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Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y(T, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Res 2022; 51:D1519-D1530. [PMID: 36399478 PMCID: PMC9825471 DOI: 10.1093/nar/gkac1009] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based proteomics has become the method of choice to profile the composition of the ECM, or the matrisome, of tissues. To assist non-specialists with the reuse of ECM proteomic datasets, we released MatrisomeDB (https://matrisomedb.org) in 2020. Here, we report the expansion of the database to include 25 new curated studies on the ECM of 24 new tissues in addition to datasets on tissues previously included, more than doubling the size of the original database and achieving near-complete coverage of the in-silico predicted matrisome. We further enhanced data visualization by maps of peptides and post-translational-modifications detected onto domain-based representations and 3D structures of ECM proteins. We also referenced external resources to facilitate the design of targeted mass spectrometry assays. Last, we implemented an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.
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Affiliation(s)
- Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Clarissa D Gomez
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Nandini Kapoor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - James M Considine
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher Grams
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yu (Tom) Gao
- Correspondence may also be addressed to Dr. Yu (Tom) Gao. Tel: +1 312 996 8087;
| | - Alexandra Naba
- To whom correspondence should be addressed. Tel: +1 312 355 5417;
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Georgieva VS, Bluhm B, Probst K, Zhu M, Heilig J, Niehoff A, Brachvogel B. Ablation of the miRNA cluster 24 in cartilage and osteoblasts impairs bone remodeling. Sci Rep 2022; 12:9116. [PMID: 35650319 PMCID: PMC9160244 DOI: 10.1038/s41598-022-13231-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs (miRNAs) post-transcriptionally regulate cartilage and bone development and function, however, only few miRNAs have been described to play a role for cartilage to bone transition in vivo. Previously, we showed that cartilage-specific deletion of the Mirc24 cluster in newborn male mice leads to impaired growth plate cartilage development due to increased RAF/MEK/ERK signaling and affects the stability of the cartilage extracellular matrix on account of decreased SOX6 and SOX9 and increased MMP13 levels. Here, we studied how Mirc24 cluster inactivation in cartilage and osteoblasts leads to an increased bone density associated with defects in collagen remodeling in trabecular bone. No changes in osteoblast distribution were observed, whereas the number of osteoclasts was reduced and TRAP activity in osteoclasts decreased. Surprisingly, an increased level of cluster-encoded miR-322 or miR-503 raises Rankl gene expression and inactivation of the cluster in chondrocytes reduces Rankl expression. These results suggest that the Mirc24 cluster regulates Rankl expression in chondrocytes at the chondro-osseous border, where the cluster is mainly expressed to modulate osteoclast formation, bone remodeling and bone integrity.
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Affiliation(s)
- Veronika S Georgieva
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany.,Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany
| | - Björn Bluhm
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany.,Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany
| | - Kristina Probst
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany.,Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany
| | - Mengjie Zhu
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany.,Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany
| | - Juliane Heilig
- Institute of Biomechanics and Orthopaedics, German Sport University Cologne, 50933, Cologne, Germany.,Cologne Center for Musculoskeletal Biomechanics (CCMB), University of Cologne, 50931, Cologne, Germany
| | - Anja Niehoff
- Institute of Biomechanics and Orthopaedics, German Sport University Cologne, 50933, Cologne, Germany.,Cologne Center for Musculoskeletal Biomechanics (CCMB), University of Cologne, 50931, Cologne, Germany
| | - Bent Brachvogel
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany. .,Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, 50931, Cologne, Germany.
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Zhang J, Hao X, Chi R, Liu J, Shang X, Deng X, Qi J, Xu T. Whole Transcriptome Mapping Identifies an Immune- and Metabolism-Related Non-coding RNA Landscape Remodeled by Mechanical Stress in IL-1β-Induced Rat OA-like Chondrocytes. Front Genet 2022; 13:821508. [PMID: 35309149 PMCID: PMC8927047 DOI: 10.3389/fgene.2022.821508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Osteoarthritis (OA) is a common degenerative joint disease. The aims of this study are to explore the effects of mechanical stress on whole transcriptome landscape and to identify a non-coding transcriptome signature of mechanical stress. Methods: Next-generation RNA sequencing (RNA-seq) was performed on IL-1β-induced OA-like chondrocytes stimulated by mechanical stress. Integrated bioinformatics analysis was performed and further verified by experimental validations. Results: A total of 5,022 differentially expressed mRNAs (DEMs), 88 differentially expressed miRNAs (DEMIs), 1,259 differentially expressed lncRNAs (DELs), and 393 differentially expressed circRNAs (DECs) were identified as the transcriptome response to mechanical stress. The functional annotation of the DEMs revealed the effects of mechanical stress on chondrocyte biology, ranging from cell fate, metabolism, and motility to endocrine, immune response, and signaling transduction. Among the DELs, ∼92.6% were identified as the novel lncRNAs. According to the co-expressing DEMs potentially regulated by the responsive DELs, we found that these DELs were involved in the modification of immune and metabolism. Moreover, immune- and metabolism-relevant DELs exhibited a notable involvement in the competing endogenous RNA (ceRNA) regulation networks. Silencing lncRNA TCONS_00029778 attenuated cellular senescence induced by mechanical stress. Moreover, the expression of Cd80 was elevated by mechanical stress, which was rescued by silencing TCONS_00029778. Conclusion: The transcriptome landscape of IL-1β-induced OA-like chondrocytes was remarkably remodeled by mechanical stress. This study identified an immune- and metabolism-related ncRNA transcriptome signature responsive to mechanical stress and provides an insight of ncRNAs into chondrocyte biology and OA.
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Affiliation(s)
- Jiaming Zhang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxia Hao
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruimin Chi
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiawei Liu
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingru Shang
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaofeng Deng
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Qi
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jun Qi, ; Tao Xu,
| | - Tao Xu
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jun Qi, ; Tao Xu,
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Sox6, A Potential Target for MicroRNAs in Cardiometabolic Disease. Curr Hypertens Rep 2022; 24:145-156. [DOI: 10.1007/s11906-022-01175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/25/2022]
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Bubb K, Holzer T, Nolte JL, Krüger M, Wilson R, Schlötzer-Schrehardt U, Brinckmann J, Altmüller J, Aszodi A, Fleischhauer L, Clausen-Schaumann H, Probst K, Brachvogel B. Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage. J Biol Chem 2021; 297:101224. [PMID: 34560099 PMCID: PMC8503590 DOI: 10.1016/j.jbc.2021.101224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Energy metabolism and extracellular matrix (ECM) function together orchestrate and maintain tissue organization, but crosstalk between these processes is poorly understood. Here, we used single-cell RNA-Seq (scRNA-Seq) analysis to uncover the importance of the mitochondrial respiratory chain for ECM homeostasis in mature cartilage. This tissue produces large amounts of a specialized ECM to promote skeletal growth during development and maintain mobility throughout life. A combined approach of high-resolution scRNA-Seq, mass spectrometry/matrisome analysis, and atomic force microscopy was applied to mutant mice with cartilage-specific inactivation of respiratory chain function. This genetic inhibition in cartilage results in the expansion of a central area of 1-month-old mouse femur head cartilage, showing disorganized chondrocytes and increased deposition of ECM material. scRNA-Seq analysis identified a cell cluster-specific decrease in mitochondrial DNA-encoded respiratory chain genes and a unique regulation of ECM-related genes in nonarticular chondrocytes. These changes were associated with alterations in ECM composition, a shift in collagen/noncollagen protein content, and an increase of collagen crosslinking and ECM stiffness. These results demonstrate that mitochondrial respiratory chain dysfunction is a key factor that can promote ECM integrity and mechanostability in cartilage and presumably also in many other tissues.
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Affiliation(s)
- Kristina Bubb
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Tatjana Holzer
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janica L Nolte
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marcus Krüger
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - Ursula Schlötzer-Schrehardt
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Brinckmann
- Department of Dermatology, Institute of Virology and Cell Biology, University of Lübeck, Lübeck, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Attila Aszodi
- Department for Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Lutz Fleischhauer
- Department for Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany; Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany
| | - Hauke Clausen-Schaumann
- Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany
| | - Kristina Probst
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany.
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