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Naba A. Mechanisms of assembly and remodelling of the extracellular matrix. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00767-3. [PMID: 39223427 DOI: 10.1038/s41580-024-00767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
The extracellular matrix (ECM) is the complex meshwork of proteins and glycans that forms the scaffold that surrounds and supports cells. It exerts key roles in all aspects of metazoan physiology, from conferring physical and mechanical properties on tissues and organs to modulating cellular processes such as proliferation, differentiation and migration. Understanding the mechanisms that orchestrate the assembly of the ECM scaffold is thus crucial to understand ECM functions in health and disease. This Review discusses novel insights into the compositional diversity of matrisome components and the mechanisms that lead to tissue-specific assemblies and architectures tailored to support specific functions. The Review then highlights recently discovered mechanisms, including post-translational modifications and metabolic pathways such as amino acid availability and the circadian clock, that modulate ECM secretion, assembly and remodelling in homeostasis and human diseases. Last, the Review explores the potential of 'matritherapies', that is, strategies to normalize ECM composition and architecture to achieve a therapeutic benefit.
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Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, USA.
- University of Illinois Cancer Center, Chicago, IL, USA.
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2
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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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3
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Usui Y, Hanashima A, Hashimoto K, Kimoto M, Ohira M, Mohri S. Comparative analysis of ventricular stiffness across species. Physiol Rep 2024; 12:e16013. [PMID: 38644486 PMCID: PMC11033294 DOI: 10.14814/phy2.16013] [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: 09/20/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024] Open
Abstract
Investigating ventricular diastolic properties is crucial for understanding the physiological cardiac functions in organisms and unraveling the pathological mechanisms of cardiovascular disorders. Ventricular stiffness, a fundamental parameter that defines ventricular diastolic functions in chordates, is typically analyzed using the end-diastolic pressure-volume relationship (EDPVR). However, comparing ventricular stiffness accurately across chambers of varying maximum volume capacities has been a long-standing challenge. As one of the solutions to this problem, we propose calculating a relative ventricular stiffness index by applying an exponential approximation formula to the EDPVR plot data of the relationship between ventricular pressure and values of normalized ventricular volume by the ventricular weight. This article reviews the potential, utility, and limitations of using normalized EDPVR analysis in recent studies. Herein, we measured and ranked ventricular stiffness in differently sized and shaped chambers using ex vivo ventricular pressure-volume analysis data from four animals: Wistar rats, red-eared slider turtles, masu salmon, and cherry salmon. Furthermore, we have discussed the mechanical effects of intracellular and extracellular viscoelastic components, Titin (Connectin) filaments, collagens, physiological sarcomere length, and other factors that govern ventricular stiffness. Our review provides insights into the comparison of ventricular stiffness in different-sized ventricles between heterologous and homologous species, including non-model organisms.
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Grants
- JP22K15155 Japan Society for the Promotion of Science, Grant/Award Number
- JP20K21453 Japan Society for the Promotion of Science, Grant/Award Number
- JP20H04508 Japan Society for the Promotion of Science, Grant/Award Number
- JP21K19933 Japan Society for the Promotion of Science, Grant/Award Number
- JP20H04521 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H02092 Japan Society for the Promotion of Science, Grant/Award Number
- JP23H00556 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H06272 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H00859 Japan Society for the Promotion of Science, Grant/Award Number
- JP25560214 Japan Society for the Promotion of Science, Grant/Award Number
- JP16K01385 Japan Society for the Promotion of Science, Grant/Award Number
- JP26282127 Japan Society for the Promotion of Science, Grant/Award Number
- The Futaba research grant program
- Research Grant from the Kawasaki Foundation in 2016 from Medical Science and Medical Welfare
- Medical Research Grant in 2010 from Takeda Science Foundation
- R03S005 Research Project Grant from Kawasaki Medical School
- R03B050 Research Project Grant from Kawasaki Medical School
- R01B054 Research Project Grant from Kawasaki Medical School
- H30B041 Research Project Grant from Kawasaki Medical School
- H30B016 Research Project Grant from Kawasaki Medical School
- H27B10 Research Project Grant from Kawasaki Medical School
- R02B039 Research Project Grant from Kawasaki Medical School
- H28B80 Research Project Grant from Kawasaki Medical School
- R05B016 Research Project Grant from Kawasaki Medical School
- Japan Society for the Promotion of Science, Grant/Award Number
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Affiliation(s)
- Yuu Usui
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Akira Hanashima
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Ken Hashimoto
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Misaki Kimoto
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Momoko Ohira
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Satoshi Mohri
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
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Dong Y, Yang Y, Wang H, Feng D, Nist E, Yapundich N, Spurlock B, Craft M, Qian L, Liu J. Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells. SCIENCE ADVANCES 2024; 10:eadk4694. [PMID: 38381829 PMCID: PMC10881044 DOI: 10.1126/sciadv.adk4694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Cardiac regeneration requires coordinated participation of multiple cell types whereby their communications result in transient activation of proregenerative cell states. Although the molecular characteristics and lineage origins of these activated cell states and their contribution to cardiac regeneration have been studied, the extracellular signaling and the intrinsic genetic program underlying the activation of the transient functional cell states remain largely unexplored. In this study, we delineated the chromatin landscapes of the noncardiomyocytes (nonCMs) of the regenerating heart at the single-cell level and inferred the cis-regulatory architectures and trans-acting factors that control cell type-specific gene expression programs. Moreover, further motif analysis and cell-specific genetic manipulations suggest that the macrophage-derived inflammatory signal tumor necrosis factor-α, acting via its downstream transcription factor complex activator protein-1, functions cooperatively with discrete transcription regulators to activate respective nonCM cell types critical for cardiac regeneration. Thus, our study defines the regulatory architectures and intercellular communication principles in zebrafish heart regeneration.
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Affiliation(s)
- Yanhan Dong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haofei Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dong Feng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth Nist
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicholas Yapundich
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian Spurlock
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Madison Craft
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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Panda P, Sarohi V, Basak T, Kasturi P. Elucidation of Site-Specific Ubiquitination on Chaperones in Response to Mutant Huntingtin. Cell Mol Neurobiol 2023; 44:3. [PMID: 38102300 DOI: 10.1007/s10571-023-01446-1] [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: 08/23/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Huntington's disease (HD) is one of the prominent neurodegenerative diseases, characterized by the progressive decline of neuronal function, due to the accumulation and aggregation of misfolded proteins. Pathological progression of HD is hallmarked by the aberrant aggregation of the huntingtin protein (HTT) and subsequent neurotoxicity. Molecular chaperones (heat shock proteins, HSPs) play a pivotal role in maintaining proteostasis by facilitating protein refolding, degradation, or sequestration to limit the accumulation of misfolded proteins during neurotoxicity. However, the role of post-translational modifications such as ubiquitination among HSPs during HD is less known. In this study, we aimed to elucidate HSPs ubiquitin code in the context of HD pathogenesis. In a comprehensive proteomic analysis, we identified site-specific ubiquitination events in HSPs associated with HTT in HD-affected brain regions. To assess the impact of ubiquitination on HSPs during HD, we quantified the abundance of ubiquitinated lysine sites in both the rat cortex/striatum and in the mouse primary cortical neurons. Strikingly, we observed highly tissue-specific alterations in the relative ubiquitination levels of HSPs under HD conditions, emphasizing the importance of spatial perturbed post-translational modifications (PTMs) in shaping disease pathology. These ubiquitination events, combined with other PTMs on HSPs, are likely to influence the phase transitions of HTT. In conclusion, our study uncovered differential site-specific ubiquitination of molecular chaperones and offers a comprehensive view of the intricate relationship between protein aggregation, and PTMs in the context of Huntington's disease.
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Affiliation(s)
- Prajnadipta Panda
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Vivek Sarohi
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India.
| | - Prasad Kasturi
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India.
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Castillo-Casas JM, Caño-Carrillo S, Sánchez-Fernández C, Franco D, Lozano-Velasco E. Comparative Analysis of Heart Regeneration: Searching for the Key to Heal the Heart-Part II: Molecular Mechanisms of Cardiac Regeneration. J Cardiovasc Dev Dis 2023; 10:357. [PMID: 37754786 PMCID: PMC10531542 DOI: 10.3390/jcdd10090357] [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: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Cardiovascular diseases are the leading cause of death worldwide, among which ischemic heart disease is the most representative. Myocardial infarction results from occlusion of a coronary artery, which leads to an insufficient blood supply to the myocardium. As it is well known, the massive loss of cardiomyocytes cannot be solved due the limited regenerative ability of the adult mammalian hearts. In contrast, some lower vertebrate species can regenerate the heart after an injury; their study has disclosed some of the involved cell types, molecular mechanisms and signaling pathways during the regenerative process. In this 'two parts' review, we discuss the current state-of-the-art of the main response to achieve heart regeneration, where several processes are involved and essential for cardiac regeneration.
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Affiliation(s)
- Juan Manuel Castillo-Casas
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain; (J.M.C.-C.); (S.C.-C.); (C.S.-F.); (D.F.)
| | - Sheila Caño-Carrillo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain; (J.M.C.-C.); (S.C.-C.); (C.S.-F.); (D.F.)
| | - Cristina Sánchez-Fernández
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain; (J.M.C.-C.); (S.C.-C.); (C.S.-F.); (D.F.)
- Medina Foundation, 18007 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain; (J.M.C.-C.); (S.C.-C.); (C.S.-F.); (D.F.)
- Medina Foundation, 18007 Granada, Spain
| | - Estefanía Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain; (J.M.C.-C.); (S.C.-C.); (C.S.-F.); (D.F.)
- Medina Foundation, 18007 Granada, Spain
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7
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Extracellular Matrix-Based Approaches in Cardiac Regeneration: Challenges and Opportunities. Int J Mol Sci 2022; 23:ijms232415783. [PMID: 36555424 PMCID: PMC9779713 DOI: 10.3390/ijms232415783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiac development is characterized by the active proliferation of different cardiac cell types, in particular cardiomyocytes and endothelial cells, that eventually build the beating heart. In mammals, these cells lose their regenerative potential early after birth, representing a major obstacle to our current capacity to restore the myocardial structure and function after an injury. Increasing evidence indicates that the cardiac extracellular matrix (ECM) actively regulates and orchestrates the proliferation, differentiation, and migration of cardiac cells within the heart, and that any change in either the composition of the ECM or its mechanical properties ultimately affect the behavior of these cells throughout one's life. Thus, understanding the role of ECMs' proteins and related signaling pathways on cardiac cell proliferation is essential to develop effective strategies fostering the regeneration of a damaged heart. This review provides an overview of the components of the ECM and its mechanical properties, whose function in cardiac regeneration has been elucidated, with a major focus on the strengths and weaknesses of the experimental models so far exploited to demonstrate the actual pro-regenerative capacity of the components of the ECM and to translate this knowledge into new therapies.
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Sarohi V, Chakraborty S, Basak T. Exploring the cardiac ECM during fibrosis: A new era with next-gen proteomics. Front Mol Biosci 2022; 9:1030226. [PMID: 36483540 PMCID: PMC9722982 DOI: 10.3389/fmolb.2022.1030226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 10/24/2023] Open
Abstract
Extracellular matrix (ECM) plays a critical role in maintaining elasticity in cardiac tissues. Elasticity is required in the heart for properly pumping blood to the whole body. Dysregulated ECM remodeling causes fibrosis in the cardiac tissues. Cardiac fibrosis leads to stiffness in the heart tissues, resulting in heart failure. During cardiac fibrosis, ECM proteins get excessively deposited in the cardiac tissues. In the ECM, cardiac fibroblast proliferates into myofibroblast upon various kinds of stimulations. Fibroblast activation (myofibroblast) contributes majorly toward cardiac fibrosis. Other than cardiac fibroblasts, cardiomyocytes, epithelial/endothelial cells, and immune system cells can also contribute to cardiac fibrosis. Alteration in the expression of the ECM core and ECM-modifier proteins causes different types of cardiac fibrosis. These different components of ECM culminated into different pathways inducing transdifferentiation of cardiac fibroblast into myofibroblast. In this review, we summarize the role of different ECM components during cardiac fibrosis progression leading to heart failure. Furthermore, we highlight the importance of applying mass-spectrometry-based proteomics to understand the key changes occurring in the ECM during fibrotic progression. Next-gen proteomics studies will broaden the potential to identify key targets to combat cardiac fibrosis in order to achieve precise medicine-development in the future.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Sanchari Chakraborty
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
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Ning T, Ning C, Li S, Mo C, Liu Z, Wang H. Integrative proteomics and phosphoproteomics profiling on osteogenic differentiation of periodontal ligament stem cell. Proteomics 2022; 22:e2200067. [PMID: 36044325 DOI: 10.1002/pmic.202200067] [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: 03/02/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 12/29/2022]
Abstract
This study aims to elucidate the phosphorylated profile of periodontal ligament stem cells (PDLSCs) osteogenic differentiation, which contributes to the promotion of periodontium regeneration. PDLSCs cultured in the osteogenic induction medium for 14 days were analyzed by proteomics and phosphoproteomics. Potential functions of phosphorylated differentially expressed proteins (DEPs) were annotated and enriched based on Gene Ontology (GO). Furtherly, overlapped DEPs were identified and conducted protein-protein interaction (PPI) network united with the top 20 up/downregulated phosphorylated DEPs. Hub phosphorylated DEPs were analyzed by Cytoscape, and the protein kinase phosphorylation network was predicted by iGPS. Proteomics identified 87 upregulated and 227 downregulated DEPs. Phosphoproteomics identified 460 upregulated and 393 downregulated phosphorylated DEPs, and they were primarily enriched in mitochondrial function and ion-channel related terms. Furthermore, 63 overlapped DEPs were recognized for more accurate predictions. Among the top 10 hub phosphorylated DEPs, only Integrin alpha-5 (ITGA5) expressed upregulated phosphorylation, and half of them belonged to extracellular matrix (ECM) proteins. In addition, numerous kinases corresponding to four interactive hub phosphorylated DEPs were predicted, including Collagen alpha-2(I) (COL1A2), Syndecan-1 (SDC1), Fibrillin-1 (FBN1), and ITGA5. Our findings established a basis for further elucidation of the phosphorylation of PDLSCs osteogenic differentiation, and COL1A2/SDC1/ITGA5/FBN1 phosphorylated network may dominate this process.
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Affiliation(s)
- Tingting Ning
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Caiyu Ning
- Forestry and Landscape Architecture College, South China Agricultural University, Guangzhou, Guangdong, China
| | - Siwei Li
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Chuzi Mo
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhao Liu
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - He Wang
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
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