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Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Ramos Y, Rice SJ, Ali SA, Pastrello C, Jurisica I, Thomas Appleton C, Rockel JS, Kapoor M. Three decades of advancements in osteoarthritis research: insights from transcriptomic, proteomic, and metabolomic studies. Osteoarthritis Cartilage 2024; 32:385-397. [PMID: 38049029 DOI: 10.1016/j.joca.2023.11.019] [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: 10/10/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is a complex disease involving contributions from both local joint tissues and systemic sources. Patient characteristics, encompassing sociodemographic and clinical variables, are intricately linked with OA rendering its understanding challenging. Technological advancements have allowed for a comprehensive analysis of transcripts, proteomes and metabolomes in OA tissues/fluids through omic analyses. The objective of this review is to highlight the advancements achieved by omic studies in enhancing our understanding of OA pathogenesis over the last three decades. DESIGN We conducted an extensive literature search focusing on transcriptomics, proteomics and metabolomics within the context of OA. Specifically, we explore how these technologies have identified individual transcripts, proteins, and metabolites, as well as distinctive endotype signatures from various body tissues or fluids of OA patients, including insights at the single-cell level, to advance our understanding of this highly complex disease. RESULTS Omic studies reveal the description of numerous individual molecules and molecular patterns within OA-associated tissues and fluids. This includes the identification of specific cell (sub)types and associated pathways that contribute to disease mechanisms. However, there remains a necessity to further advance these technologies to delineate the spatial organization of cellular subtypes and molecular patterns within OA-afflicted tissues. CONCLUSIONS Leveraging a multi-omics approach that integrates datasets from diverse molecular detection technologies, combined with patients' clinical and sociodemographic features, and molecular and regulatory networks, holds promise for identifying unique patient endophenotypes. This holistic approach can illuminate the heterogeneity among OA patients and, in turn, facilitate the development of tailored therapeutic interventions.
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Affiliation(s)
- Muhammad Farooq Rai
- Department of Anatomy and Cellular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Kelsey H Collins
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Annemarie Lang
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen Geurts
- Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC -Hospital Universitario A Coruña, SERGAS, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - Yolande Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shabana Amanda Ali
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada.
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Zhu Q, Tan M, Wang C, Chen Y, Wang C, Zhang J, Gu Y, Guo Y, Han J, Li L, Jiang R, Fan X, Xie H, Wang L, Gu Z, Liu D, Shi J, Feng X. Single-cell RNA sequencing analysis of the temporomandibular joint condyle in 3 and 4-month-old human embryos. Cell Biosci 2023; 13:130. [PMID: 37468984 DOI: 10.1186/s13578-023-01069-5] [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: 01/11/2023] [Accepted: 06/13/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The temporomandibular joint (TMJ) is a complex joint consisting of the condyle, the temporal articular surface, and the articular disc. Functions such as mastication, swallowing and articulation are accomplished by the movements of the TMJ. To date, the TMJ has been studied more extensively, but the types of TMJ cells, their differentiation, and their interrelationship during growth and development are still unclear and the study of the TMJ is limited. The aim of this study was to establish a molecular cellular atlas of the human embryonic temporomandibular joint condyle (TMJC) by single-cell RNA sequencing, which will contribute to understanding and solving clinical problems. RESULTS Human embryos at 3 and 4 months of age are an important stage of TMJC development. We performed a comprehensive transcriptome analysis of TMJC tissue from human embryos at 3 and 4 months of age using single-cell RNA sequencing. A total of 16,624 cells were captured and the gene expression profiles of 15 cell clusters in human embryonic TMJC were determined, including 14 known cell types and one previously unknown cell type, "transition state cells (TSCs)". Immunofluorescence assays confirmed that TSCs are not the same cell cluster as mesenchymal stem cells (MSCs). Pseudotime trajectory and RNA velocity analysis revealed that MSCs transformed into TSCs, which further differentiated into osteoblasts, hypertrophic chondrocytes and tenocytes. In addition, chondrocytes (CYTL1high + THBS1high) from secondary cartilage were detected only in 4-month-old human embryonic TMJC. CONCLUSIONS Our study provides an atlas of differentiation stages of human embryonic TMJC tissue cells, which will contribute to an in-depth understanding of the pathophysiology of the TMJC tissue repair process and ultimately help to solve clinical problems.
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Affiliation(s)
- Qianqi Zhu
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Miaoying Tan
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Chengniu Wang
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, 226001, China
| | - Yufei Chen
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, 226001, China
| | - Chenfei Wang
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Junqi Zhang
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Yijun Gu
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Yuqi Guo
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Jianpeng Han
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Lei Li
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Rongrong Jiang
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Xudong Fan
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Huimin Xie
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Liang Wang
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China
| | - Zhifeng Gu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China.
| | - Dong Liu
- School of Life Science, Nantong Laboratory of Development and Diseases Second Affiliated Hospital Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
| | - Jianwu Shi
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, 226001, China.
| | - Xingmei Feng
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of, Nantong University, Nantong, 226001, China.
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Rizzo MG, Best TM, Huard J, Philippon M, Hornicek F, Duan Z, Griswold AJ, Kaplan LD, Hare JM, Kouroupis D. Therapeutic Perspectives for Inflammation and Senescence in Osteoarthritis Using Mesenchymal Stem Cells, Mesenchymal Stem Cell-Derived Extracellular Vesicles and Senolytic Agents. Cells 2023; 12:1421. [PMID: 37408255 PMCID: PMC10217382 DOI: 10.3390/cells12101421] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 07/07/2023] Open
Abstract
Osteoarthritis (OA) is the most common cause of disability worldwide among the elderly. Alarmingly, the incidence of OA in individuals less than 40 years of age is rising, likely due to the increase in obesity and post-traumatic osteoarthritis (PTOA). In recent years, due to a better understanding of the underlying pathophysiology of OA, several potential therapeutic approaches targeting specific molecular pathways have been identified. In particular, the role of inflammation and the immune system has been increasingly recognized as important in a variety of musculoskeletal diseases, including OA. Similarly, higher levels of host cellular senescence, characterized by cessation of cell division and the secretion of a senescence-associated secretory phenotype (SASP) within the local tissue microenvironments, have also been linked to OA and its progression. New advances in the field, including stem cell therapies and senolytics, are emerging with the goal of slowing disease progression. Mesenchymal stem/stromal cells (MSCs) are a subset of multipotent adult stem cells that have demonstrated the potential to modulate unchecked inflammation, reverse fibrosis, attenuate pain, and potentially treat patients with OA. Numerous studies have demonstrated the potential of MSC extracellular vesicles (EVs) as cell-free treatments that comply with FDA regulations. EVs, including exosomes and microvesicles, are released by numerous cell types and are increasingly recognized as playing a critical role in cell-cell communication in age-related diseases, including OA. Treatment strategies for OA are being developed that target senescent cells and the paracrine and autocrine secretions of SASP. This article highlights the encouraging potential for MSC or MSC-derived products alone or in combination with senolytics to control patient symptoms and potentially mitigate the progression of OA. We will also explore the application of genomic principles to the study of OA and the potential for the discovery of OA phenotypes that can motivate more precise patient-driven treatments.
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Affiliation(s)
- Michael G. Rizzo
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.G.R.); (T.M.B.)
| | - Thomas M. Best
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.G.R.); (T.M.B.)
| | - Johnny Huard
- Center for Regenerative and Personalized Medicine (CRPM), Steadman Philippon Research Institute, Vail, CO 81657, USA (M.P.)
| | - Marc Philippon
- Center for Regenerative and Personalized Medicine (CRPM), Steadman Philippon Research Institute, Vail, CO 81657, USA (M.P.)
| | - Francis Hornicek
- Department of Orthopedics, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (F.H.); (Z.D.)
| | - Zhenfeng Duan
- Department of Orthopedics, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (F.H.); (Z.D.)
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Lee D. Kaplan
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.G.R.); (T.M.B.)
| | - Joshua M. Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Dimitrios Kouroupis
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.G.R.); (T.M.B.)
- Diabetes Research Institute, Cell Transplant Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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4
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Poulsen RC, Jain L, Dalbeth N. Re-thinking osteoarthritis pathogenesis: what can we learn (and what do we need to unlearn) from mouse models about the mechanisms involved in disease development. Arthritis Res Ther 2023; 25:59. [PMID: 37046337 PMCID: PMC10100340 DOI: 10.1186/s13075-023-03042-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
Efforts to develop effective disease-modifying drugs to treat osteoarthritis have so far proved unsuccessful with a number of promising drug candidates from pre-clinical studies failing to show efficacy in clinical trials. It is therefore timely to re-evaluate our current understanding of osteoarthritis pathogenesis and the similarities and differences in disease development between commonly used pre-clinical mouse models and human patients. There is substantial heterogeneity between patients presenting with osteoarthritis and mounting evidence that the pathways involved in osteoarthritis (e.g. Wnt signalling) differ between patient sub-groups. There is also emerging evidence that the pathways involved in osteoarthritis differ between the STR/ort mouse model (the most extensively studied mouse model of spontaneously occurring osteoarthritis) and injury-induced osteoarthritis mouse models. For instance, while canonical Wnt signalling is upregulated in the synovium and cartilage at an early stage of disease in injury-induced osteoarthritis mouse models, this does not appear to be the case in the STR/ort mouse. Such findings may prove insightful for understanding the heterogeneity in mechanisms involved in osteoarthritis pathogenesis in human disease. However, it is important to recognise that there are differences between mice and humans in osteoarthritis pathogenesis. A much more extensive array of pathological changes are evident in osteoarthritic joints in individual mice with osteoarthritis compared to individual patients. There are also specified differences in the pathways involved in disease development. For instance, although increased TGF-β signalling is implicated in osteoarthritis development in both mouse models of osteoarthritis and human disease, in mice, this is mainly mediated through TGF-β3 whereas in humans, it is through TGF-β1. Studies in other tissues have shown TGF-β1 is more potent than TGF-β3 in inducing the switch to SMAD1/5 signalling that occurs in osteoarthritic cartilage and that TGF-β1 and TGF-β3 have opposing effects on fibrosis. It is therefore possible that the relative contribution of TGF-β signalling to joint pathology in osteoarthritis differs between murine models and humans. Understanding the similarities and differences in osteoarthritis pathogenesis between mouse models and humans is critical for understanding the translational potential of findings from pre-clinical studies.
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Affiliation(s)
- Raewyn C Poulsen
- Department of Pharmacology & Clinical Pharmacology, Faculty of Medical & Health Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
| | - Lekha Jain
- Department of Pharmacology & Clinical Pharmacology, Faculty of Medical & Health Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, Faculty of Medical & Health Sciences, University of Auckland, Auckland, New Zealand
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Pennitz P, Goekeri C, Trimpert J, Wyler E, Ebenig A, Weissfuss C, Mühlebach MD, Witzenrath M, Nouailles G. Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis. STAR Protoc 2023; 4:101957. [PMID: 36542521 PMCID: PMC9765304 DOI: 10.1016/j.xpro.2022.101957] [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: 10/10/2022] [Revised: 11/08/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
In infectious disease research, single-cell RNA sequencing allows dissection of host-pathogen interactions. As a prerequisite, we provide a protocol to transform solid and complex organs such as lungs into representative diverse, viable single-cell suspensions. Our protocol describes performance of vascular perfusion, pneumonectomy, enzymatic digestion, and mechanical dissociation of lung tissue, as well as red blood cell lysis and counting of isolated cells. A challenge remains, however, to further increase the proportion of pulmonary endothelial cells without compromising on viability. For complete details on the use and execution of this protocol, please refer to Nouailles et al. (2021),1 Wyler et al. (2022),2 and Ebenig et al. (2022).3.
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Affiliation(s)
- Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Cyprus International University, Faculty of Medicine, Nicosia, Cyprus.
| | - Jakob Trimpert
- Freie Universität Berlin, Institute of Virology, Berlin, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Aileen Ebenig
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Chantal Weissfuss
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Michael D Mühlebach
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany; German Center for Infection Research (DZIF), Gießen-Marburg-Langen, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.
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Takács R, Póliska S, Juhász T, Barna KB, Matta C. Isolation of High-Quality Total RNA from Small Animal Articular Cartilage for Next-Generation Sequencing. Curr Protoc 2023; 3:e692. [PMID: 36880775 DOI: 10.1002/cpz1.692] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Articular cartilage is characterized by a low density of chondrocytes surrounded by an abundant extracellular matrix (ECM) consisting of a dense mixture of collagens, proteoglycans, and glycosaminoglycans. Due to its low cellularity and high proteoglycan content, it is particularly challenging to extract high-quality total RNA suitable for sensitive high-throughput downstream applications such as RNA sequencing (RNA-Seq). Available protocols for high-quality RNA isolation from articular chondrocytes are inconsistent, resulting in suboptimal yield and compromised quality. This poses a significant difficulty in the application of RNA-Seq to study the cartilage transcriptome. Current protocols rely either on dissociation of cartilage ECM by collagenase digestion or pulverizing cartilage using various methods prior to RNA extraction. However, protocols for cartilage processing vary significantly depending on the species and source of cartilage within the body. Protocols for isolating RNA from human or large mammal (e.g., horse or cattle) cartilage samples are available, but this is not the case for chicken cartilage, despite the species being extensively used in cartilage research. Here, we present two improved RNA isolation protocols based on pulverization of fresh articular cartilage using a cryogenic mill or on enzymatic digestion using 1.2% (w/v) collagenase II. Our protocols optimize the collection and tissue processing steps to minimize RNA degradation and enhance RNA purity. Our results show that RNA purified from chicken articular cartilage using these methods has appropriate quality for RNA-Seq experiments. The procedure is applicable for RNA extraction from cartilage from other species such as dog, cat, sheep, and goat. The workflow for RNA-Seq analysis is also described here. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of total RNA from pulverized chicken articular cartilage Alternate Protocol: Extraction of total RNA from collagen-digested articular cartilage Support Protocol: Dissection of chicken articular cartilage from the knee joint Basic Protocol 2: RNA sequencing of total RNA from chicken articular cartilage.
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Affiliation(s)
- Roland Takács
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Juhász
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztina B Barna
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Csaba Matta
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Swahn H, Li K, Duffy T, Olmer M, D'Lima DD, Mondala TS, Natarajan P, Head SR, Lotz MK. Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. Ann Rheum Dis 2023; 82:403-415. [PMID: 36564153 PMCID: PMC10076001 DOI: 10.1136/ard-2022-223227] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Single-cell level analysis of articular cartilage and meniscus tissues from human healthy and osteoarthritis (OA) knees. METHODS Single-cell RNA sequencing (scRNA-seq) analyses were performed on articular cartilage and meniscus tissues from healthy (n=6, n=7) and OA (n=6, n=6) knees. Expression of genes of interest was validated using immunohistochemistry and RNA-seq and function was analysed by gene overexpression and depletion. RESULTS scRNA-seq analyses of human knee articular cartilage (70 972 cells) and meniscus (78 017 cells) identified a pathogenic subset that is shared between both tissues. This cell population is expanded in OA and has strong OA and senescence gene signatures. Further, this subset has critical roles in extracellular matrix (ECM) and tenascin signalling and is the dominant sender of signals to all other cartilage and meniscus clusters and a receiver of TGFβ signalling. Fibroblast activating protein (FAP) is also a dysregulated gene in this cluster and promotes ECM degradation. Regulons that are controlled by transcription factor ZEB1 are shared between the pathogenic subset in articular cartilage and meniscus. In meniscus and cartilage cells, FAP and ZEB1 promote expression of genes that contribute to OA pathogenesis, including senescence. CONCLUSIONS These single-cell studies identified a senescent pathogenic cell cluster that is present in cartilage and meniscus and has FAP and ZEB1 as main regulators which are novel and promising therapeutic targets for OA-associated pathways in both tissues.
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Affiliation(s)
- Hannah Swahn
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Kun Li
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Tomas Duffy
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Merissa Olmer
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Darryl D D'Lima
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
- Shiley Center for Orthopaedic Research and Education at Scripps Clinic, Scripps Health, La Jolla, California, USA
| | - Tony S Mondala
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Padmaja Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Steven R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Martin K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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Resource: A Cellular Developmental Taxonomy of the Bone Marrow Mesenchymal Stem Cell Population in Mice. Hemasphere 2023; 7:e823. [PMID: 36741354 PMCID: PMC9891453 DOI: 10.1097/hs9.0000000000000823] [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: 07/08/2022] [Accepted: 11/29/2022] [Indexed: 02/03/2023] Open
Abstract
Mesenchymal stem cells (MSCs) play pivotal roles in tissue (re)generation. In the murine bone marrow, they are thought to reside within the Sca-1+ CD51+ bone marrow stromal cell population. Here, using scRNAseq, we aimed to delineate the cellularheterogeneity of this MSC-enriched population throughout development. At the fetal stage, the MSC population is relatively homogeneous with subsets predicted to contain stem/progenitor cells, based on transcriptional modeling and marker expression. These subsets decline in relative size throughout life, with postnatal emergence of specialized clusters, including hematopoietic stem/progenitor cell (HSPC) niches. In fetal development, these stromal HSPC niches are lacking, but subsets of endothelial cells express HSPC factors, suggesting that they may provide initial niches for emerging hematopoiesis. This cellular taxonomy of the MSC population upon development is anticipated to provide a resource aiding the prospective identification of cellular subsets and molecular mechanisms driving bone marrow (re)generation.
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Application of Single-Cell and Spatial Omics in Musculoskeletal Disorder Research. Int J Mol Sci 2023; 24:ijms24032271. [PMID: 36768592 PMCID: PMC9917071 DOI: 10.3390/ijms24032271] [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: 11/30/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Musculoskeletal disorders, including fractures, scoliosis, heterotopic ossification, osteoporosis, osteoarthritis, disc degeneration, and muscular injury, etc., can occur at any stage of human life. Understanding the occurrence and development mechanism of musculoskeletal disorders, as well as the changes in tissues and cells during therapy, might help us find targeted treatment methods. Single-cell techniques provide excellent tools for studying alterations at the cellular level of disorders. However, the application of these techniques in research on musculoskeletal disorders is still limited. This review summarizes the current single-cell and spatial omics used in musculoskeletal disorders. Cell isolation, experimental methods, and feasible experimental designs for single-cell studies of musculoskeletal system diseases have been reviewed based on tissue characteristics. Then, the paper summarizes the latest findings of single-cell studies in musculoskeletal disorders from three aspects: bone and ossification, joint, and muscle and tendon disorders. Recent discoveries about the cell populations involved in these diseases are highlighted. Furthermore, the therapeutic responses of musculoskeletal disorders, especially single-cell changes after the treatments of implants, stem cell therapies, and drugs are described. Finally, the application potential and future development directions of single-cell and spatial omics in research on musculoskeletal diseases are discussed.
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Shen P, Wu P, Maleitzke T, Reisener MJ, Heinz GA, Heinrich F, Durek P, Gwinner C, Winkler T, Pumberger M, Perka C, Mashreghi MF, Löhning M. Optimization of chondrocyte isolation from human articular cartilage to preserve the chondrocyte transcriptome. Front Bioeng Biotechnol 2022; 10:1046127. [DOI: 10.3389/fbioe.2022.1046127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
The isolation of chondrocytes from human articular cartilage for single-cell RNA sequencing requires extensive and prolonged tissue digestion at 37 C. Modulations of the transcriptional activity likely take place during this period such that the transcriptomes of isolated human chondrocytes no longer match their original status in vivo. Here, we optimized the human chondrocyte isolation procedure to maximally preserve the in vivo transcriptome. Cartilage tissues were transferred into a hypoxia chamber (4% O2) immediately after being removed from OA patients and minced finely. Collagenase II at concentrations of 0.02%, 0.1%, 0.25%, 0.5%, 1%, and 2% was applied for 0.5, 1, 2, 4, and 18 h to digest the minced tissue. Actinomycin D (ActD) was added to test its capacity in stabilizing the transcriptome. Cell yield, viability, cell size, and transcriptome were determined using counter chamber, flow cytometry, and RNA sequencing (RNA-seq). Collagenase II at 2% concentration released small chondrocytes from cartilage matrix during the first digestion hour and started to release large cells thereafter, reaching a complete release at 4 h. During 4-h digestions, collagenase II at 2% and 1% but not at lower concentrations yielded maximal release also of the large chondrocyte population. RNA-seq analysis revealed that a 4-h digestion period with 1% or 2% collagenase II plus Actinomycin D optimally preserved the transcriptome. Thus, this study provides an isolation protocol for single chondrocytes from human articular cartilage optimized for transcriptome preservation and RNA-seq analysis.
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Pennitz P, Kirsten H, Friedrich VD, Wyler E, Goekeri C, Obermayer B, Heinz GA, Mashreghi MF, Büttner M, Trimpert J, Landthaler M, Suttorp N, Hocke AC, Hippenstiel S, Tönnies M, Scholz M, Kuebler WM, Witzenrath M, Hoenzke K, Nouailles G. A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics. Eur Respir Rev 2022; 31:31/165/220056. [PMID: 35896273 DOI: 10.1183/16000617.0056-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and recruited cells are essential for maintaining organ functionality. We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus auratus), rat (Rattus norvegicus) and mouse (Mus musculus) by employing RNA velocity and intercellular communication based on ligand-receptor co-expression, among other techniques. Specifically, we demonstrated a workflow for interspecies data integration, applied a single unified gene nomenclature, performed cell-specific clustering and identified marker genes for each species. Overall, integrative approaches combining newly sequenced as well as publicly available datasets could help identify species-specific transcriptomic signatures in both healthy and diseased lung tissue and select appropriate models for future respiratory research.
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Affiliation(s)
- Peter Pennitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Both authors contributed equally to this work
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Both authors contributed equally to this work
| | - Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Gitta A Heinz
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Maren Büttner
- University of Bonn, Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Systems Medicine, Bonn, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institute of Virology, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Humboldt-Universität zu Berlin, Institute for Biology, IRI Life Sciences, Berlin, Germany
| | - Norbert Suttorp
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Andreas C Hocke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Stefan Hippenstiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Mario Tönnies
- HELIOS Clinic Emil von Behring, Department of Pneumology and Department of Thoracic Surgery, Chest Hospital Heckeshorn, Berlin, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Wolfgang M Kuebler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Physiology, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Katja Hoenzke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
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12
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Young D, Barter M, Soul J. Osteoarthritis year in review: genetics, genomics, epigenetics. Osteoarthritis Cartilage 2022; 30:216-225. [PMID: 34774787 PMCID: PMC8811265 DOI: 10.1016/j.joca.2021.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In this review, we have highlighted the advances over the past year in genetics, genomics and epigenetics in the field of osteoarthritis (OA). METHODS A literature search of PubMed was performed using the criteria: "osteoarthritis" and one of the following terms "genetic(s), genomic(s), epigenetic(s), polymorphism, noncoding ribonucleic acid (RNA), microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing (RNA-seq), single cell sequencing, transcriptomics, or deoxyribonucleic acid (DNA) methylation between April 01, 2020 and April 30, 2021. RESULTS In total we identified 765 unique publications, which eventually reduced to 380 of relevance to the field as judged by two assessors. Many of these studies included multiple search terms. We summarised advances relating to genetics, functional genetics, genomics and epigenetics, focusing on our personal key papers during the year. CONCLUSIONS This year few studies have identified new genetic variants contributing to OA susceptibility, but a focus has been on refining risk loci or their functional validation. The use of new technologies together with investigating the cross-talk between multiple tissue types, greater sample sizes and/or better patient classification (OA subtypes) will continue to increase our knowledge of disease mechanisms and progress towards understanding and treating OA.
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Affiliation(s)
- D.A. Young
- Address correspondence and reprint requests to: D.A. Young, Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. Tel.: 44-191-2418831.
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