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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [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: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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Ma J, Subramaniam P, Yancey JR, Farrington AA, McGlade EC, Renshaw PF, Yurgelun-Todd DA. Elevated circulating soluble interleukin-2 receptor (sCD25) level is associated with prefrontal excitatory-inhibitory imbalance in individuals with chronic pain: A proton MRS study. Brain Behav Immun 2024; 120:1-9. [PMID: 38772429 PMCID: PMC11269041 DOI: 10.1016/j.bbi.2024.05.020] [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: 12/02/2023] [Revised: 04/29/2024] [Accepted: 05/18/2024] [Indexed: 05/23/2024] Open
Abstract
Aberrant neuronal excitability in the anterior cingulate cortex (ACC) is implicated in cognitive and affective pain processing. Such excitability may be amplified by activated circulating immune cells, including T lymphocytes, that interact with the central nervous system. Here, we conducted a study of individuals with chronic pain using magnetic resonance spectroscopy (MRS) to investigate the clinical evidence for the interaction between peripheral immune activation and prefrontal excitatory-inhibitory imbalance. In thirty individuals with chronic musculoskeletal pain, we assessed markers of peripheral immune activation, including soluble interleukin-2 receptor alpha chain (sCD25) levels, as well as brain metabolites, including Glx (glutamate + glutamine) to GABA+ (γ-aminobutyric acid + macromolecules/homocarnosine) ratio in the ACC. We found that the circulating level of sCD25 was associated with prefrontal Glx/GABA+. Greater prefrontal Glx/GABA+ was associated with higher pain catastrophizing, evaluative pain ratings, and anxiodepressive symptoms. Further, the interaction effect of sCD25 and prefrontal Glx/GABA+ on pain catastrophizing was significant, indicating the joint association of these two markers with pain catastrophizing. Our results provide the first evidence suggesting that peripheral T cellular activation, as reflected by elevated circulating sCD25 levels, may be linked to prefrontal excitatory-inhibitory imbalance in individuals with chronic pain. The interaction between these two systems may play a role as a potential mechanism underlying pain catastrophizing. Further prospective and treatment studies are needed to elucidate the specific role of the immune and brain interaction in pain catastrophizing.
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Affiliation(s)
- Jiyoung Ma
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Punitha Subramaniam
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - James R Yancey
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA; George E. Wahlen Department of Veterans Affairs Medical Center, VISN 19 Mental Illness Research, Education and Clinical Center, Salt Lake City, UT, USA
| | - Amy A Farrington
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Erin C McGlade
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA; George E. Wahlen Department of Veterans Affairs Medical Center, VISN 19 Mental Illness Research, Education and Clinical Center, Salt Lake City, UT, USA
| | - Perry F Renshaw
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA; George E. Wahlen Department of Veterans Affairs Medical Center, VISN 19 Mental Illness Research, Education and Clinical Center, Salt Lake City, UT, USA
| | - Deborah A Yurgelun-Todd
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA; Diagnostic Neuroimaging Laboratory, Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA; George E. Wahlen Department of Veterans Affairs Medical Center, VISN 19 Mental Illness Research, Education and Clinical Center, Salt Lake City, UT, USA.
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3
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Xiong HY, Wyns A, Campenhout JV, Hendrix J, De Bruyne E, Godderis L, Schabrun S, Nijs J, Polli A. Epigenetic Landscapes of Pain: DNA Methylation Dynamics in Chronic Pain. Int J Mol Sci 2024; 25:8324. [PMID: 39125894 PMCID: PMC11312850 DOI: 10.3390/ijms25158324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Chronic pain is a prevalent condition with a multifaceted pathogenesis, where epigenetic modifications, particularly DNA methylation, might play an important role. This review delves into the intricate mechanisms by which DNA methylation and demethylation regulate genes associated with nociception and pain perception in nociceptive pathways. We explore the dynamic nature of these epigenetic processes, mediated by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) enzymes, which modulate the expression of pro- and anti-nociceptive genes. Aberrant DNA methylation profiles have been observed in patients with various chronic pain syndromes, correlating with hypersensitivity to painful stimuli, neuronal hyperexcitability, and inflammatory responses. Genome-wide analyses shed light on differentially methylated regions and genes that could serve as potential biomarkers for chronic pain in the epigenetic landscape. The transition from acute to chronic pain is marked by rapid DNA methylation reprogramming, suggesting its potential role in pain chronicity. This review highlights the importance of understanding the temporal dynamics of DNA methylation during this transition to develop targeted therapeutic interventions. Reversing pathological DNA methylation patterns through epigenetic therapies emerges as a promising strategy for pain management.
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Affiliation(s)
- Huan-Yu Xiong
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Arne Wyns
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Jente Van Campenhout
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
| | - Jolien Hendrix
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
- Research Foundation—Flanders (FWO), 1000 Brussels, Belgium
| | - Elke De Bruyne
- Translational Oncology Research Center (TORC), Team Hematology and Immunology (HEIM), Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
| | - Siobhan Schabrun
- The School of Physical Therapy, University of Western Ontario, London, ON N6A 3K7, Canada;
- The Gray Centre for Mobility and Activity, Parkwood Institute, St. Joseph’s Healthcare, London, ON N6A 4V2, Canada
| | - Jo Nijs
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Chronic Pain Rehabilitation, Department of Physical Medicine and Physiotherapy, University Hospital Brussels, 1090 Brussels, Belgium
- Department of Health and Rehabilitation, Unit of Physiotherapy, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 41390 Göterbog, Sweden
| | - Andrea Polli
- Pain in Motion Research Group (PAIN), Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (H.-Y.X.); (A.W.); (J.V.C.); (J.H.); (A.P.)
- Department of Public Health and Primary Care, Centre for Environment & Health, KU Leuven, 3000 Leuven, Belgium;
- Research Foundation—Flanders (FWO), 1000 Brussels, Belgium
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Ramos YFM, Rice SJ, Ali SA, Pastrello C, Jurisica I, Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Thomas Appleton C, Rockel JS, Kapoor M. Evolution and advancements in genomics and epigenomics in OA research: How far we have come. Osteoarthritis Cartilage 2024; 32:858-868. [PMID: 38428513 DOI: 10.1016/j.joca.2024.02.656] [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: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most prevalent musculoskeletal disease affecting articulating joint tissues, resulting in local and systemic changes that contribute to increased pain and reduced function. Diverse technological advancements have culminated in the advent of high throughput "omic" technologies, enabling identification of comprehensive changes in molecular mediators associated with the disease. Amongst these technologies, genomics and epigenomics - including methylomics and miRNomics, have emerged as important tools to aid our biological understanding of disease. DESIGN In this narrative review, we selected articles discussing advancements and applications of these technologies to OA biology and pathology. We discuss how genomics, deoxyribonucleic acid (DNA) methylomics, and miRNomics have uncovered disease-related molecular markers in the local and systemic tissues or fluids of OA patients. RESULTS Genomics investigations into the genetic links of OA, including using genome-wide association studies, have evolved to identify 100+ genetic susceptibility markers of OA. Epigenomic investigations of gene methylation status have identified the importance of methylation to OA-related catabolic gene expression. Furthermore, miRNomic studies have identified key microRNA signatures in various tissues and fluids related to OA disease. CONCLUSIONS Sharing of standardized, well-annotated omic datasets in curated repositories will be key to enhancing statistical power to detect smaller and targetable changes in the biological signatures underlying OA pathogenesis. Additionally, continued technological developments and analysis methods, including using computational molecular and regulatory networks, are likely to facilitate improved detection of disease-relevant targets, in-turn, supporting precision medicine approaches and new treatment strategies for OA.
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Affiliation(s)
- Yolande F M Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sarah J Rice
- Biosciences Institute, International Centre for Life, 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, Ontario, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad Farooq Rai
- Department of Biological Sciences, Center for Biotechnology, College of Medicine & Health Sciences, Khalifa University, 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, A Coruña, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.
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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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Waheed A, Rai MF. Osteoarthritis year in review 2023: genetics, genomics, and epigenetics. Osteoarthritis Cartilage 2024; 32:128-137. [PMID: 37979669 DOI: 10.1016/j.joca.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
OBJECTIVE To elucidate the scientific advances made in the last 12 months within the realm of osteoarthritis genetics, genomics, and epigenetics. This review paper highlights major research publications that enhance our current understanding of the role of genetics, genomics, and epigenetics in osteoarthritis. METHODS A systematic literature search was conducted on pubmed.ncbi.nlm.nih.gov on "March 17, 2023", using the following keywords: "osteoarthritis" in combination with any of these terms: "genetic(s)", "mutation(s)", "genomic(s)", "epigenetic(s)", "DNA methylation", "noncoding RNA", "lncRNA", "circular RNA", "microRNA", "transcriptomic(s)", "RNA sequencing", "single cell RNA sequencing", or "single nucleus RNA sequencing". The selection comprised original research articles published in the English language between the OARSI congresses of 2022 and 2023. RESULTS A total of 2178 research articles were identified, which subsequently reduced to 67 unique articles relevant to the field. Current trends in osteoarthritis genetics research involve meta-analyses of various cohorts to explore the impact of gene variants on osteoarthritis-related outcomes, such as pain. Early developmental changes within the joint were also found to influence osteoarthritis through genetic variations. Researchers also prioritize testing the mechanisms and functions of miRNAs, circRNAs, and lncRNAs. Potential drug targets began to emerge; however, independent validation studies are lacking. Single cell RNA sequencing studies revealed unique immune cell populations in the knee; however, no study reported single nucleus RNA sequencing analysis. CONCLUSIONS This review focused on recent advances in the above-mentioned themes within the field of osteoarthritis. These advances improve our understanding of the disease's complexity and guide us toward functional assessments of genetic/epigenetic outcomes and toward their translational and clinical applications.
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Affiliation(s)
- Amina Waheed
- Department of Biology, University of Wisconsin-Madison, Madison, WI, United States
| | - Muhammad Farooq Rai
- Department of Anatomy and Cellular Biology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates; Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States; Department of Biomedical Engineering, Saint Louis University School of Science and Engineering, St. Louis, MO, United States.
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