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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] [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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Lyubetskaya A, Rabe B, Fisher A, Lewin A, Neuhaus I, Brett C, Brett T, Pereira E, Golhar R, Kebede S, Font-Tello A, Mosure K, Van Wittenberghe N, Mavrakis KJ, MacIsaac K, Chen BJ, Drokhlyansky E. Assessment of spatial transcriptomics for oncology discovery. CELL REPORTS METHODS 2022; 2:100340. [PMID: 36452860 PMCID: PMC9701619 DOI: 10.1016/j.crmeth.2022.100340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/05/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for oncology discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis, which provides a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell-type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.
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Affiliation(s)
- Anna Lyubetskaya
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Brian Rabe
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Andrew Fisher
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Anne Lewin
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Isaac Neuhaus
- Research and Early Development, Bristol Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, USA
| | - Constance Brett
- Aggregate Genius, Inc., 560 Fulford-Ganges Road, Salt Spring Island, BC V8K 2K1, Canada
| | - Todd Brett
- Aggregate Genius, Inc., 560 Fulford-Ganges Road, Salt Spring Island, BC V8K 2K1, Canada
| | - Ethel Pereira
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Ryan Golhar
- Research and Early Development, Bristol Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, USA
| | - Sami Kebede
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Alba Font-Tello
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Kathy Mosure
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Nicholas Van Wittenberghe
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Konstantinos J. Mavrakis
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Kenzie MacIsaac
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Benjamin J. Chen
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
| | - Eugene Drokhlyansky
- Research and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA
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3
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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: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [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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4
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Yuzhalin AE. Parallels between the extracellular matrix roles in developmental biology and cancer biology. Semin Cell Dev Biol 2021; 128:90-102. [PMID: 34556419 DOI: 10.1016/j.semcdb.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 12/28/2022]
Abstract
Interaction of a tumor with its microenvironment is an emerging field of investigation, and the crosstalk between cancer cells and the extracellular matrix is of particular interest, since cancer patients with abundant and stiff extracellular matrices display a poorer prognosis. At the post-juvenile stage, the extracellular matrix plays predominantly a structural role by providing support to cells and tissues; however, during development, matrix proteins exert a plethora of diverse signals to guide the movement and determine the fate of pluripotent cells. Taking a closer look at the communication between the extracellular matrix and cells of a developing body may bring new insights into cancer biology and identify cancer weaknesses. This review discusses parallels between the extracellular matrix roles during development and tumor growth.
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Affiliation(s)
- Arseniy E Yuzhalin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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5
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Parajuli G, Tekguc M, Wing JB, Hashimoto A, Okuzaki D, Hirata T, Sasaki A, Itokazu T, Handa H, Sugino H, Nishikawa Y, Metwally H, Kodama Y, Tanaka S, Sabe H, Yamashita T, Sakaguchi S, Kishimoto T, Hashimoto S. Arid5a Promotes Immune Evasion by Augmenting Tryptophan Metabolism and Chemokine Expression. Cancer Immunol Res 2021; 9:862-876. [PMID: 34006522 DOI: 10.1158/2326-6066.cir-21-0014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022]
Abstract
The acquisition of mesenchymal traits leads to immune evasion in various cancers, but the underlying molecular mechanisms remain unclear. In this study, we found that the expression levels of AT-rich interaction domain-containing protein 5a (Arid5a), an RNA-binding protein, were substantially increased in mesenchymal tumor subtypes. The deletion of Arid5a in tumor cell lines enhanced antitumor immunity in immunocompetent mice, but not in immunodeficient mice, suggesting a role for Arid5a in immune evasion. Furthermore, an Arid5a-deficient tumor microenvironment was shown to have robust antitumor immunity, as manifested by suppressed infiltration of granulocytic myeloid-derived suppressor cells and regulatory T cells. In addition, infiltrated T cells were more cytotoxic and less exhausted. Mechanistically, Arid5a stabilized Ido1 and Ccl2 mRNAs and augmented their expression, resulting in enhanced tryptophan catabolism and an immunosuppressive tumor microenvironment. Thus, our findings demonstrate the role of Arid5a beyond inflammatory diseases and suggest Arid5a as a promising target for the treatment of immunotolerant malignant tumors.See related Spotlight by Van den Eynde, p. 854.
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Affiliation(s)
- Gyanu Parajuli
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Murat Tekguc
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - James B Wing
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ari Hashimoto
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takeshi Hirata
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
| | - Atsushi Sasaki
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
| | - Takahide Itokazu
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Haruka Handa
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hirokazu Sugino
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Nishikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hozaifa Metwally
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yuzo Kodama
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Hisataka Sabe
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shimon Sakaguchi
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Tadamitsu Kishimoto
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
| | - Shigeru Hashimoto
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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Drew J, Machesky LM. The liver metastatic niche: modelling the extracellular matrix in metastasis. Dis Model Mech 2021; 14:dmm048801. [PMID: 33973625 PMCID: PMC8077555 DOI: 10.1242/dmm.048801] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Dissemination of malignant cells from primary tumours to metastatic sites is a key step in cancer progression. Disseminated tumour cells preferentially settle in specific target organs, and the success of such metastases depends on dynamic interactions between cancer cells and the microenvironments they encounter at secondary sites. Two emerging concepts concerning the biology of metastasis are that organ-specific microenvironments influence the fate of disseminated cancer cells, and that cancer cell-extracellular matrix interactions have important roles at all stages of the metastatic cascade. The extracellular matrix is the complex and dynamic non-cellular component of tissues that provides a physical scaffold and conveys essential adhesive and paracrine signals for a tissue's function. Here, we focus on how extracellular matrix dynamics contribute to liver metastases - a common and deadly event. We discuss how matrix components of the healthy and premetastatic liver support early seeding of disseminated cancer cells, and how the matrix derived from both cancer and liver contributes to the changes in niche composition as metastasis progresses. We also highlight the technical developments that are providing new insights into the stochastic, dynamic and multifaceted roles of the liver extracellular matrix in permitting and sustaining metastasis. An understanding of the contribution of the extracellular matrix to different stages of metastasis may well pave the way to targeted and effective therapies against metastatic disease.
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Affiliation(s)
- James Drew
- CRUK Beatson Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Laura M. Machesky
- CRUK Beatson Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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