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Yoshimoto M, Sadamori K, Tokumura K, Tanaka Y, Fukasawa K, Hinoi E. Bioinformatic analysis reveals potential relationship between chondrocyte senescence and protein glycosylation in osteoarthritis pathogenesis. Front Endocrinol (Lausanne) 2023; 14:1153689. [PMID: 37265706 PMCID: PMC10229820 DOI: 10.3389/fendo.2023.1153689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/04/2023] [Indexed: 06/03/2023] Open
Abstract
Osteoarthritis (OA) is the most common degenerative and progressive joint disease. Cellular senescence is an irreversible cell cycle arrest progressive with age, while protein glycosylation is the most abundant post-translational modification, regulating various cellular and biological pathways. The implication of either chondrocyte senescence or protein glycosylation in the OA pathogenesis has been extensively and individually studied. In this study, we aimed to investigate the possible relationship between chondrocyte senescence and protein glycosylation on the pathogenesis of OA using single-cell RNA sequencing datasets of clinical OA specimens deposited in the Gene Expression Omnibus database with a different cohort. We demonstrated that both cellular senescence signal and protein glycosylation pathways in chondrocytes are validly associated with OA pathogenesis. In addition, the cellular senescence signal is well-connected to the O-linked glycosylation pathway in OA chondrocyte and vice-versa. The expression levels of the polypeptide N-acetylgalactosaminyltransferase (GALNT) family, which is essential for the biosynthesis of O-Glycans at the early stage, are highly upregulated in OA chondrocytes. Moreover, the expression levels of the GALNT family are prominently associated with chondrocyte senescence as well as pathological features of OA. Collectively, these findings uncover a crucial relationship between chondrocyte senescence and O-linked glycosylation on the OA pathophysiology, thereby revealing a potential target for OA.
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Affiliation(s)
- Makoto Yoshimoto
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Koki Sadamori
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Kazuya Tokumura
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Yuki Tanaka
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Kazuya Fukasawa
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Eiichi Hinoi
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
- Center for One Medicine Innovative Translational Research, Division of Innovative Modality Development, Gifu University, Gifu, Japan
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Richard D, Pregizer S, Venkatasubramanian D, Raftery RM, Muthuirulan P, Liu Z, Capellini TD, Craft AM. Lineage-specific differences and regulatory networks governing human chondrocyte development. eLife 2023; 12:e79925. [PMID: 36920035 PMCID: PMC10069868 DOI: 10.7554/elife.79925] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (TFs) (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages and sheds new light on human cartilage development and biology.
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Affiliation(s)
- Daniel Richard
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Steven Pregizer
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
| | - Divya Venkatasubramanian
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Rosanne M Raftery
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
| | | | - Zun Liu
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Terence D Capellini
- Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - April M Craft
- Department of Orthopedic Research, Boston Children’s HospitalBostonUnited States
- Department of Orthopedic Surgery, Harvard Medical SchoolBostonUnited States
- Harvard Stem Cell InstituteCambridgeUnited States
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Gomez-Picos P, Ovens K, Eames BF. Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation. Front Cell Dev Biol 2022; 10:876825. [PMID: 35784462 PMCID: PMC9247276 DOI: 10.3389/fcell.2022.876825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
To explain how cartilage appeared in different parts of the vertebrate body at discrete times during evolution, we hypothesize that different embryonic populations co-opted expression of a core gene regulatory network (GRN) driving chondrocyte differentiation. To test this hypothesis, laser-capture microdissection coupled with RNA-seq was used to reveal chondrocyte transcriptomes in the developing chick humerus and ceratobranchial, which are mesoderm- and neural crest-derived, respectively. During endochondral ossification, two general types of chondrocytes differentiate. Immature chondrocytes (IMM) represent the early stages of cartilage differentiation, while mature chondrocytes (MAT) undergo additional stages of differentiation, including hypertrophy and stimulating matrix mineralization and degradation. Venn diagram analyses generally revealed a high degree of conservation between chondrocyte transcriptomes of the limb and head, including SOX9, COL2A1, and ACAN expression. Typical maturation genes, such as COL10A1, IBSP, and SPP1, were upregulated in MAT compared to IMM in both limb and head chondrocytes. Gene co-expression network (GCN) analyses of limb and head chondrocyte transcriptomes estimated the core GRN governing cartilage differentiation. Two discrete portions of the GCN contained genes that were differentially expressed in limb or head chondrocytes, but these genes were enriched for biological processes related to limb/forelimb morphogenesis or neural crest-dependent processes, respectively, perhaps simply reflecting the embryonic origin of the cells. A core GRN driving cartilage differentiation in limb and head was revealed that included typical chondrocyte differentiation and maturation markers, as well as putative novel “chondrocyte” genes. Conservation of a core transcriptional program during chondrocyte differentiation in both the limb and head suggest that the same core GRN was co-opted when cartilage appeared in different regions of the skeleton during vertebrate evolution.
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Affiliation(s)
- Patsy Gomez-Picos
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Katie Ovens
- Department of Computer Science, University of Calgary, Calgary, AB, Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: B. Frank Eames,
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Zhang X, McFarland TJ, Vartanian K, Zhu Y, Harrington CA, Chu CQ. RNA isolation from micro-quantity of articular cartilage for quantitative gene expression by microarray analysis. Int J Med Sci 2022; 19:98-104. [PMID: 34975303 PMCID: PMC8692110 DOI: 10.7150/ijms.65343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Isolation of quality RNA from articular cartilage has been challenging due to low cellularity and the high abundance of extracellular matrix and proteoglycan proteins. Recently developed methods for isolation of high quality RNA from cartilage are more applicable to larger cartilage specimens typically weighing at least 25 mg. While these methods generate RNA suitable for analysis, they are less successful with smaller tissue inputs. For the study of small focal defect cartilage specimens an improved RNA extraction method is needed. Here we report a protocol for direct RNA isolation from less than 3 mg of wet weight rabbit articular cartilage for quantitative microarray gene profiling. This protocol is useful for identifying differentially expressed genes in chondrocytes following focal cartilage repair and can potentially be adopted for gene expression analysis of cartilage biopsy specimens from human joints.
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Affiliation(s)
- Xiaowei Zhang
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, Oregon 97239
- Section of Rheumatology, VA Portland Health Care System, Portland, Oregon 97239
| | - Trevor J. McFarland
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
| | - Kristina Vartanian
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
| | - Yong Zhu
- Vivoscript, Inc, P. O. Box 63025, Irvine, CA 92602
| | - Christina A. Harrington
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
- Department of Molecular and Medical Genetics, Oregon Health & Science University; Portland, Oregon 97239
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, Oregon 97239
- Section of Rheumatology, VA Portland Health Care System, Portland, Oregon 97239
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Back to basics: Transcriptomics studies for deep phenotyping of osteoarthritis. OSTEOARTHRITIS AND CARTILAGE OPEN 2021; 3:100166. [DOI: 10.1016/j.ocarto.2021.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
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Attur M, Duan X, Cai L, Han T, Zhang W, Tycksen ED, Samuels J, Brophy RH, Abramson SB, Rai MF. Periostin loss-of-function protects mice from post-traumatic and age-related osteoarthritis. Arthritis Res Ther 2021; 23:104. [PMID: 33832532 PMCID: PMC8028178 DOI: 10.1186/s13075-021-02477-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background Elevated levels of periostin (Postn) in the cartilage and bone are associated with osteoarthritis (OA). However, it remains unknown whether Postn loss-of-function can delay or prevent the development of OA. In this study, we sought to better understand the role of Postn in OA development and assessed the functional impact of Postn deficiency on post-traumatic and age-related OA in mice. Methods The effects of Postn deficiency were studied in two murine experimental OA models using Postn−/− (n = 32) and littermate wild-type (wt) mice (n = 36). Post-traumatic OA was induced by destabilization of the medial meniscus (DMM) in 10-week-old mice (n = 20); age-related OA was analyzed in 24-month-old mice (n = 13). Cartilage degeneration was assessed histologically using the OARSI scoring system, and synovitis was evaluated by measuring the synovial lining cell layer and the cells density in the synovial stroma. Bone changes were measured by μCT analysis. Serum levels of Postn were determined by ELISA. Expression of Postn and collagenase-3 (MMP-13) was measured by immunostaining. RNA-seq was performed on chondrocytes isolated from 21-day old Postn−/− (n = 3) and wt mice (n = 3) to discover genes and pathways altered by Postn knockout. Results Postn−/− mice exhibited significantly reduced cartilage degeneration and OARSI score relative to wt mice in post-traumatic OA after 8 weeks (maximum: 2.37 ± 0.74 vs. 4.00 ± 1.20, P = 0.011; summed: 9.31 ± 2.52 vs. 21.44 ± 6.01, P = 0.0002) and spontaneous OA (maximum: 1.93 ± 0.45 vs. 3.58 ± 1.16, P = 0.014; summed: 6.14 ± 1.57 vs. 11.50 ± 3.02, P = 0.003). Synovitis was significantly lower in Postn−/− mice than wt only in the DMM model (1.88 ± 1.01 vs. 3.17 ± 0.63; P = 0.039). Postn−/− mice also showed lower trabecular bone parameters such as BV/TV, vBMD, Tb.Th, and Tb.N and high Tb. Sp in both models. Postn−/− mice had negligible levels of serum Postn compared with wt. Immunofluorescent studies of cartilage indicated that Postn−/− mice expressed lower MMP-13 levels than wt mice. RNA-seq revealed that cell-cell-adhesion and cell-differentiation processes were enriched in Postn−/− mice, while those related to cell-cycle and DNA-repair were enriched in wt mice. Conclusions Postn deficiency protects against DMM-induced post-traumatic and age-related spontaneous OA. RNA-seq findings warrant further investigations to better understand the mechanistic role of Postn and its potential as a therapeutic target in OA. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02477-z.
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Affiliation(s)
- Mukundan Attur
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, Langone Orthopedic Hospital, 550 1st Avenue, New York, NY, 10016, USA.
| | - Xin Duan
- Department of Orthopaedic Surgery, Washington University School of Medicine at Barnes-Jewish Hospital MS 8233, 425 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Lei Cai
- Department of Orthopaedic Surgery, Washington University School of Medicine at Barnes-Jewish Hospital MS 8233, 425 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Tianzhen Han
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, Langone Orthopedic Hospital, 550 1st Avenue, New York, NY, 10016, USA.,Present address: Bluestone Center for Clinical Research, NYU College of Dentistry, New York, NY, 10010, USA
| | - Weili Zhang
- Department of Orthopaedic Surgery, Washington University School of Medicine at Barnes-Jewish Hospital MS 8233, 425 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Eric D Tycksen
- Genome Technology Access Center, McDonell Genome Institute, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Jonathan Samuels
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, Langone Orthopedic Hospital, 550 1st Avenue, New York, NY, 10016, USA
| | - Robert H Brophy
- Department of Orthopaedic Surgery, Washington University School of Medicine at Barnes-Jewish Hospital MS 8233, 425 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Steven B Abramson
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, Langone Orthopedic Hospital, 550 1st Avenue, New York, NY, 10016, USA
| | - Muhammad Farooq Rai
- Department of Orthopaedic Surgery, Washington University School of Medicine at Barnes-Jewish Hospital MS 8233, 425 South Euclid Avenue, St. Louis, MO, 63110, USA. .,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, 63110, MO, USA.
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Ratneswaran A, Kapoor M. Osteoarthritis year in review: genetics, genomics, epigenetics. Osteoarthritis Cartilage 2021; 29:151-160. [PMID: 33227439 DOI: 10.1016/j.joca.2020.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In this review, we have highlighted advances in genetics, genomics and epigenetics in the field of osteoarthritis (OA) over the past year. METHODS A literature search was performed using PubMed and the criteria: "osteoarthritis" and one of the following terms "genetic(s), genomic(s), epigenetic(s), epigenomic(s), noncoding RNA, microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing, single cell sequencing, or DNA methylation between April 1, 2019 and April 30, 2020. RESULTS We identified 653 unique publications, many studies spanned multiple search terms. We summarized advances relating to evolutionary genetics, pain, ethnicity specific risk factors, functional studies of gene variants, and interactions between coding and non-coding RNAs in OA pathogenesis. CONCLUSIONS Studies have identified variants contributing to OA susceptibility, candidate biomarkers for diagnosis and prognosis, as well as promising therapeutic candidates. Validation in multiple cohorts, multi-omics strategies, and machine learning aided computational analyses have all contributed to the strength of published literature. Open access data-sets, greater sample sizes to capture broader populations and understanding disease mechanisms by investigating the interactions between multiple tissue types will further aid in progress towards understanding and curing OA.
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Affiliation(s)
- A Ratneswaran
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada; Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - M Kapoor
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada; Krembil Research Institute, University Health Network, Toronto, ON, Canada; Department of Surgery, Faculty of Medicine, University of Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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