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Chandran RR, Vijayaraj P, Garcia-Milian R, King J, Castillo K, Chen L, Kwon Y, William S, Rickabaugh TM, Langerman J, Choi W, Sen C, Lever JEP, Li Q, Pavelkova N, Plosa EJ, Rowe SM, Plath K, Clair G, Gomperts BN. Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599411. [PMID: 38948715 PMCID: PMC11212876 DOI: 10.1101/2024.06.17.599411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The distal bronchioles in Idiopathic Pulmonary Fibrosis (IPF) exhibit histopathological abnormalities such as bronchiolization, peribronchiolar fibrosis and honeycomb cysts that contribute to the overall architectural remodeling of lung tissue seen in the disease. Here we describe an additional histopathologic finding of epithelial desquamation in patients with IPF, wherein epithelial cells detach from the basement membrane of the distal bronchioles. To understand the mechanism driving this pathology, we performed spatial transcriptomics of the epithelial cells and spatial proteomics of the basement membrane of the distal bronchioles from IPF patients and patients with no prior history of lung disease. Our findings reveal a downregulation of cell junctional components, upregulation of epithelial-mesenchymal transition signatures and dysregulated basement membrane matrix in IPF distal bronchioles, facilitating epithelial desquamation. Further, functional assays identified regulation between Collagen IV in the matrix, and the junctional genes JUP and PLEC , that is crucial for maintaining distal bronchiolar homeostasis. In IPF, this balanced regulation between matrix and cell-junctions is disrupted, leading to loss of epithelial adhesion, peribronchiolar fibrosis and epithelial desquamation. Overall, our study suggests that in IPF the interplay between the loss of cell junctions and a dysregulated matrix results in desquamation of distal bronchiolar epithelium and lung remodeling, exacerbating the disease. One Sentence Summary Two-way regulation of cell junctional proteins and matrix proteins drives cellular desquamation and fibrosis in the distal bronchioles of patients with Idiopathic Pulmonary Fibrosis.
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Frattini T, Devos H, Makridakis M, Roubelakis MG, Latosinka A, Mischak H, Schanstra JP, Vlahou A, Saulnier-Blache JS. Benefits and limits of decellularization on mass-spectrometry-based extracellular matrix proteome analysis of mouse kidney. Proteomics 2024:e2400052. [PMID: 38896836 DOI: 10.1002/pmic.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
The extracellular matrix (ECM) is composed of collagens, ECM glycoproteins, and proteoglycans (also named core matrisome proteins) that are critical for tissue structure and function, and matrisome-associated proteins that balance the production and degradation of the ECM proteins. The identification and quantification of core matrisome proteins using mass spectrometry is often hindered by their low abundance and their propensity to form macromolecular insoluble structures. In this study, we aimed to investigate the added value of decellularization in identifying and quantifying core matrisome proteins in mouse kidney. The decellularization strategy combined freeze-thaw cycles and sodium dodecyl sulphate treatment. We found that decellularization preserved 95% of the core matrisome proteins detected in non-decellularized kidney and revealed few additional ones. Decellularization also led to an average of 59 times enrichment of 96% of the core matrisome proteins as the result of the successful removal of cellular and matrisome-associated proteins. However, the enrichment varied greatly among core matrisome proteins, resulting in a misrepresentation of the native ECM composition in decellularized kidney. This should be brought to the attention of the matrisome research community, as it highlights the need for caution when interpreting proteomic data obtained from a decellularized organ.
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Affiliation(s)
- Teresa Frattini
- Institut National de la Santé et de la Recherche Médicale, U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Hanne Devos
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens, Greece
| | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens, Greece
| | - Maria G Roubelakis
- Laboratory of Cell and Gene Therapy, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Laboratory of Biology, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | | | | | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale, U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens, Greece
| | - Jean-Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale, U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
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Liang Z, Li J, Lin H, Zhang S, Liu F, Rao Z, Chen J, Feng Y, Zhang K, Quan D, Lin Z, Bai Y, Huang Q. Understanding the multi-functionality and tissue-specificity of decellularized dental pulp matrix hydrogels for endodontic regeneration. Acta Biomater 2024; 181:202-221. [PMID: 38692468 DOI: 10.1016/j.actbio.2024.04.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Dental pulp is the only soft tissue in the tooth which plays a crucial role in maintaining intrinsic multi-functional behaviors of the dentin-pulp complex. Nevertheless, the restoration of fully functional pulps after pulpitis or pulp necrosis, termed endodontic regeneration, remained a major challenge for decades. Therefore, a bioactive and in-situ injectable biomaterial is highly desired for tissue-engineered pulp regeneration. Herein, a decellularized matrix hydrogel derived from porcine dental pulps (pDDPM-G) was prepared and characterized through systematic comparison against the porcine decellularized nerve matrix hydrogel (pDNM-G). The pDDPM-G not only exhibited superior capabilities in facilitating multi-directional differentiation of dental pulp stem cells (DPSCs) during 3D culture, but also promoted regeneration of pulp-like tissues after DPSCs encapsulation and transplantation. Further comparative proteomic and transcriptome analyses revealed the differential compositions and potential mechanisms that endow the pDDPM-G with highly tissue-specific properties. Finally, it was realized that the abundant tenascin C (TNC) in pDDPM served as key factor responsible for the activation of Notch signaling cascades and promoted DPSCs odontoblastic differentiation. Overall, it is believed that pDDPM-G is a sort of multi-functional and tissue-specific hydrogel-based material that holds great promise in endodontic regeneration and clinical translation. STATEMENT OF SIGNIFICANCE: Functional hydrogel-based biomaterials are highly desirable for endodontic regeneration treatments. Decellularized extracellular matrix (dECM) preserves most extracellular matrix components of its native tissue, exhibiting unique advantages in promoting tissue regeneration and functional restoration. In this study, we prepared a porcine dental pulp-derived dECM hydrogel (pDDPM-G), which exhibited superior performance in promoting odontogenesis, angiogenesis, and neurogenesis of the regenerating pulp-like tissue, further showed its tissue-specificity compared to the peripheral nerve-derived dECM hydrogel. In-depth proteomic and transcriptomic analyses revealed that the activation of tenascin C-Notch axis played an important role in facilitating odontogenic regeneration. This biomaterial-based study validated the great potential of the dental pulp-specific pDDPM-G for clinical applications, and provides a springboard for research strategies in ECM-related regenerative medicine.
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Affiliation(s)
- Zelin Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Junda Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Hongkun Lin
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Sien Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Fan Liu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Zilong Rao
- Guangdong Engineering Technology Research Centre for Functional Biomaterials, PCFM Lab, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiaxin Chen
- Guangdong Engineering Technology Research Centre for Functional Biomaterials, PCFM Lab, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuwen Feng
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China
| | - Kexin Zhang
- Guangdong Engineering Technology Research Centre for Functional Biomaterials, PCFM Lab, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Daping Quan
- Guangdong Engineering Technology Research Centre for Functional Biomaterials, PCFM Lab, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengmei Lin
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China.
| | - Ying Bai
- Guangdong Engineering Technology Research Centre for Functional Biomaterials, PCFM Lab, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.
| | - Qiting Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, China.
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4
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Joshi A, Nigam A, Narayan Mudgal L, Mondal B, Basak T. ColPTMScape: An open access knowledge base for tissue-specific collagen PTM maps. Matrix Biol Plus 2024; 22:100144. [PMID: 38469247 PMCID: PMC10926295 DOI: 10.1016/j.mbplus.2024.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Collagen is a key component of the extracellular matrix (ECM). In the remodeling of ECM, a remarkable variation in collagen post-translational modifications (PTMs) occurs. This makes collagen a potential target for understanding extracellular matrix remodeling during pathological conditions. Over the years, scientists have gathered a huge amount of data about collagen PTM during extracellular matrix remodeling. To make such information easily accessible in a consolidated space, we have developed ColPTMScape (https://colptmscape.iitmandi.ac.in/), a dedicated knowledge base for collagen PTMs. The identified site-specific PTMs, quantitated PTM sites, and PTM maps of collagen chains are deliverables to the scientific community, especially to matrix biologists. Through this knowledge base, users can easily gain information related to the difference in the collagen PTMs across different tissues in different organisms.
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Affiliation(s)
- Ashutosh Joshi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Ayush Nigam
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Lalit Narayan Mudgal
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Bhaskar Mondal
- School of Chemical Sciences, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
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Phothichailert S, Samoun S, Fournier BP, Isaac J, Nelwan SC, Osathanon T, Nowwarote N. MSCs-Derived Decellularised Matrix: Cellular Responses and Regenerative Dentistry. Int Dent J 2024; 74:403-417. [PMID: 38494389 PMCID: PMC11123543 DOI: 10.1016/j.identj.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
The decellularised extracellular matrix (dECM) of in vitro cell culture is a naturally derived biomaterial formed by the removal of cellular components. The compositions of molecules in the extracellular matrix (ECM) differ depending on various factors, including the culture conditions. Cell-derived ECM provides a 3-dimensional structure that has a complex influence on cell signalling, which in turn affects cell survival and differentiation. This review describes the effects of dECM derived from mesenchymal stem cells (MSCs) on cell responses, including cell migration, cell proliferation, and cell differentiation in vitro. Published articles were searched in the PubMed databases in 2005 to 2022, with assigned keywords (MSCs and decellularisation and cell culture). The 41 articles were reviewed, with the following criteria. (1) ECM was produced exclusively from MSCs; (2) decellularisation processes were performed; and (3) the dECM production was discussed in terms of culture systems and specific supplementations that are suitable for creating the dECM biomaterials. The dECM derived from MSCs supports cell adhesion, enhances cell proliferation, and promotes cell differentiation. Importantly, dECM derived from dental MSCs shows promise in regenerative dentistry applications. Therefore, the literature strongly supports cell-based dECMs as a promising option for innovative tissue engineering approaches for regenerative medicine.
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Affiliation(s)
- Suphalak Phothichailert
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Shirel Samoun
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Universite, INSERM UMRS1138, Molecular Oral Pathophysiology, Paris, France
| | - Benjamin P Fournier
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Universite, INSERM UMRS1138, Molecular Oral Pathophysiology, Paris, France; Department of Oral Biology, Faculty of Dentistry, Université Paris Cité, Paris, France
| | - Juliane Isaac
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Universite, INSERM UMRS1138, Molecular Oral Pathophysiology, Paris, France; Department of Oral Biology, Faculty of Dentistry, Université Paris Cité, Paris, France
| | - Sindy Cornelia Nelwan
- Department of Pediatric Dentistry, Faculty of Dental Medicine, Universitas Airlangga, Airlangga, Indonesia
| | - Thanaphum Osathanon
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand; Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
| | - Nunthawan Nowwarote
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Universite, INSERM UMRS1138, Molecular Oral Pathophysiology, Paris, France; Department of Oral Biology, Faculty of Dentistry, Université Paris Cité, Paris, France.
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6
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Daulagala AC, Cetin M, Nair-Menon J, Jimenez DW, Bridges MC, Bradshaw AD, Sahin O, Kourtidis A. The epithelial adherens junction component PLEKHA7 regulates ECM remodeling and cell behavior through miRNA-mediated regulation of MMP1 and LOX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596237. [PMID: 38853930 PMCID: PMC11160653 DOI: 10.1101/2024.05.28.596237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epithelial adherens junctions (AJs) are cell-cell adhesion complexes that are influenced by tissue mechanics, such as those emanating from the extracellular matrix (ECM). Here, we introduce a mechanism whereby epithelial AJs can also regulate the ECM. We show that the AJ component PLEKHA7 regulates levels and activity of the key ECM remodeling components MMP1 and LOX in well-differentiated colon epithelial cells, through the miR-24 and miR-30c miRNAs. PLEKHA7 depletion in epithelial cells results in LOX-dependent ECM remodeling in culture and in the colonic mucosal lamina propria in mice. Furthermore, PLEKHA7-depleted cells exhibit increased migration and invasion rates that are MMP1- and LOX- dependent, and form colonies in 3D cultures that are larger in size and acquire aberrant morphologies in stiffer matrices. These results reveal an AJ-mediated mechanism, through which epithelial cells drive ECM remodeling to modulate their behavior, including acquisition of phenotypes that are hallmarks of conditions such as fibrosis and tumorigenesis.
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Affiliation(s)
- Amanda C. Daulagala
- Department of Regenerative Medicine and Cell Biology, Medical University South Carolina, Charleston, SC
| | - Metin Cetin
- Department of Biochemistry and Molecular Biology, Medical University South Carolina, Charleston, SC
| | - Joyce Nair-Menon
- Department of Regenerative Medicine and Cell Biology, Medical University South Carolina, Charleston, SC
| | - Douglas W. Jimenez
- Department of Regenerative Medicine and Cell Biology, Medical University South Carolina, Charleston, SC
| | - Mary Catherine Bridges
- Department of Regenerative Medicine and Cell Biology, Medical University South Carolina, Charleston, SC
| | - Amy D. Bradshaw
- Department of Medicine, Medical University South Carolina, Charleston, SC
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Medical University South Carolina, Charleston, SC
| | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University South Carolina, Charleston, SC
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7
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Guvatova ZG, Kobelyatskaya AA, Kudasheva ER, Pudova EA, Bulavkina EV, Churov AV, Tkacheva ON, Moskalev AA. Matrisome Transcriptome Dynamics during Tissue Aging. Life (Basel) 2024; 14:593. [PMID: 38792614 PMCID: PMC11121957 DOI: 10.3390/life14050593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The extracellular matrix (ECM) is a complex three-dimensional network of macromolecules that provides structural support for the cells and plays a significant role in tissue homeostasis and repair. Growing evidence indicates that dysregulation of ECM remodeling contributes to various pathological conditions in the body, including age-associated diseases. In this work, gene expression data of normal human tissues obtained from the Genotype-Tissue Expression project, as well as data from MatrisomeDB 2.0, the ECM-protein knowledge database, are used to estimate the age-dependent matrisome transcriptome dynamics in the blood, heart, brain, liver, kidneys, lungs, and muscle. Differential gene expression (DE) analysis revealed dozens of matrisome genes encoding both structural elements of the ECM and ECM-associated proteins, which had a tissue-specific expression profile with age. Among common DE genes that changed expression with age in at least three tissues, COL18A1, MFAP1, IGFBP7, AEBP1, LTBP2, LTBP4, LG14, EFEMP1, PRELP, BGN, FAM20B, CTSC, CTSS, and CLEC2B were observed. The findings of the study also reveal that there are sex-specific alterations during aging in the matrisome gene expression. Taken together, the results obtained in this work may help in understanding the role of the ECM in tissue aging and might prove valuable for the future development of the field of ECM research in general.
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Affiliation(s)
- Zulfiya G. Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia
| | | | - Eveline R. Kudasheva
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia
| | - Elena A. Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta V. Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey V. Churov
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia
| | - Olga N. Tkacheva
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, 129226 Moscow, Russia
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Rojas MG, Pereira-Simon S, Zigmond ZM, Varona Santos J, Perla M, Santos Falcon N, Stoyell-Conti FF, Salama A, Yang X, Long X, Duque JC, Salman LH, Tabbara M, Martinez L, Vazquez-Padron RI. Single-Cell Analyses Offer Insights into the Different Remodeling Programs of Arteries and Veins. Cells 2024; 13:793. [PMID: 38786017 PMCID: PMC11119253 DOI: 10.3390/cells13100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Arteries and veins develop different types of occlusive diseases and respond differently to injury. The biological reasons for this discrepancy are not well understood, which is a limiting factor for the development of vein-targeted therapies. This study contrasts human peripheral arteries and veins at the single-cell level, with a focus on cell populations with remodeling potential. Upper arm arteries (brachial) and veins (basilic/cephalic) from 30 organ donors were compared using a combination of bulk and single-cell RNA sequencing, proteomics, flow cytometry, and histology. The cellular atlases of six arteries and veins demonstrated a 7.8× higher proportion of contractile smooth muscle cells (SMCs) in arteries and a trend toward more modulated SMCs. In contrast, veins showed a higher abundance of endothelial cells, pericytes, and macrophages, as well as an increasing trend in fibroblasts. Activated fibroblasts had similar proportions in both types of vessels but with significant differences in gene expression. Modulated SMCs and activated fibroblasts were characterized by the upregulation of MYH10, FN1, COL8A1, and ITGA10. Activated fibroblasts also expressed F2R, POSTN, and COMP and were confirmed by F2R/CD90 flow cytometry. Activated fibroblasts from veins were the top producers of collagens among all fibroblast populations from both types of vessels. Venous fibroblasts were also highly angiogenic, proinflammatory, and hyper-responders to reactive oxygen species. Differences in wall structure further explain the significant contribution of fibroblast populations to remodeling in veins. Fibroblasts are almost exclusively located outside the external elastic lamina in arteries, while widely distributed throughout the venous wall. In line with the above, ECM-targeted proteomics confirmed a higher abundance of fibrillar collagens in veins vs. more basement ECM components in arteries. The distinct cellular compositions and transcriptional programs of reparative populations in arteries and veins may explain differences in acute and chronic wall remodeling between vessels. This information may be relevant for the development of antistenotic therapies.
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Affiliation(s)
- Miguel G. Rojas
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Simone Pereira-Simon
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | | | - Javier Varona Santos
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Mikael Perla
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Nieves Santos Falcon
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Filipe F. Stoyell-Conti
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Alghidak Salama
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Xiaofeng Yang
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Xiaochun Long
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Juan C. Duque
- Department of Medicine, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Loay H. Salman
- Division of Nephrology and Hypertension, Albany Medical College, Albany, NY 12208, USA
| | - Marwan Tabbara
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Laisel Martinez
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
| | - Roberto I. Vazquez-Padron
- Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (M.G.R.); (S.P.-S.); (J.V.S.); (A.S.)
- Bruce W. Carter Veterans Affairs Medical Center, Miami, FL 33125, USA;
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9
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Ortega JA, Soares de Aguiar GP, Chandravanshi P, Levy N, Engel E, Álvarez Z. Exploring the properties and potential of the neural extracellular matrix for next-generation regenerative therapies. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1962. [PMID: 38723788 DOI: 10.1002/wnan.1962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/24/2024]
Abstract
The extracellular matrix (ECM) is a dynamic and complex network of proteins and molecules that surrounds cells and tissues in the nervous system and orchestrates a myriad of biological functions. This review carefully examines the diverse interactions between cells and the ECM, as well as the transformative chemical and physical changes that the ECM undergoes during neural development, aging, and disease. These transformations play a pivotal role in shaping tissue morphogenesis and neural activity, thereby influencing the functionality of the central nervous system (CNS). In our comprehensive review, we describe the diverse behaviors of the CNS ECM in different physiological and pathological scenarios and explore the unique properties that make ECM-based strategies attractive for CNS repair and regeneration. Addressing the challenges of scalability, variability, and integration with host tissues, we review how advanced natural, synthetic, and combinatorial matrix approaches enhance biocompatibility, mechanical properties, and functional recovery. Overall, this review highlights the potential of decellularized ECM as a powerful tool for CNS modeling and regenerative purposes and sets the stage for future research in this exciting field. This article is categorized under: Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement Therapeutic Approaches and Drug Discovery > Nanomedicine for Neurological Disease Implantable Materials and Surgical Technologies > Nanomaterials and Implants.
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Affiliation(s)
- J Alberto Ortega
- Department of Pathology and Experimental Therapeutics, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet del Llobregat, Spain
| | - Gisele P Soares de Aguiar
- Department of Pathology and Experimental Therapeutics, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet del Llobregat, Spain
| | - Palash Chandravanshi
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Natacha Levy
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elisabeth Engel
- IMEM-BRT Group, Department of Materials Science and Engineering, EEBE, Technical University of Catalonia (UPC), Barcelona, Spain
- Biomaterials for Regenerative Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CIBER en Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
| | - Zaida Álvarez
- Biomaterials for Neural Regeneration Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CIBER en Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois, USA
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10
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Gao Y, Wu R, Pei Z, Ke C, Zeng D, Li X, Zhang Y. Cell cycle associated protein 1 associates with immune infiltration and ferroptosis in gastrointestinal cancer. Heliyon 2024; 10:e28794. [PMID: 38586390 PMCID: PMC10998105 DOI: 10.1016/j.heliyon.2024.e28794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Background Cell Cycle-Associated Protein 1 (CAPRIN1) play an important role in cell proliferation, oxidative stress, and inflammatory response. Nonetheless, its role in tumor immunity and ferroptosis is largely unknown in gastrointestinal cancer patients. Methods Through comprehensive bioinformatics, we investigate CAPRIN1 expression patterns and its role in diagnosis, functional signaling pathways, tumor immune infiltration and ferroptosis of different gastrointestinal cancer subtypes. Besides, immunohistochemistry (IHC) and immune blot were used to validate our esophagus cancer clinical data. The ferroptotic features of CAPRIN1 in vitro were assessed through knockdown assays in esophagus cancer cells. Results CAPRIN1 expression was significantly upregulated, correlated with poor prognosis, and served as an independent risk factor for most gastrointestinal cancer. Moreover, CAPRIN1 overexpression positively correlated with gene markers of most infiltrating immune cells, and immune checkpoints. CAPRIN1 knockdown significantly decreased the protein level of major histocompatibility complex class I molecules. We also identified a link between CAPRIN1 and ferroptosis-related genes in gastrointestinal cancer. Knockdown of CAPRIN1 significantly increased the production of lipid reactive oxygen species and malondialdehyde. Inhibition of CAPRIN1 expression promoted ferroptotic cell death induced by RAS-selective lethal 3 and erastin in human esophagus cancer cells. Conclusion Collectively, our results demonstrate that CAPRIN1 is aberrantly expressed in gastrointestinal cancer, is associated with poor prognosis, and could potentially influence immune infiltration and ferroptosis.
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Affiliation(s)
- Yan Gao
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P.R. China
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Ruimin Wu
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Zhijun Pei
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Changbin Ke
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Daobing Zeng
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiaohui Li
- Department of Pharmacy, Taihe Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P.R. China
- State Key Laboratory of Shaanxi for Natural Medicines Research and Engineering, Xi'an Jiaotong University, Xi'an, 710061, China
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11
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Qu N, Chen D, Ma B, Zhang L, Wang Q, Wang Y, Wang H, Ni Z, Wang W, Liao T, Xiang J, Wang Y, Jin S, Xue D, Wu W, Wang Y, Ji Q, He H, Piao HL, Shi R. Integrated proteogenomic and metabolomic characterization of papillary thyroid cancer with different recurrence risks. Nat Commun 2024; 15:3175. [PMID: 38609408 PMCID: PMC11014849 DOI: 10.1038/s41467-024-47581-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Although papillary thyroid cancer (PTC) has a good prognosis, its recurrence rate is high and remains a core concern in the clinic. Molecular factors contributing to different recurrence risks (RRs) remain poorly defined. Here, we perform an integrative proteogenomic and metabolomic characterization of 102 Chinese PTC patients with different RRs. Genomic profiling reveals that mutations in MUC16 and TERT promoter as well as multiple gene fusions like NCOA4-RET are enriched by the high RR. Integrative multi-omics analyses further describe the multi-dimensional characteristics of PTC, especially in metabolism pathways, and delineate dominated molecular patterns of different RRs. Moreover, the PTC patients are clustered into four subtypes (CS1: low RR and BRAF-like; CS2: high RR and metabolism type, worst prognosis; CS3: high RR and immune type, better prognosis; CS4: high RR and BRAF-like) based on the omics data. Notably, the subtypes display significant differences considering BRAF and TERT promoter mutations, metabolism and immune pathway profiles, epithelial cell compositions, and various clinical factors (especially RRs and prognosis) as well as druggable targets. This study can provide insights into the complex molecular characteristics of PTC recurrences and help promote early diagnosis and precision treatment of recurrent PTC.
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Affiliation(s)
- Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lijun Zhang
- Department of General Surgery, Ganmei Affiliated Hospital of Kunming Medical University (The First People's Hospital of Kunming), Kunming, Yunnan, China
- Department of Surgery, Kunming Medical University, Kunming, Yunnan, China
| | - Qiuping Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yuting Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongping Wang
- Department of Endocrinology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaoxian Ni
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Xiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yulong Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi Jin
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dixin Xue
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weili Wu
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Hui He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Laparoscopic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Hai-Long Piao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- Department of Biochemistry & Molecular Biology, School of Life Sciences, China Medical University, Shenyang, China.
| | - Rongliang Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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12
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Mogal MR, Jame JA, Sohel M, Mozibullah M, Mahmod MR, Junayed A, Kar N, Arbia L, Al Mamun A, Sikder MA. Integrated bioinformatics analysis reveals upregulated extracellular matrix hub genes in pancreatic cancer: Implications for diagnosis, prognosis, immune infiltration, and therapeutic strategies. Cancer Rep (Hoboken) 2024; 7:e2059. [PMID: 38639039 PMCID: PMC11027013 DOI: 10.1002/cnr2.2059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/20/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to therapeutic interventions. The primary objective of this present study was to identify extracellular matrix (ECM)-related hub genes (HGs) and their corresponding molecular signatures, with the intent of potentially utilizing them as biomarkers for diagnostic, prognostic, and therapeutic applications. METHODS Three microarray datasets were sourced from the NCBI database to acquire upregulated differentially expressed genes (DEGs), while MatrisomeDB was employed for filtering ECM-related genes. Subsequently, a protein-protein interaction (PPI) network was established using the STRING database. The created network was visually inspected through Cytoscape, and HGs were identified using the CytoHubba plugin tool. Furthermore, enrichment analysis, expression pattern analysis, clinicopathological correlation, survival analysis, immune cell infiltration analysis, and examination of chemical compounds were carried out using Enrichr, GEPIA2, ULCAN, Kaplan Meier plotter, TIMER2.0, and CTD web platforms, respectively. The diagnostic and prognostic significance of HGs was evaluated through the ROC curve analysis. RESULTS Ten genes associated with ECM functions were identified as HGs among 131 DEGs obtained from microarray datasets. Notably, the expression of these HGs exhibited significantly (p < 0.05) higher in PC, demonstrating a clear association with tumor advancement. Remarkably, higher expression levels of these HGs were inversely correlated with the likelihood of patient survival. Moreover, ROC curve analysis revealed that identified HGs are promising biomarkers for both diagnostic (AUC > 0.75) and prognostic (AUC > 0.64) purposes. Furthermore, we observed a positive correlation between immune cell infiltration and the expression of most HGs. Lastly, our study identified nine compounds with significant interaction profiles that could potentially act as effective chemical agents targeting the identified HGs. CONCLUSION Taken together, our findings suggest that COL1A1, KRT19, MMP1, COL11A1, SDC1, ITGA2, COL1A2, POSTN, FN1, and COL5A1 hold promise as innovative biomarkers for both the diagnosis and prognosis of PC, and they present as prospective targets for therapeutic interventions aimed at impeding the progression PC.
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Affiliation(s)
- Md Roman Mogal
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Jasmin Akter Jame
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Rashel Mahmod
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Asadullah Junayed
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Newton Kar
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Lubatul Arbia
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Abdullah Al Mamun
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Asaduzzaman Sikder
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
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13
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Fu Y, Zhou Y, Wang K, Li Z, Kong W. Extracellular Matrix Interactome in Modulating Vascular Homeostasis and Remodeling. Circ Res 2024; 134:931-949. [PMID: 38547250 DOI: 10.1161/circresaha.123.324055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The ECM (extracellular matrix) is a major component of the vascular microenvironment that modulates vascular homeostasis. ECM proteins include collagens, elastin, noncollagen glycoproteins, and proteoglycans/glycosaminoglycans. ECM proteins form complex matrix structures, such as the basal lamina and collagen and elastin fibers, through direct interactions or lysyl oxidase-mediated cross-linking. Moreover, ECM proteins directly interact with cell surface receptors or extracellular secreted molecules, exerting matricellular and matricrine modulation, respectively. In addition, extracellular proteases degrade or cleave matrix proteins, thereby contributing to ECM turnover. These interactions constitute the ECM interactome network, which is essential for maintaining vascular homeostasis and preventing pathological vascular remodeling. The current review mainly focuses on endogenous matrix proteins in blood vessels and discusses the interaction of these matrix proteins with other ECM proteins, cell surface receptors, cytokines, complement and coagulation factors, and their potential roles in maintaining vascular homeostasis and preventing pathological remodeling.
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Affiliation(s)
- Yi Fu
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics (Y.Z.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Kai Wang
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Zhuofan Li
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Wei Kong
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
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14
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Debnath K, Qayoom I, O'Donnell S, Ekiert J, Wang C, Sanborn MA, Liu C, Rivera A, Cho IS, Saichellappa S, Toth PT, Mehta D, Rehman J, Du X, Gao Y, Shin JW. Matrimeres are systemic nanoscale mediators of tissue integrity and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586585. [PMID: 38585943 PMCID: PMC10996590 DOI: 10.1101/2024.03.25.586585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tissue barriers must be rapidly restored after injury to promote regeneration. However, the mechanism behind this process is unclear, particularly in cases where the underlying extracellular matrix is still compromised. Here, we report the discovery of matrimeres as constitutive nanoscale mediators of tissue integrity and function. We define matrimeres as non-vesicular nanoparticles secreted by cells, distinguished by a primary composition comprising at least one matrix protein and DNA molecules serving as scaffolds. Mesenchymal stromal cells assemble matrimeres from fibronectin and DNA within acidic intracellular compartments. Drawing inspiration from this biological process, we have achieved the successful reconstitution of matrimeres without cells. This was accomplished by using purified matrix proteins, including fibronectin and vitronectin, and DNA molecules under optimal acidic pH conditions, guided by the heparin-binding domain and phosphate backbone, respectively. Plasma fibronectin matrimeres circulate in the blood at homeostasis but exhibit a 10-fold decrease during systemic inflammatory injury in vivo . Exogenous matrimeres rapidly restore vascular integrity by actively reannealing endothelial cells post-injury and remain persistent in the host tissue matrix. The scalable production of matrimeres holds promise as a biologically inspired platform for regenerative nanomedicine.
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15
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Macdonald JK, Mehta AS, Drake RR, Angel PM. Molecular analysis of the extracellular microenvironment: from form to function. FEBS Lett 2024; 598:602-620. [PMID: 38509768 PMCID: PMC11049795 DOI: 10.1002/1873-3468.14852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.
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Affiliation(s)
- Jade K Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
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16
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Guo Q, Ping L, Dammer EB, Yin L, Xu K, Shantaraman A, Fox EJ, Golde TE, Johnson ECB, Roberts BR, Lah JJ, Levey AI, Seyfried NT. Heparin-enriched plasma proteome is significantly altered in Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-3933136. [PMID: 38464223 PMCID: PMC10925398 DOI: 10.21203/rs.3.rs-3933136/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Introduction Heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology in Alzheimer's disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry-based proteomic approaches. Methods We employed heparin affinity chromatography, followed by off-line fractionation and tandem mass tag mass spectrometry (TMT-MS), to capture and enrich HBPs in plasma obtained from AD (n=62) and control (n=47) samples. These profiles were then correlated to a consensus AD brain proteome, as well as with Aβ, tau and phosphorylated tau (pTau) CSF biomarkers from the same individuals. We then leveraged published human postmortem brain proteome datasets to assess the overlap with the heparin-enriched plasma proteome. Results Heparin-enrichment from plasma was highly reproducible, enriched well-known HBPs like APOE and thrombin, and depleted high-abundance proteins such as albumin. A total of 2865 proteins, spanning 10 orders of magnitude were detectable. Utilizing a consensus AD brain protein co-expression network, we observed that specific plasma HBPs exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes highlighting the complex interplay between the two compartments. Elevated HBPs in AD plasma, when compared to controls, included members of the matrisome module in brain that accumulate within Aβ deposits, such as SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB, and APOE. Additionally, heparin enriched plasma proteins demonstrated significant correlations with conventional AD CSF biomarkers, including Aβ, total tau, pTau, and plasma pTau from the same individuals. Conclusion These findings support the utility of a heparin-affinity approach for enriching amyloid-associated proteins, as well as a wide spectrum of plasma biomarkers that reflect pathological changes in the AD brain.
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Affiliation(s)
- Qi Guo
- Emory University School of Medicine
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17
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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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18
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Brodeur A, Roy V, Touzel-Deschênes L, Bianco S, Droit A, Fradette J, Ruel J, Gros-Louis F. Transcriptomic Analysis of Mineralized Adipose-Derived Stem Cell Tissues for Calcific Valve Disease Modelling. Int J Mol Sci 2024; 25:2291. [PMID: 38396969 PMCID: PMC10889332 DOI: 10.3390/ijms25042291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Calcific aortic valve disease (CAVD) is characterized by the fibrosis and mineralization of the aortic valve, which leads to aortic stenosis and heart failure. At the cellular level, this is due to the osteoblastic-like differentiation of valve interstitial cells (VICs), resulting in the calcification of the tissue. Unfortunately, human VICs are not readily available to study CAVD pathogenesis and the implicated mechanisms in vitro; however, adipose-derived stromal/stem cells (ASCs), carrying the patient's specific genomic features, have emerged as a promising cell source to model cardiovascular diseases due to their multipotent nature, availability, and patient-specific characteristics. In this study, we describe a comprehensive transcriptomic analysis of tissue-engineered, scaffold-free, ASC-embedded mineralized tissue sheets using bulk RNA sequencing. Bioinformatic and gene set enrichment analyses revealed the up-regulation of genes associated with the organization of the extracellular matrix (ECM), suggesting that the ECM could play a vital role in the enhanced mineralization observed in these tissue-engineered ASC-embedded sheets. Upon comparison with publicly available gene expression datasets from CAVD patients, striking similarities emerged regarding cardiovascular diseases and ECM functions, suggesting a potential link between ECM gene expression and CAVDs pathogenesis. A matrisome-related sub-analysis revealed the ECM microenvironment promotes the transcriptional activation of the master gene runt-related transcription factor 2 (RUNX2), which is essential in CAVD development. Tissue-engineered ASC-embedded sheets with enhanced mineralization could be a valuable tool for research and a promising avenue for the identification of more effective aortic valve replacement therapies.
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Affiliation(s)
- Alyssa Brodeur
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 5C3, Canada; (A.B.); (V.R.); (L.T.-D.); (J.F.)
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
| | - Vincent Roy
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 5C3, Canada; (A.B.); (V.R.); (L.T.-D.); (J.F.)
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
| | - Lydia Touzel-Deschênes
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 5C3, Canada; (A.B.); (V.R.); (L.T.-D.); (J.F.)
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
| | - Stéphanie Bianco
- Department of Molecular Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1V 5C3, Canada; (S.B.); (A.D.)
- Computational Biology Laboratory, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1V 4G2, Canada
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1V 5C3, Canada; (S.B.); (A.D.)
- Computational Biology Laboratory, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1V 4G2, Canada
| | - Julie Fradette
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 5C3, Canada; (A.B.); (V.R.); (L.T.-D.); (J.F.)
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
| | - Jean Ruel
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
- Department of Mechanical Engineering, Faculty of Sciences and Engineering, Laval University, Quebec City, QC G1V 0A6, Canada
| | - François Gros-Louis
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 5C3, Canada; (A.B.); (V.R.); (L.T.-D.); (J.F.)
- Division of Regenerative Medicine, CHU de Quebec Université Laval Research Centre, Quebec City, QC G1J 5B3, Canada;
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19
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Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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20
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Pally D, Naba A. Extracellular matrix dynamics: A key regulator of cell migration across length-scales and systems. Curr Opin Cell Biol 2024; 86:102309. [PMID: 38183892 PMCID: PMC10922734 DOI: 10.1016/j.ceb.2023.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/11/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
The interactions between cells and their surrounding extracellular matrix (ECM) are dynamic and play critical roles in cell migration during development, health, and diseases. Recent advances have highlighted the complexity and diversity of ECM compositions, or "matrisomes", of tissues resulting in ECMs of different physical, mechanical, and biochemical properties. Investigating the effects of these properties on cell-ECM interactions in the context of cell migration have led to a better understanding of the principles underlying tissue morphogenesis, wound healing, immune response, or cancer metastasis. These new insights into the interplay between ECM dynamics and cell migration can lead to the identification of unique opportunities for therapeutic interventions.
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Affiliation(s)
- Dharma Pally
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
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21
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Moutin EB, Bons J, Giavara G, Lourenco F, Pan D, Burton JB, Shah S, Colombé M, Gascard P, Tlsty T, Schilling B, Winton DJ. Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon. Cell Mol Gastroenterol Hepatol 2024; 17:639-656. [PMID: 38199279 PMCID: PMC10905044 DOI: 10.1016/j.jcmgh.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is both a consequence and a mediator of disease progression. Despite previous characterization of epithelial and stromal remodeling during inflammatory bowel disease, a complete understanding of its impact on disease progression is lacking. METHODS A comprehensive proteomic pipeline using data-independent acquisition was applied to decellularized colon samples from the Muc2 knockout (Muc2KO) mouse model of colitis for an in-depth characterization of extracellular matrix remodeling. Unique proteomic profiles of the matrisomal landscape were extracted from prepathologic and overt colitis. Integration of proteomics and transcriptomics data sets extracted from the same murine model produced network maps describing the orchestrating role of matrisomal proteins in tissue remodeling during the progression of colitis. RESULTS The in-depth proteomic workflow used here allowed the addition of 34 proteins to the known colon matrisomal signature. Protein signatures of prepathologic and pathologic colitic states were extracted, differentiating the 2 states by expression of small leucine-rich proteoglycans. We outlined the role of this class and other matrisomal proteins in tissue remodeling during colitis, as well as the potential for coordinated regulation of cell types by matrisomal ligands. CONCLUSIONS Our work highlights a central role for matrisomal proteins in tissue remodeling during colitis and defines orchestrating nodes that can be exploited in the selection of therapeutic targets.
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Affiliation(s)
- Elisa B Moutin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Giada Giavara
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Filipe Lourenco
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Deng Pan
- Department of Pathology, University of California, San Francisco, California
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, California
| | - Mathilde Colombé
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Philippe Gascard
- Department of Pathology, University of California, San Francisco, California
| | - Thea Tlsty
- Department of Pathology, University of California, San Francisco, California
| | | | - Douglas J Winton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom.
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22
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Carretta M, Thorseth ML, Schina A, Agardy DA, Johansen AZ, Baker KJ, Khan S, Rømer AMA, Fjæstad KY, Linder H, Kuczek DE, Donia M, Grøntved L, Madsen DH. Dissecting tumor microenvironment heterogeneity in syngeneic mouse models: insights on cancer-associated fibroblast phenotypes shaped by infiltrating T cells. Front Immunol 2024; 14:1320614. [PMID: 38259467 PMCID: PMC10800379 DOI: 10.3389/fimmu.2023.1320614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Murine syngeneic tumor models have been used extensively for cancer research for several decades and have been instrumental in driving the discovery and development of cancer immunotherapies. These tumor models are very simplistic cancer models, but recent reports have, however, indicated that the different inoculated cancer cell lines can lead to the formation of unique tumor microenvironments (TMEs). To gain more knowledge from studies based on syngeneic tumor models, it is essential to obtain an in-depth understanding of the cellular and molecular composition of the TME in the different models. Additionally, other parameters that are important for cancer progression, such as collagen content and mechanical tissue stiffness across syngeneic tumor models have not previously been reported. Here, we compare the TME of tumors derived from six common syngeneic tumor models. Using flow cytometry and transcriptomic analyses, we show that strikingly unique TMEs are formed by the different cancer cell lines. The differences are reflected as changes in abundance and phenotype of myeloid, lymphoid, and stromal cells in the tumors. Gene expression analyses support the different cellular composition of the TMEs and indicate that distinct immunosuppressive mechanisms are employed depending on the tumor model. Cancer-associated fibroblasts (CAFs) also acquire very different phenotypes across the tumor models. These differences include differential expression of genes encoding extracellular matrix (ECM) proteins, matrix metalloproteinases (MMPs), and immunosuppressive factors. The gene expression profiles suggest that CAFs can contribute to the formation of an immunosuppressive TME, and flow cytometry analyses show increased PD-L1 expression by CAFs in the immunogenic tumor models, MC38 and CT26. Comparison with CAF subsets identified in other studies shows that CAFs are skewed towards specific subsets depending on the model. In athymic mice lacking tumor-infiltrating cytotoxic T cells, CAFs express lower levels of PD-L1 and lower levels of fibroblast activation markers. Our data underscores that CAFs can be involved in the formation of an immunosuppressive TME.
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Affiliation(s)
- Marco Carretta
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Marie-Louise Thorseth
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Aimilia Schina
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Dennis Alexander Agardy
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Astrid Zedlitz Johansen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Kevin James Baker
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Shawez Khan
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Anne Mette Askehøj Rømer
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Klaire Yixin Fjæstad
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Hannes Linder
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Dorota Ewa Kuczek
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Daniel Hargbøl Madsen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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23
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Bacchetti R, Yuan S, Rainero E. ADAMTS Proteases: Their Multifaceted Role in the Regulation of Cancer Metastasis. DISEASES & RESEARCH 2024; 4:40-52. [PMID: 38948119 PMCID: PMC7616120 DOI: 10.54457/dr.202401004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cancer leads to nearly 10 million deaths worldwide per year. The tumour microenvironment (TME) is fundamental for tumour growth and progression. A key component of the TME, the extracellular matrix (ECM) has recently become a focus of interest in cancer research. Dysregulation of ECM synthesis and proteolysis leads to uncontrolled tumour growth and metastasis. Matrix remodelling enzymes, secreted by cancer cells and stromal cells, modify the overall structure and organisation of ECM proteins, therefore influencing biochemical interactions, tissue integrity and tissue turnover. While A Disintegrin and Metalloproteinases (ADAMs)' and matrix metalloproteinases' role in cancer has been deeply investigated, other proteolytic enzymes, like ADAMs with thrombospondin(-like) motifs (ADAMTSs) have been gaining interest due to their roles in modulating cancer cell-ECM interactions and oncogenic signalling pathways. In this review, we will discuss the dysregulation of ADAMTSs in cancer and their roles in regulating cancer development and progression, via ECM remodelling and cell signalling modulation.
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Affiliation(s)
- Rachele Bacchetti
- School of Biosciences, Department of Biomedical science, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Shengnan Yuan
- School of Biosciences, Department of Biomedical science, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Elena Rainero
- School of Biosciences, Department of Biomedical science, Firth Court, Western Bank, Sheffield S10 2TN, UK
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24
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Santamaria S. Web-Based Resources to Investigate Protease Function. Methods Mol Biol 2024; 2747:1-18. [PMID: 38038927 DOI: 10.1007/978-1-0716-3589-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
In 2001, the release of the first draft of the human genome marked the beginning of the Big Data era for biological sciences. Since then, the complexity of datasets generated by laboratories worldwide has increased exponentially. Public repositories such as the Protein Data Bank, which has exceeded the 200000 entries in 2023, have been instrumental not only to collect, organize, and distill this enormous research output but also to promote further research enterprises. The achievements of artificial intelligence programs such as AlphaFold would not have been possible without the collective efforts of countless researchers who made their work publicly available. Here, I provide a practical, but far from exhaustive, list of resources useful to investigate protease function.
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Affiliation(s)
- Salvatore Santamaria
- Department of Biochemical Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK.
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25
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Morais MRPT, Tian P, O'cualain R, Lawless C, Lennon R. Protocol to characterize basement membranes during kidney development using mass spectrometry-based label-free quantitative proteomics. STAR Protoc 2023; 4:102741. [PMID: 38039136 PMCID: PMC10722381 DOI: 10.1016/j.xpro.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Basement membranes are specialized extracellular matrices formed by highly insoluble structural proteins and extracellular matrix (ECM)-bound components that provide structural and signaling support to tissues and are dynamic during development. Here, we present a mass spectrometry-based label-free quantitative proteomics protocol to investigate basement membranes and define their composition using samples from human kidney organoids and mouse fetal kidneys. This protocol facilitates the study of basement membrane and other ECM components during development to improve our understanding of matrix regulation and function. For complete details on the use and execution of this protocol, please refer to Morais et al.1.
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Affiliation(s)
- Mychel R P T Morais
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK.
| | - Ronan O'cualain
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK.
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26
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Zhao P, Yang F, Jia X, Xiao Y, Hua C, Xing M, Lyu G. Extracellular Matrices as Bioactive Materials for In Situ Tissue Regeneration. Pharmaceutics 2023; 15:2771. [PMID: 38140112 PMCID: PMC10747903 DOI: 10.3390/pharmaceutics15122771] [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: 08/19/2023] [Revised: 10/28/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Bioactive materials based on a nature-derived extracellular matrix (NECM) represent a category of biomedical devices with versatile therapeutic applications in the realms of tissue repair and engineering. With advancements in decellularization technique, the inherent bioactive molecules and the innate nano-structural and mechanical properties are preserved in three-dimensional scaffolds mainly composed of collagens. Techniques such as electrospinning, three-dimensional printing, and the intricate fabrication of hydrogels are developed to mimic the physical structures, biosignalling and mechanical cues of ECM. Until now, there has been no approach that can fully account for the multifaceted properties and diverse applications of NECM. In this review, we introduce the main proteins composing NECMs and explicate the importance of them when used as therapeutic devices in tissue repair. Nano-structural features of NECM and their applications regarding tissue repair are summarized. The origins, degradability, and mechanical property of and immune responses to NECM are also introduced. Furthermore, we review their applications, and clinical features thereof, in the repair of acute and chronic wounds, abdominal hernia, breast deformity, etc. Some typical marketed devices based on NECM, their indications, and clinical relevance are summarized.
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Affiliation(s)
- Peng Zhao
- Burn & Trauma Treatment Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
- Engineering Research Center of the Ministry of Education for Wound Repair Technology, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi 214000, China; (F.Y.); (Y.X.)
| | - Fengbo Yang
- Engineering Research Center of the Ministry of Education for Wound Repair Technology, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi 214000, China; (F.Y.); (Y.X.)
| | - Xiaoli Jia
- Engineering Research Center of the Ministry of Education for Wound Repair Technology, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi 214000, China; (F.Y.); (Y.X.)
| | - Yuqin Xiao
- Engineering Research Center of the Ministry of Education for Wound Repair Technology, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi 214000, China; (F.Y.); (Y.X.)
| | - Chao Hua
- Burn & Trauma Treatment Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Malcolm Xing
- Department of Mechanical Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Guozhong Lyu
- Burn & Trauma Treatment Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
- Engineering Research Center of the Ministry of Education for Wound Repair Technology, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi 214000, China; (F.Y.); (Y.X.)
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27
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Neilson LJ, Cartwright D, Risteli M, Jokinen EM, McGarry L, Sandvik T, Nikolatou K, Hodge K, Atkinson S, Vias M, Kay EJ, Brenton JD, Carlin LM, Bryant DM, Salo T, Zanivan S. Omentum-derived matrix enables the study of metastatic ovarian cancer and stromal cell functions in a physiologically relevant environment. Matrix Biol Plus 2023; 19-20:100136. [PMID: 38223308 PMCID: PMC10784634 DOI: 10.1016/j.mbplus.2023.100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/20/2023] [Accepted: 11/12/2023] [Indexed: 01/16/2024] Open
Abstract
High-grade serous (HGS) ovarian cancer is the most lethal gynaecological disease in the world and metastases is a major cause. The omentum is the preferential metastatic site in HGS ovarian cancer patients and in vitro models that recapitulate the original environment of this organ at cellular and molecular level are being developed to study basic mechanisms that underpin this disease. The tumour extracellular matrix (ECM) plays active roles in HGS ovarian cancer pathology and response to therapy. However, most of the current in vitro models use matrices of animal origin and that do not recapitulate the complexity of the tumour ECM in patients. Here, we have developed omentum gel (OmGel), a matrix made from tumour-associated omental tissue of HGS ovarian cancer patients that has unprecedented similarity to the ECM of HGS omental tumours and is simple to prepare. When used in 2D and 3D in vitro assays to assess cancer cell functions relevant to metastatic ovarian cancer, OmGel performs as well as or better than the widely use Matrigel and does not induce additional phenotypic changes to ovarian cancer cells. Surprisingly, OmGel promotes pronounced morphological changes in cancer associated fibroblasts (CAFs). These changes were associated with the upregulation of proteins that define subsets of CAFs in tumour patient samples, highlighting the importance of using clinically and physiologically relevant matrices for in vitro studies. Hence, OmGel provides a step forward to study the biology of HGS omental metastasis. Metastasis in the omentum are also typical of other cancer types, particularly gastric cancer, implying the relevance of OmGel to study the biology of other highly lethal cancers.
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Affiliation(s)
| | - Douglas Cartwright
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Maija Risteli
- Research Unit of Population Health, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Elina M. Jokinen
- Department of Bacteriology and Immunology, Translational Immunology Research Program, University of Helsinki, Finland
| | - Lynn McGarry
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - Toni Sandvik
- Research Unit of Population Health, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Konstantina Nikolatou
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kelly Hodge
- Cancer Research UK Scotland Institute, Glasgow, UK
| | | | - Maria Vias
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Emily J. Kay
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Leo M. Carlin
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David M. Bryant
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Tuula Salo
- Research Unit of Population Health, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
- Department of Pathology, University of Helsinki, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sara Zanivan
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
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28
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Long AM, Lee G, Demonbreun AR, McNally EM. Extracellular matrix contribution to disease progression and dysfunction in myopathy. Am J Physiol Cell Physiol 2023; 325:C1244-C1251. [PMID: 37746696 PMCID: PMC10855263 DOI: 10.1152/ajpcell.00182.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/27/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Myopathic processes affect skeletal muscle and heart. In the muscular dystrophies, which are a subset of myopathies, muscle cells are gradually replaced by fibrosis and fat, impairing muscle function as well as regeneration and repair. In addition to skeletal muscle, these genetic disorders often also affect the heart, where fibrofatty infiltration progressively accumulates in the myocardium, impairing heart function. Although considerable effort has focused on gene-corrective and gene-replacement approaches to stabilize myofibers and cardiomyocytes, the continual and ongoing deposition of extracellular matrix itself contributes to tissue and organ dysfunction. Transcriptomic and proteomic profiling, along with high-resolution imaging and biophysical measurements, have been applied to define extracellular matrix components and their role in contributing to cardiac and skeletal muscle weakness. More recently, decellularization methods have been adapted to an on-slide format to preserve the spatial geography of the extracellular matrix, allowing new insight into matrix remodeling and its direct role in suppressing regeneration in muscle. This review highlights recent literature with focus on the extracellular matrix and molecular mechanisms that contribute to muscle and heart fibrotic disorders. We will also compare how the myopathic matrix differs from healthy matrix, emphasizing how the pathological matrix contributes to disease.
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Affiliation(s)
- Ashlee M Long
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - GaHyun Lee
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Alexis R Demonbreun
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
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Jin Y, Cai Q, Wang L, Ji J, Sun Y, Jiang J, Wang C, Wu J, Zhang B, Zhao L, Qi F, Yu B, Zhang J. Paracrine activin B-NF-κB signaling shapes an inflammatory tumor microenvironment in gastric cancer via fibroblast reprogramming. J Exp Clin Cancer Res 2023; 42:269. [PMID: 37858201 PMCID: PMC10585924 DOI: 10.1186/s13046-023-02861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Important roles of INHBB in various malignancies are increasingly identified. The underlying mechanisms in gastric cancer (GC) microenvironment are still greatly unexplored. METHODS The clinical significance of INHBB and the correlation between INHBB and p-p65 in GC were assessed through analyzing publicly available databases and human paraffin embedded GC tissues. The biological crosstalk of INHBB between GC cells and fibroblasts was explored both in vitro and in vivo. RNA-seq analyses were performed to determine the mechanisms which regulating fibroblasts reprogramming. Luciferase reporter assay and chromatin immunoprecipitation (CHIP) assay were used to verify the binding relationship of p65 and INHBB in GC cells. RESULTS Our study showed that INHBB level was significantly higher in GC, and that increased INHBB was associated with poor survival. INHBB positively regulates the proliferation, migration, and invasion of GC cells in vitro. Also, activin B promotes the occurrence of GC by reprogramming fibroblasts into cancer-associated fibroblasts (CAFs). The high expression of INHBB in GC cells activates the NF-κB pathway of normal gastric fibroblasts by secreting activin B, and promotes fibroblasts proliferation, migration, and invasion. In addition, activin B activates NF-κB pathway by controlling TRAF6 autoubiquitination to induce TAK1 phosphorylation in fibroblasts. Fibroblasts activated by activin B can induce the activation of p65 phosphorylation of GC cells by releasing pro-inflammatory factors IL-1β. p65 can directly bind to the INHBB promoter and increase the INHBB transcription of GC cells, thus establishing a positive regulatory feedback loop to promote the progression of GC. CONCLUSIONS GC cells p65/INHBB/activin B and fibroblasts p65/IL-1β signal loop led to the formation of a whole tumor-promoting inflammatory microenvironment, which might be a promising therapeutic target for GC.
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Affiliation(s)
- Yangbing Jin
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Qu Cai
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Lingquan Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Jun Ji
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Ying Sun
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Jinling Jiang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Chao Wang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Junwei Wu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Benyan Zhang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Liqin Zhao
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Feng Qi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China
| | - Beiqin Yu
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China.
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, 200025, Shanghai, China.
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Dylag AM, Misra RS, Bandyopadhyay G, Poole C, Huyck HL, Jehrio MG, Haak J, Deutsch GH, Dvorak C, Olson HM, Paurus V, Katzman PJ, Woo J, Purkerson JM, Adkins JN, Mariani TJ, Clair GC, Pryhuber GS. New insights into the natural history of bronchopulmonary dysplasia from proteomics and multiplexed immunohistochemistry. Am J Physiol Lung Cell Mol Physiol 2023; 325:L419-L433. [PMID: 37489262 PMCID: PMC10642360 DOI: 10.1152/ajplung.00130.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a disease of prematurity related to the arrest of normal lung development. The objective of this study was to better understand how proteome modulation and cell-type shifts are noted in BPD pathology. Pediatric human donors aged 1-3 yr were classified based on history of prematurity and histopathology consistent with "healed" BPD (hBPD, n = 3) and "established" BPD (eBPD, n = 3) compared with respective full-term born (n = 6) age-matched term controls. Proteins were quantified by tandem mass spectroscopy with selected Western blot validations. Multiplexed immunofluorescence (MxIF) microscopy was performed on lung sections to enumerate cell types. Protein abundances and MxIF cell frequencies were compared among groups using ANOVA. Cell type and ontology enrichment were performed using an in-house tool and/or EnrichR. Proteomics detected 5,746 unique proteins, 186 upregulated and 534 downregulated, in eBPD versus control with fewer proteins differentially abundant in hBPD as compared with age-matched term controls. Cell-type enrichment suggested a loss of alveolar type I, alveolar type II, endothelial/capillary, and lymphatics, and an increase in smooth muscle and fibroblasts consistent with MxIF. Histochemistry and Western analysis also supported predictions of upregulated ferroptosis in eBPD versus control. Finally, several extracellular matrix components mapping to angiogenesis signaling pathways were altered in eBPD. Despite clear parsing by protein abundance, comparative MxIF analysis confirms phenotypic variability in BPD. This work provides the first demonstration of tandem mass spectrometry and multiplexed molecular analysis of human lung tissue for critical elucidation of BPD trajectory-defining factors into early childhood.NEW & NOTEWORTHY We provide new insights into the natural history of bronchopulmonary dysplasia in donor human lungs after the neonatal intensive care unit hospitalization. This study provides new insights into how the proteome and histopathology of BPD changes in early childhood, uncovering novel pathways for future study.
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Affiliation(s)
- Andrew M Dylag
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Cory Poole
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Heidie L Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew G Jehrio
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Jeannie Haak
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Gail H Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington, University of Washington, Seattle, Washington, United States
| | - Carly Dvorak
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Heather M Olson
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Vanessa Paurus
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Philip J Katzman
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, United States
| | - Jongmin Woo
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Jeffrey M Purkerson
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Joshua N Adkins
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Geremy C Clair
- Pacific Northwest National Laboratories, Richland, Washington, United States
| | - Gloria S Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
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Novoseletskaya ES, Evdokimov PV, Efimenko AY. Extracellular matrix-induced signaling pathways in mesenchymal stem/stromal cells. Cell Commun Signal 2023; 21:244. [PMID: 37726815 PMCID: PMC10507829 DOI: 10.1186/s12964-023-01252-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
The extracellular matrix (ECM) is a crucial component of the stem cell microenvironment, or stem-cell niches, and contributes to the regulation of cell behavior and fate. Accumulating evidence indicates that different types of stem cells possess a large variety of molecules responsible for interactions with the ECM, mediating specific epigenetic rearrangements and corresponding changes in transcriptome profile. Signals from the ECM are crucial at all stages of ontogenesis, including embryonic and postnatal development, as well as tissue renewal and repair. The ECM could regulate stem cell transition from a quiescent state to readiness to perceive the signals of differentiation induction (competence) and the transition between different stages of differentiation (commitment). Currently, to unveil the complex networks of cellular signaling from the ECM, multiple approaches including screening methods, the analysis of the cell matrixome, and the creation of predictive networks of protein-protein interactions based on experimental data are used. In this review, we consider the existing evidence regarded the contribution of ECM-induced intracellular signaling pathways into the regulation of stem cell differentiation focusing on mesenchymal stem/stromal cells (MSCs) as well-studied type of postnatal stem cells totally depended on signals from ECM. Furthermore, we propose a system biology-based approach for the prediction of ECM-mediated signal transduction pathways in target cells. Video Abstract.
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Affiliation(s)
- Ekaterina Sergeevna Novoseletskaya
- Faculty of Biology, Dayun New Town, Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen, Guangdong Province, P. R. China.
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia.
| | - Pavel Vladimirovich Evdokimov
- Materials Science Department, Lomonosov Moscow State University, Leninskie Gory, 1, Building 73, 119991, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-3, Moscow, Russia
| | - Anastasia Yurievna Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosov Ave., 27/1, 119991, Moscow, Russia
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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] [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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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. J Cell Sci 2023; 136:jcs261255. [PMID: 37555624 PMCID: PMC10499032 DOI: 10.1242/jcs.261255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays crucial roles in all aspects of life - from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we have previously defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the 'matrisome' and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate '-omics' datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application and an R package. The web application can be used by anyone interested in annotating, classifying and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Fl-00290 Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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Eckersley A, Morais MR, Ozols M, Lennon R. Peptide location fingerprinting identifies structural alterations within basement membrane components in ageing kidney. Matrix Biol 2023; 121:167-178. [PMID: 37437747 DOI: 10.1016/j.matbio.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/04/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
During ageing, the glomerular and tubular basement membranes (BM) of the kidney undergo a progressive decline in function that is underpinned by histological changes, including glomerulosclerosis and tubular interstitial fibrosis and atrophy. This BM-specific ageing is thought to result from damage accumulation to long-lived extracellular matrix (ECM) protein structures. Determining which BM proteins are susceptible to these structure-associated changes, and the possible mechanisms and downstream consequences, is critical to understand age-related kidney degeneration and to identify markers for therapeutic intervention. Peptide location fingerprinting (PLF) is an emerging proteomic mass spectrometry analysis technique capable of identifying ECM proteins with structure-associated differences that may occur by damage modifications in ageing. Here, we apply PLF as a bioinformatic screening tool to identify BM proteins with structure-associated differences between young and aged human glomerular and tubulointerstitial compartments. Several functional regions within key BM components displayed alterations in tryptic peptide yield, reflecting potential age-dependent shifts in molecular (e.g. laminin-binding regions in agrin) and cellular (e.g. integrin-binding regions in laminins 521 and 511) interactions, oxidation (e.g. collagen IV) and the fragmentation and release of matrikines (e.g. canstatin and endostatin from collagens IV and XVIII). Furthermore, we found that periostin and the collagen IV α2 chain exhibited structure-associated differences in ageing that were conserved between human kidney and previously analysed mouse lung, revealing BM components that harbour shared susceptibilities across species and organs.
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Affiliation(s)
- Alexander Eckersley
- Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
| | - Mychel Rpt Morais
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Wellcome Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Matiss Ozols
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Rachel Lennon
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Wellcome Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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Swahn H, Olmer M, Lotz MK. RNA-binding proteins that are highly expressed and enriched in healthy cartilage but suppressed in osteoarthritis. Front Cell Dev Biol 2023; 11:1208315. [PMID: 37457300 PMCID: PMC10349536 DOI: 10.3389/fcell.2023.1208315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives: RNA-binding proteins (RBPs) have diverse and essential biological functions, but their role in cartilage health and disease is largely unknown. The objectives of this study were (i) map the global landscape of RBPs expressed and enriched in healthy cartilage and dysregulated in osteoarthritis (OA); (ii) prioritize RBPs for their potential role in cartilage and in OA pathogenesis and as therapeutic targets. Methods: Our published bulk RNA-sequencing (RNA-seq) data of healthy and OA human cartilage, and a census of 1,542 RBPs were utilized to identify RBPs that are expressed in healthy cartilage and differentially expressed (DE) in OA. Next, our comparison of healthy cartilage RNA-seq data to 37 transcriptomes in the Genotype-Tissue Expression (GTEx) database was used to determine RBPs that are enriched in cartilage. Finally, expression of RBPs was analyzed in our single cell RNA-sequencing (scRNA-seq) data from healthy and OA human cartilage. Results: Expression of RBPs was higher than nonRBPs in healthy cartilage. In OA cartilage, 188 RBPs were differentially expressed, with a greater proportion downregulated. Ribosome biogenesis was enriched in the upregulated RBPs, while splicing and transport were enriched in the downregulated. To further prioritize RBPs, we selected the top 10% expressed RBPs in healthy cartilage and those that were cartilage-enriched according to GTEx. Intersecting these criteria, we identified Tetrachlorodibenzodioxin (TCDD) Inducible Poly (ADP-Ribose) Polymerase (TIPARP) as a candidate RBP. TIPARP was downregulated in OA. scRNA-seq data revealed TIPARP was most significantly downregulated in the "pathogenic cluster". Conclusion: Our global analyses reveal expression patterns of RBPs in healthy and OA cartilage. We also identified TIPARP and other RBPs as novel mediators in OA pathogenesis and as potential therapeutic targets.
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Debnath K, Heras KL, Rivera A, Lenzini S, Shin JW. Extracellular vesicle-matrix interactions. NATURE REVIEWS. MATERIALS 2023; 8:390-402. [PMID: 38463907 PMCID: PMC10919209 DOI: 10.1038/s41578-023-00551-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/24/2023] [Indexed: 03/12/2024]
Abstract
The extracellular matrix in microenvironments harbors a variety of signals to control cellular functions and the materiality of tissues. Most efforts to synthetically reconstitute the matrix by biomaterial design have focused on decoupling cell-secreted and polymer-based cues. Cells package molecules into nanoscale lipid membrane-bound extracellular vesicles and secrete them. Thus, extracellular vesicles inherently interact with the meshwork of the extracellular matrix. In this Review, we discuss various aspects of extracellular vesicle-matrix interactions. Cells receive feedback from the extracellular matrix and leverage intracellular processes to control the biogenesis of extracellular vesicles. Once secreted, various biomolecular and biophysical factors determine whether extracellular vesicles are locally incorporated into the matrix or transported out of the matrix to be taken up by other cells or deposited into tissues at a distal location. These insights can be utilized to develop engineered biomaterials where EV release and retention can be precisely controlled in host tissue to elicit various biological and therapeutic outcomes.
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Affiliation(s)
- Koushik Debnath
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kevin Las Heras
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy (UPV/EHU)
- Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain
| | - Ambar Rivera
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Stephen Lenzini
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jae-Won Shin
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537378. [PMID: 37131773 PMCID: PMC10153148 DOI: 10.1101/2023.04.18.537378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays critical roles in all aspects of life: from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the "matrisome" and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate -omics datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application ( https://sites.google.com/uic.edu/matrisome/tools/matrisome-analyzer ) and an R package ( https://github.com/Matrisome/MatrisomeAnalyzeR ). The web application can be used by anyone interested in annotating, classifying, and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options. SUMMARY STATEMENT Matrisome AnalyzeR is a suite of tools, including a web-based app and an R package, designed to facilitate the annotation and quantification of extracellular matrix components in big datasets.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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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: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
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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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Phase-specific signatures of wound fibroblasts and matrix patterns define cancer-associated fibroblast subtypes. Matrix Biol 2023; 119:19-56. [PMID: 36914141 DOI: 10.1016/j.matbio.2023.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/23/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
Healing wounds and cancers present remarkable cellular and molecular parallels, but the specific roles of the healing phases are largely unknown. We developed a bioinformatics pipeline to identify genes and pathways that define distinct phases across the time-course of healing. Their comparison to cancer transcriptomes revealed that a resolution phase wound signature is associated with increased severity in skin cancer and enriches for extracellular matrix-related pathways. Comparisons of transcriptomes of early- and late-phase wound fibroblasts vs skin cancer-associated fibroblasts (CAFs) identified an "early wound" CAF subtype, which localizes to the inner tumor stroma and expresses collagen-related genes that are controlled by the RUNX2 transcription factor. A "late wound" CAF subtype localizes to the outer tumor stroma and expresses elastin-related genes. Matrix imaging of primary melanoma tissue microarrays validated these matrix signatures and identified collagen- vs elastin-rich niches within the tumor microenvironment, whose spatial organization predicts survival and recurrence. These results identify wound-regulated genes and matrix patterns with prognostic potential in skin cancer.
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Apte SS, Naba A. Beyond the matrisome: New frontiers in ECM research. Matrix Biol 2023; 115:133-138. [PMID: 36572230 DOI: 10.1016/j.matbio.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.
| | - 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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