Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives
Alexandra Naba
Abstract
•ECM alterations cause or accompany diseases and disorders of all organ systems.•Proteomics is a method of choice to profile the composition of the ECM of tissues.•ECM proteomics can identify novel prognostic and diagnostic biomarkers.•ECM proteomics can uncover proteins playing functional roles in disease etiology.•Further technical advances are needed to capture the diversity of ECM proteoforms 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 posttranslationally 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 first part of 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. Lastly, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. Mass spectrometry–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. 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 posttranslationally 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 first part of 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. Lastly, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. Mass spectrometry–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. The extracellular matrix (ECM) is a complex assembly of proteins forming the architectural scaffold of all multicellular organisms (1Hynes R.O. The evolution of metazoan extracellular matrix.J. Cell Biol. 2012; 196: 671-679Crossref PubMed Scopus (177) Google Scholar, 2Adams J.C. Extracellular matrix evolution: an overview.in: Keeley F.W. Mecham R.P. Evolution of Extracellular Matrix. Springer, Berlin, Heidelberg2013: 1-25https://doi.org/10.1007/978-3-642-36002-2_1Crossref Google Scholar, 3Karamanos N.K. Theocharis A.D. Piperigkou Z. Manou D. Passi A. Skandalis S.S. et al.A guide to the composition and functions of the extracellular matrix.FEBS J. 2021; 288: 6850-6912Crossref PubMed Scopus (34) Google Scholar). As such, the ECM guides cell polarization and serves as a substrate to cell migration, it organizes cells into tissues and tissues into organs, and confers mechanical properties to tissues. In addition to its structural roles, the ECM exerts signaling functions through mechanotransduction (4Humphrey J.D. Dufresne E.R. Schwartz M.A. Mechanotransduction and extracellular matrix homeostasis.Nat. Rev. Mol. Cell Biol. 2014; 15: 802-812Crossref PubMed Scopus (1185) Google Scholar, 5Dooling L.J. Saini K. Anlaş A.A. Discher D.E. Tissue mechanics coevolves with fibrillar matrisomes in healthy and fibrotic tissues.Matrix Biol. 2022; 111: 153-188Crossref PubMed Scopus (0) Google Scholar). It also provides biochemical cues interpreted by cells via cell-surface receptors (e.g., integrins (6Kanchanawong P. Calderwood D.A. Organization, dynamics and mechanoregulation of integrin-mediated cell–ECM adhesions.Nat. Rev. Mol. Cell Biol. 2022; 24: 142-161Crossref PubMed Scopus (7) Google Scholar), syndecans, adhesion GPCRs (7Liebscher I. Cevheroğlu O. Hsiao C.C. Maia A.F. Schihada H. Scholz N. et al.A guide to adhesion GPCR research.FEBS J. 2021; 289: 7610-7630Crossref PubMed Scopus (5) Google Scholar)) that orchestrate most, if not all, cellular functions, from cell proliferation and survival to adhesion and migration, to stemness and differentiation. The ECM thus plays critical roles during development, growth, and other physiological processes including wound healing and aging (8Yamada K.M. Collins J.W. Cruz Walma D.A. Doyle A.D. Morales S.G. Lu J. et al.Extracellular matrix dynamics in cell migration, invasion and tissue morphogenesis.Int. J. Exp. Pathol. 2019; 100: 144-152Crossref PubMed Scopus (47) Google Scholar, 9Dzamba B.J. DeSimone D.W. Extracellular matrix (ECM) and the sculpting of embryonic tissues.Curr. Top Dev. Biol. 2018; 130: 245-274Crossref PubMed Scopus (49) Google Scholar, 10Karamanos N.K. Theocharis A.D. Neill T. Iozzo R.V. Matrix modeling and remodeling: a biological interplay regulating tissue homeostasis and diseases.Matrix Biol. 2019; 75–76: 1-11Crossref PubMed Scopus (156) Google Scholar, 11Lausecker F. Lennon R. Randles M.J. The kidney matrisome in health, aging, and disease.Kidney Int. 2022; 102: 1000-1012Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar, 12Ewald C.Y. The matrisome during aging and longevity: a systems-level approach toward defining matreotypes promoting healthy aging.Gerontology. PubMed Scopus Google Scholar). the ECM is multicellular The ECM is a that and structural by and of ECM by in ECM disorders of the extracellular PubMed Scopus (0) Google Scholar), by an ECM and or by ECM in disorders and diseases affecting all physiological P. K. Z. Extracellular matrix and in development and Biol. PubMed Scopus Google Scholar, J. Z. the extracellular matrix in development and Rev. Mol. Cell Biol. 2014; 15: PubMed Scopus Google Scholar, A.D. Manou D. N.K. The extracellular matrix as a in J. 2019; PubMed Scopus Google including the (e.g., F. T. The Rev. PubMed Scopus Google Scholar), the (e.g., D. T. fibrosis signals from the extracellular matrix the of Biol. 2018; PubMed Scopus Google Scholar), of the of Biol. 2014; PubMed Scopus Google the (e.g., J. F. in and PubMed Scopus Google the fibrosis J.C. A. N. K. J. et al.Extracellular matrix in development, homeostasis and Biol. 2018; PubMed Scopus Google and the (e.g., fibrosis P. Extracellular matrix in kidney a 2019; PubMed Scopus Google Scholar, Lennon R. in kidney 2018; PubMed Scopus Google to a In ECM is a of fibrosis P. The in and Biol. 2018; PubMed Scopus Google and cancer The extracellular matrix the of 2014; 15: PubMed Scopus Google Scholar, The matrix in Rev. 2021; PubMed Scopus Google Scholar, J. A. Z. of extracellular matrix in and PubMed Scopus Google Scholar). The of ECM in the of by the has been to be of prognostic with cancer of the in and of a prognostic Pathol. 2021; PubMed Scopus (5) Google Scholar, H. H. et in the biological and its prognostic 2018; PubMed Scopus (0) Google Scholar). of the cancer F. L.J. J. et as an to in J. PubMed Google are ECM ECM proteins the of the they can be the of N. H. et of and fibrosis a the extracellular A. 2019; PubMed Scopus (0) Google Scholar, F. et of the of a of in with Google Scholar, D. cancer historical and PubMed Scopus Google or by of a a ECM protein and an N. D. a novel of 2012; PubMed Scopus Google Scholar, et with of in a PubMed Scopus (0) Google Scholar, N. N.K. et of to cancer 2019; PubMed Scopus Google Scholar). Lastly, it has been that the or properties of the ECM or be a therapeutic approach in contexts A. R. O. extracellular matrix diseases of the Biol. 2018; PubMed Scopus Google Scholar, D. and Biol. 2018; PubMed Scopus Google Scholar, of the 2021; PubMed Scopus Google Scholar, A. to the PubMed Scopus Google Scholar, extracellular matrix to from to clinical 2018; PubMed Scopus Google Scholar, K. J. biological clinical and Rev. 15: PubMed Scopus Google Scholar). The ECM thus a reservoir of and therapeutic proteins (e.g., or of proteins (e.g., of the ECM have been the ECM as a R. The extracellular an Rev. PubMed Scopus Google and the extracellular matrix in J. Exp. Pathol. 2018; PubMed Scopus (0) Google Scholar). The biochemical properties ECM proteins to into an architectural scaffold of mechanical and have hindered our ability to the composition of the ECM. The structural proteins of the ECM to be large, ECM proteins and extracellular including and and proteins that to the of the of P. J. J. of in the of 2019; PubMed Scopus Google Scholar), and ECM proteins also into via (e.g., M.J. the of A. PubMed Scopus Google Scholar, and Rev. PubMed Scopus Google (e.g., DeSimone D.W. their and in Biol. PubMed Scopus Google and (e.g., J. A. and 2021; PubMed Scopus Google Scholar), The Biol. PubMed Scopus Google biochemical properties to ECM proteins highly to biochemical approaches and or of their ECM proteins are in proteomic datasets. to this is the from a the ECM represents a of healthy organ and tissue The second limiting the of the ECM is its in of protein The ECM is of and highly structural ECM can there are in the of and also as or in This is not unique to the and advances in and to protein and that not be have been to capture the of and are now to ECM proteomics The first profiling the protein composition of the ECM of the or ECM other or to the of ECM proteins that be by to the of to a structural ECM the this was and these have been in the of ECM proteomics R. challenges, and recent PubMed Scopus (0) Google Scholar, M.J. J. A. of and PubMed Scopus (0) Google Scholar, R. O. et changes in in extracellular matrix that PubMed Scopus Google Scholar, R. A.F. et profiling of extracellular matrix and and Cell Full Text Full Text PDF PubMed Scopus Google Scholar, D. R. of PubMed Scopus Google Scholar, O. J. A. J. et method extracellular matrix Cell Full Text Full Text PDF PubMed Scopus Google Scholar). with to the unique challenges by ECM protein by in the of extracellular proteins A. K. of extracellular in the Cell Full Text Full Text PDF PubMed Scopus Google Scholar, A. K. A. A. et al.Extracellular matrix composition and in a proteomics Cell Full Text Full Text PDF PubMed Scopus Google Scholar). ECM to be in not may how can we novel ECM proteins or proteins not to be in these the third our to in an the protein composition of the ECM of was the of a to As a in the of ECM proteins as proteins in proteins in cell–ECM or proteins not in the ECM. proteins to be as to the ECM. This a to to identify of diseased It thus that and approaches be needed to the of the ECM. This review the latest in ECM from in and to the application of ECM proteomics the of and therapeutic discovery with a cancer. As part of the this clinical or of diseases that translational ECM proteomics is also to the ECM of multicellular Z. M.A. D.W. D.W. et extracellular matrix Scopus Google Scholar, A. I. D. et of extracellular matrix during Cell 2019; Full Text Full Text PDF PubMed Scopus (0) Google Scholar, et of the extracellular 2014; Scopus Google Scholar), K. R. et al.Extracellular matrix in the and Biol. PubMed Scopus Google Scholar), or et and functional of extracellular matrix in Cell 2021; Full Text Full Text PDF PubMed Google or to the ECM by cells in are to of the ECM in the of development, health, and In this review it is that other can be to of the including the of ECM proteins R. J. and of matrisome Cell 2019; Full Text Full Text PDF PubMed Scopus Google Scholar, N. D. et and in protein the of of 2022; PubMed Scopus (0) Google Scholar, to to extracellular 2021; Full Text Full Text PDF PubMed Scopus Google Scholar, guide to strategies Cell 2021; Full Text Full Text PDF PubMed Google Scholar), the of of ECM proteins in matrisome Biol. 2022; PubMed Scopus (0) Google Scholar), or the and of ECM proteins K. A. et extracellular matrix proteins in tissues by 2018; PubMed Scopus Google Scholar, A. of the extracellular matrix from tissue 2021; PubMed Scopus Google Scholar). In we in this an a approach to define the protein composition of the ECM of tissues A. H. R.O. The in and in by proteomics of and extracellular Cell 2012; Full Text Full Text PDF PubMed Scopus Google Scholar). to overcome of the by or ECM proteins in we to In we first of the of and ECM proteins to proteins by in or ECM that in and not and that ECM be in the we that ECM proteins and thus with protein with a of to capture a of ECM we to the correct and of all ECM we the and as represents of the of the of and is in and of and is P. J. J. of in the of 2019; PubMed Scopus Google Scholar). In we a to and ECM In we and the of ECM proteins J. and in extracellular matrix Biol. PubMed Scopus Google Scholar, J. a of the ECM and a the and of biological 2012; PubMed Scopus (0) Google to an ECM A. H. R.O. The in and in by proteomics of and extracellular Cell 2012; Full Text Full Text PDF PubMed Scopus Google Scholar, A. R.O. of an ECM an Biol. 2012; PubMed Scopus Google Scholar, R.O. A. of the of extracellular matrix and Biol. 2012; Scopus Google Scholar, A. The matrisome of from to Extracellular Matrix Google that we the This was by in the to the of a of ECM the The of and by Google Scholar). In we to the of the to the of to structural ECM the including ECM and The also proteins not to the of the ECM are in ECM homeostasis and signaling functions, as ECM and of with ECM proteins A. H. R.O. The in and in by proteomics of and extracellular Cell 2012; Full Text Full Text PDF PubMed Scopus Google Scholar, A. R.O. of an ECM an Biol. 2012; PubMed Scopus Google Scholar, R.O. A. of the of extracellular matrix and Biol. 2012; Scopus Google Scholar, A. The matrisome of from to Extracellular Matrix Google Scholar). The of an to ECM and the of the matrisome in the of the ECM of and over including matrisome and as the from the and of the matrix and A. H. R.O. The in and in by proteomics of and extracellular Cell 2012; Full Text Full Text PDF PubMed Scopus Google Scholar). via an A. H. R.O. The in and in by proteomics of and extracellular Cell 2012; Full Text Full Text PDF PubMed Scopus Google and a and A. R.O. of extracellular matrix proteins from tissues and into Exp. Scholar, A. A. D. H. et of the extracellular matrix of and diseased tissues PubMed Scopus Google Scholar), and the of available or to in with have our to and the past decade, proteomics has the method of choice to profile the protein composition of the ECM. in the in the to or ECM proteins or in the ECM protein or to all are a in are to our the and have devised an that proteins of to and an T. et and profiling of the extracellular in and Biol. PubMed Scopus Google Scholar). to not the also of by to a profile of the ECM of the T. et and profiling of the extracellular in and Biol. PubMed Scopus Google Scholar), fibrotic and et profiling of cells in and J. 196: PubMed Scopus Google Scholar), aging I. et of the aging by cell and tissue 2019; PubMed Scopus Google Scholar), the of the J. J. M.J. F. et the cell of Full Text Full Text PDF PubMed Scopus (0) Google Scholar). of of matrisome proteins in the is of the that in the of matrisome proteins it is a it a of In it is to that the of matrisome proteins in of or can to the of matrisome proteins not yet or to matrisome proteins in the extracellular not as into the ECM is a powerful in changes in matrisome protein in physiological or The to approaches ECM including the of approaches to proteins or M.J. A. et extracellular matrix PubMed Scopus Google Scholar, A. O. et extracellular matrix proteomics to and tissue J. Cell Biol. PubMed Scopus Google Scholar). and an and the of ECM protein and to profile the ECM of tissues et and of extracellular matrix Cell 2021; Full Text Full Text PDF Google Scholar). this the of the of matrisome the of the ECM. recent of in the ECM ECM protein have that there is a in the matrisome proteins and that there are as of proteins uniquely or et and of extracellular matrix Cell 2021; Full Text Full Text PDF Google Scholar, in the proteomic profiling of the matrisome and Rev. 2021; PubMed Scopus (0) Google Scholar, A. F. P. A. of extracellular matrix the of the matrisome by 2021; Google Scholar). The has a approach available and tissue into of and D. matrisome protein an approach to proteomic matrisome J. Mol. PubMed Scopus (0) Google Scholar). the has a and it in a approach to the ECM composition of H. A. D. et extracellular matrix PubMed Scopus (0) Google Scholar). As in the of proteins a of proteins and the of the of proteins a of matrisome As the of matrisome proteins in of or can to matrisome proteins or to matrisome proteins in the extracellular not in the ECM In the in of the was and all of protein if of that was to (e.g., or tissue is thus to protein in protein ECM protein plays a in an that may be to J. J. K. of substrate 2018; PubMed Scopus Google Scholar), and not of can be by (e.g., have other or to the of as and may the of and thus protein discovery and it is that not the profile of ECM in a of this In there is or It is thus to the and of as as of and the method that is to the of the ECM they are the of the of the ECM to the of assembly of the ECM or ECM in healthy and diseased tissue the of the past decade, ECM proteomics has proteomics as of protein or the of A. A. D. H. et of the extracellular matrix of and diseased tissues PubMed Scopus Google Scholar). the ECM a recent have also H. proteomic in 2021; PubMed Google Scholar, P. N. P. et as a tool profiling of the 2018; PubMed Scopus Google Scholar, J. J. H. D. et proteomic that extracellular matrix 2022; PubMed Scopus (0) Google Scholar, J. D. R. et and of extracellular matrix from in 2022; Scopus (0) Google Scholar). protein and of protein abundance, it is to in the of the that can proteins of and these of and are not by they the proteomic and have the we and others have that and in the of the and of matrisome proteins in A. A. D. H. et of the extracellular matrix of and diseased tissues PubMed Scopus Google Scholar, T. L.J. of and of by 15: PubMed Scopus Google Scholar). overcome the by the of matrisome protein abundance, we to a approach to all from the proteins in our A. A. T. K.M. et proteomics identify as a of cancer and to a prognostic of A. PubMed Scopus Google Scholar). we a of unique including all from the and of and the of and the of also all from and proteins with in our This in the of matrisome proteins it in a in the of matrisome to a of the proteins our A. A. T. K.M. et proteomics identify as a of cancer and to a prognostic of A. PubMed Scopus Google Scholar). of this approach is that it an to identify to be and thus may a with and a may the of overcome challenges in the ECM and the of the protein composition of the ECM the can we biological and clinical from ECM proteomic the ECM plays roles in the homeostasis of all physiological systems, of the ECM has all the past decade, ECM proteomics has thus been to a of (e.g., clinical tissues from of tissue or ECM by cells in and in the of diseases and have the application of proteomics to the ECM of the J. A. proteomics of the extracellular matrix in health and Rev. Scholar), diseases J. and the application of proteomics to the extracellular PubMed Scopus Google Scholar, of the extracellular clinical research Rev. 2018; 15: PubMed Scopus (0) Google Scholar), diseases A. The matrisome Google Scholar, The and PubMed Scopus (1) Google Scholar), diseases O. The extracellular matrix of the composition and alterations in J. PubMed Scopus Google Scholar), and diseases R. J. and of matrisome Cell 2019; Full Text Full Text PDF PubMed Scopus Google Scholar, J. Mass of extracellular matrix in Rev. 2022; PubMed Scopus (0) Google Scholar, J. the a of extracellular matrix of the in and Cell PubMed Scopus (5) Google Scholar). This thus of the past that have to the ECM of cancer a of proteomic of the cancer matrisome readers are to to our review A. The cancer from to Cell Dev. Biol. 2019; PubMed Scopus Google Scholar). In an we ECM proteomics to the protein composition of the ECM of and highly This to the of a of of A. R.O. Extracellular matrix of identify novel 2014; PubMed Scopus Google Scholar). This matrisome proteins that been with cancer as R. D. et of the development of a PubMed Scopus Google and D. et through Full Text Full Text PDF PubMed Scopus Google Scholar), and also matrisome proteins that been with this disease as the protein It also a novel ECM of we that the of of and with cancer R.O. A. K. K. extracellular matrix and and Scholar). In a we proteomics to the protein composition of the ECM of from cells in organs, the and This approach to the of cells and cells to the of the proteins by cells can be from proteins by cells J.D. A. et profiling of the ECM of cancer in PubMed Scopus (47) Google Scholar). This to the of over and matrisome proteoforms by or cells and that was characterized by a unique ECM composition by cells and cells J.D. A. et profiling of the ECM of cancer in PubMed Scopus (47) Google Scholar). by the that of the of the fibrillar is a of cancer A. and of cancer by extracellular matrix Cell Biol. 2021; PubMed Scopus Google Scholar, the PubMed Scopus Google Scholar, J.C. K.M. et is a prognostic survival in J. Pathol. Full Text Full Text PDF PubMed Scopus Google Scholar). the past there has thus been an in ECM proteomics to and identify the these and ECM proteomics to profile changes the of the fibrillar in A. et matrisome and in from 2018; PubMed Scopus Google Scholar). matrisome proteins with healthy tissue and including and that a with that of the fibrillar in In a the ECM proteomics to identify protein with the of to the and I. et cancer by the 130: PubMed Scopus Google Scholar). The that from tissues with fibrillar and and the a has been with an of The a changes in matrisome protein composition of a of cancer et profiling of the as a of 2022; PubMed Scopus Google Scholar). The the of of the first proteins with over in healthy and with of the second of proteins in in as with healthy the third including proteins with with and the proteins in in and of development as with healthy tissue with in as with et profiling of the as a of 2022; PubMed Scopus Google Scholar). The that with and of a in with cancer an of in as with tissue I. et cancer by the 130: PubMed Scopus Google Scholar). The tissue a of that the of with and This the of ECM proteomics a of and the translational of findings to the that is by and to a of cancer invasion by the of the fibrillar This the of not as a prognostic also as a have that is with an of including cancer and Scholar). The that ECM in in a P. J. K. et changes in ECM mechanics PubMed Scopus Google Scholar). this the proteomics to the ECM composition of from a or a The the of a of ECM proteins in the with the in the of as with et extracellular matrix identify as a of cancer cell invasion in and PubMed Scopus (47) Google Scholar). of the ECM proteins in as with in as with healthy E.R. in of tissues and proteomic of extracellular PubMed Scopus Google Scholar), and in highly A. R.O. Extracellular matrix of identify novel 2014; PubMed Scopus Google and a and the and the protein et extracellular matrix identify as a of cancer cell invasion in and PubMed Scopus (47) Google Scholar). This that changes in the ECM with changes during cancer The functional and prognostic of this was by that cancer and that the of the and the the functional with cancer et extracellular matrix identify as a of cancer cell invasion in and PubMed Scopus (47) Google Scholar). from the characterized the changes in the ECM composition of the of that or or a M.J. cancer cell through of and adhesion 2022; PubMed Scopus (0) Google Scholar). The that with in changes in ECM composition matrisome proteins in and in abundance, as with from the changes by matrisome proteins in and in abundance, as with with a in the of The of the and in matrisome proteins in