. Our findings provide fundamental insights into the molecular network underlying ECM homeostasis in PDL, which is vital for clinical diagnosis and development of biomimetic tissue-regeneration strategies.
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Affiliation(s)
- Lay Thant
- Division of Dental Pharmacology, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Division of Orthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Center for Advanced Oral Science, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- *Correspondence: Masaru Kaku,
| | - Yoshito Kakihara
- Division of Dental Pharmacology, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Mizukoshi
- Division of Orthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Megumi Kitami
- Division of Dental Pharmacology, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Center for Advanced Oral Science, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Moe Arai
- Division of Orthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Kohei Kitami
- Division of Orthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Daiki Kobayashi
- Omics Unit, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yutaka Yoshida
- Department of Structural Pathology, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Takeyasu Maeda
- Center for Advanced Oral Science, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Isao Saito
- Division of Orthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Katsumi Uoshima
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Makio Saeki
- Division of Dental Pharmacology, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Dussoyer M, Page A, Delolme F, Rousselle P, Nyström A, Moali C. Comparison of extracellular matrix enrichment protocols for the improved characterization of the skin matrisome by mass spectrometry. J Proteomics 2022; 251:104397. [PMID: 34678517 DOI: 10.1016/j.jprot.2021.104397] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 12/14/2022]
Abstract
A striking feature of skin organization is that the extracellular matrix (ECM) occupies a larger volume than the cells. Skin ECM also directly contributes to aging and most cutaneous diseases. In recent years, specific ECM enrichment protocols combined with in silico approaches allowed the proteomic description of the matrisome of various organs and tumor samples. Nevertheless, the skin matrisome remains under-studied and protocols allowing the efficient recovery of the diverse ECM found in skin are still to be described. Here, we compared four protocols allowing the enrichment of ECM proteins from adult mouse back skin and found that all protocols led to a significant enrichment (up to 65%) of matrisome proteins when compared to total skin lysates. The protocols based on decellularization and solubility profiling gave the best results in terms of numbers of proteins identified and confirmed that skin matrisome proteins exhibit very diverse solubility and abundance profiles. We also report the first description of the skin matrisome of healthy adult mice that includes 236 proteins comprising 95 core matrisome proteins and 141 associated matrisome proteins. These results provide a reliable basis for future characterizations of skin ECM proteins and their dysregulations in disease-specific contexts. SIGNIFICANCE: Extracellular matrix proteins are key players in skin physiopathology and have been involved in several diseases such as genetic disorders, wound healing defects, scleroderma and skin carcinoma. However, skin ECM proteins are numerous, diverse and challenging to analyze by mass spectrometry due to the multiplicity of their post-translational modifications and to the heterogeneity of their solubility profiles. Here, we performed the thorough evaluation of four ECM enrichment protocols compatible with the proteomic analysis of mouse back skin and provide the first description of the adult mouse skin matrisome in homeostasis conditions. Our work will greatly facilitate the future characterization of skin ECM alterations in preclinical mouse models and will inspire new optimizations to analyze the skin matrisome of other species and of human clinical samples.
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Affiliation(s)
- Mélissa Dussoyer
- University of Lyon, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
| | - Adeline Page
- University of Lyon, INSERM, ENS Lyon, CNRS, Protein Science Facility, SFR BioSciences, UAR3444/US8, F-69366 Lyon, France
| | - Frédéric Delolme
- University of Lyon, INSERM, ENS Lyon, CNRS, Protein Science Facility, SFR BioSciences, UAR3444/US8, F-69366 Lyon, France
| | - Patricia Rousselle
- University of Lyon, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
| | - Alexander Nyström
- Department of Clinical Dermatology/Medical Center, University of Freiburg, Freiburg, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Catherine Moali
- University of Lyon, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France.
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Erickson CB, Hill R, Pascablo D, Kazakia G, Hansen K, Bahney C. A timeseries analysis of the fracture callus extracellular matrix proteome during bone fracture healing. J Life Sci (Westlake Village) 2021; 3:1-30. [PMID: 35765657 PMCID: PMC9236279 DOI: 10.36069/jols/20220601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
While most bones fully self-heal, certain diseases require bone allograft to assist with fracture healing. Bone allografts offer promise as treatments for such fractures due to their osteogenic properties. However, current bone allografts made of decellularized bone extracellular matrix (ECM) have high failure rates, and thus grafts which improve fracture healing outcomes are needed. Understanding specific changes to the ECM proteome during normal fracture healing would enable the identification of key proteins that could be used enhance osteogenicity of bone allograft. Here, we performed a timeseries analysis of the fracture callus in mice to investigate proteomic and mineralization changes to the ECM at key stages of fracture healing. We found that changes to the ECM proteome largely coincide with the distinct phases of fracture healing. Basement membrane proteins (AGRN, COL4, LAMA), cartilage proteins (COL2A1, ACAN), and collagen crosslinking enzymes (LOXL, PLOD, ITIH) were initially upregulated, followed by bone specific proteoglycans and collagens (IBSP, COL1A1). Various tissue proteases (MMP2, 9, 13, 14; CTSK, CTSG, ELANE) were expressed at different levels throughout fracture healing. These changes coordinated with mineralization of the fracture callus, which increased steeply during the initial stages of healing. Interestingly the later timepoint was characterized by a response to wound healing and high expression of clotting factors (F2, 7, 9, 10). We identified ELANE and ITIH2 as tissue remodeling enzymes having no prior known involvement with fracture healing. This data can be further mined to identify regenerative proteins for enhanced bone graft design.
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Affiliation(s)
- Christopher B. Erickson
- Department of Biochemistry and Molecular Genetics,University of Colorado, Anschutz Medical Campus, Aurora, CO
| | - Ryan Hill
- Department of Biochemistry and Molecular Genetics,University of Colorado, Anschutz Medical Campus, Aurora, CO
| | - Donna Pascablo
- Orthopaedic Trauma Institute, University of California, San Francisco (UCSF), San Francisco, CA
| | - Galateia Kazakia
- Department of Radiology and Biomedical Imaging, University of California, San Francisco (UCSF), San Francisco, CA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics,University of Colorado, Anschutz Medical Campus, Aurora, CO
| | - Chelsea Bahney
- Stedman Philippon Research Institute (SPRI), Center for Regenerative and Personalized Medicine. Vail, CO
- Orthopaedic Trauma Institute, University of California, San Francisco (UCSF), San Francisco, CA
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Abstract
INTRODUCTION The matrisome and adhesome comprise proteins that are found within or are associated with the extracellular matrix (ECM) and adhesion complexes, respectively. Interactions between cells and their microenvironment are mediated by key matrisome and adhesome proteins, which direct fundamental processes, including growth and development. Due to their underlying complexity, it has historically been challenging to undertake mass spectrometry (MS)-based profiling of these proteins. New developments in sample preparative workflows, informatics databases, and MS techniques have enabled in-depth proteomic characterization of the matrisome and adhesome, resulting in a comprehensive understanding of the interactomes, and cellular signaling that occur at the cell-ECM interface. AREA COVERED This review summarizes recent advances in proteomic characterization of the matrisome and adhesome. It focuses on the importance of curated databases and discusses key strengths and limitations of different workflows. EXPERT OPINION MS-based proteomics has shown promise in characterizing the matrisome and topology of adhesome networks in health and disease. Moving forward, it will be important to incorporate integrative analysis to define the bidirectional signaling between the matrisome and adhesome, and adopt new methods for post-translational modification and in vivo analyses to better dissect the critical roles that these proteins play in human pathophysiology.
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Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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Park W, Gao G, Cho DW. Tissue-Specific Decellularized Extracellular Matrix Bioinks for Musculoskeletal Tissue Regeneration and Modeling Using 3D Bioprinting Technology. Int J Mol Sci 2021; 22:7837. [PMID: 34360604 PMCID: PMC8346156 DOI: 10.3390/ijms22157837] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
The musculoskeletal system is a vital body system that protects internal organs, supports locomotion, and maintains homeostatic function. Unfortunately, musculoskeletal disorders are the leading cause of disability worldwide. Although implant surgeries using autografts, allografts, and xenografts have been conducted, several adverse effects, including donor site morbidity and immunoreaction, exist. To overcome these limitations, various biomedical engineering approaches have been proposed based on an understanding of the complexity of human musculoskeletal tissue. In this review, the leading edge of musculoskeletal tissue engineering using 3D bioprinting technology and musculoskeletal tissue-derived decellularized extracellular matrix bioink is described. In particular, studies on in vivo regeneration and in vitro modeling of musculoskeletal tissue have been focused on. Lastly, the current breakthroughs, limitations, and future perspectives are described.
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Affiliation(s)
- Wonbin Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang 37673, Korea;
| | - Ge Gao
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China;
| | - Dong-Woo Cho
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang 37673, Korea;
- POSTECH-Catholic Biomedical Engineering Institute, Pohang University of Science and Technology, Pohang 37673, Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
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