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Roberts JB, Rice SJ. Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease. Curr Rheumatol Rep 2024; 26:222-234. [PMID: 38430365 PMCID: PMC11116181 DOI: 10.1007/s11926-024-01142-z] [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] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE OF REVIEW Osteoarthritis is a complex and highly polygenic disease. Over 100 reported osteoarthritis risk variants fall in non-coding regions of the genome, ostensibly conferring functional effects through the disruption of regulatory elements impacting target gene expression. In this review, we summarise the progress that has advanced our knowledge of gene enhancers both within the field of osteoarthritis and more broadly in complex diseases. RECENT FINDINGS Advances in technologies such as ATAC-seq have facilitated our understanding of chromatin states in specific cell types, bolstering the interpretation of GWAS and the identification of effector genes. Their application to osteoarthritis research has revealed enhancers as the principal regulatory element driving disease-associated changes in gene expression. However, tissue-specific effects in gene regulatory mechanisms can contribute added complexity to biological interpretation. Understanding gene enhancers and their altered activity in specific cell and tissue types is the key to unlocking the genetic complexity of osteoarthritis. The use of single-cell technologies in osteoarthritis research is still in its infancy. However, such tools offer great promise in improving our functional interpretation of osteoarthritis GWAS and the identification of druggable targets. Large-scale collaborative efforts will be imperative to understand tissue and cell-type specific molecular mechanisms underlying enhancer function in disease.
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Affiliation(s)
- Jack B Roberts
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Sarah J Rice
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK.
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2
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Hollander JM, Goraltchouk A, Rawal M, Liu J, Luppino F, Zeng L, Seregin A. Adeno-Associated Virus-Delivered Fibroblast Growth Factor 18 Gene Therapy Promotes Cartilage Anabolism. Cartilage 2023; 14:492-505. [PMID: 36879540 PMCID: PMC10807742 DOI: 10.1177/19476035231158774] [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: 10/28/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE To determine the characterization of chondrogenic properties of adeno-associated virus type 2 (AAV2)-delivered hFGF18, via analysis of effects on primary human chondrocyte proliferation, gene expression, and in vivo cartilage thickness changes in the tibia and meniscus. DESIGN Chondrogenic properties of AAV2-FGF18 were compared with recombinant human FGF18 (rhFGF18) in vitro relative to phosphate-buffered saline (PBS) and AAV2-GFP negative controls. Transcriptome analysis was performed using RNA-seq on primary human chondrocytes treated with rhFGF18 and AAV2-FGF18, relative to PBS. Durability of gene expression was assessed using AAV2-nLuc and in vivo imaging. Chondrogenesis was evaluated by measuring weight-normalized thickness in the tibial plateau and the white zone of the anterior horn of the medial meniscus in Sprague-Dawley rats. RESULTS AAV2-FGF18 elicits chondrogenesis by promoting proliferation and upregulation of hyaline cartilage-associated genes, including COL2A1 and HAS2, while downregulating fibrocartilage-associated COL1A1. This activity translates to statistically significant, dose-dependent increases in cartilage thickness in vivo within the area of the tibial plateau, following a single intra-articular injection of the AAV2-FGF18 or a regimen of 6 twice-weekly injections of rhFGF18 protein relative to AAV2-GFP. In addition, we observed AAV2-FGF18-induced and rhFGF18-induced increases in cartilage thickness of the anterior horn of the medial meniscus. Finally, the single-injection AAV2-delivered hFGF18 offers a potential safety advantage over the multi-injection protein treatment as evidenced by reduced joint swelling over the study period. CONCLUSION AAV2-delivered hFGF18 represents a promising strategy for the restoration of hyaline cartilage by promoting extracellular matrix production, chondrocyte proliferation, and increasing articular and meniscal cartilage thickness in vivo after a single intra-articular injection.
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Affiliation(s)
- Judith M. Hollander
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | | | - Miraj Rawal
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | - Jingshu Liu
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | | | - Li Zeng
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
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Winstanley-Zarach P, Rot G, Kuba S, Smagul A, Peffers MJ, Tew SR. Analysis of RNA Polyadenylation in Healthy and Osteoarthritic Human Articular Cartilage. Int J Mol Sci 2023; 24:6611. [PMID: 37047586 PMCID: PMC10094766 DOI: 10.3390/ijms24076611] [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: 01/13/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Polyadenylation (polyA) defines the 3' boundary of a transcript's genetic information. Its position can vary and alternative polyadenylation (APA) transcripts can exist for a gene. This causes variance in 3' regulatory domains and can affect coding sequence if intronic events occur. The distribution of polyA sites on articular chondrocyte transcripts has not been studied so we aimed to define their transcriptome-wide location in age-matched healthy and osteoarthritic knee articular cartilage. Total RNA was isolated from frozen tissue samples and analysed using the QuantSeq-Reverse 3' RNA sequencing approach, where each read runs 3' to 5' from within the polyA tail into the transcript and contains a distinct polyA site. Differential expression of transcripts was significant altered between healthy and osteoarthritic samples with enrichment for functionalities that were strongly associated with joint pathology. Subsequent examination of polyA site data allowed us to define the extent of site usage across all the samples. When comparing healthy and osteoarthritic samples, we found that differential use of polyadenylation sites was modest. However, in the genes affected, there was potential for the APA to have functional relevance. We have characterised the polyadenylation landscape of human knee articular chondrocytes and conclude that osteoarthritis does not elicit a widespread change in their polyadenylation site usage. This finding differentiates knee osteoarthritis from pathologies such as cancer where APA is more commonly observed.
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Affiliation(s)
- Phaedra Winstanley-Zarach
- Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Gregor Rot
- Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Shweta Kuba
- Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
- School of Health and Life Sciences, National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Aibek Smagul
- Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Mandy J. Peffers
- Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Simon R. Tew
- Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
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Li Y, Liu Q, Ma Q, Ma Z, Chen J, Yu A, Ma C, Qiu L, Shi H, Liang H, Hu M. Identification of key variants correlated with susceptibility of primary osteoporosis in the Chinese Han group. Ann Hum Genet 2023; 87:63-74. [PMID: 36479902 DOI: 10.1111/ahg.12490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Primary osteoporosis is a systemic skeletal disease characterized by reduced bone mass and vulnerability to fractures. The genetics of osteoporosis in the Chinese population remain unclear, which hinders the prevention and treatment of osteoporosis in China. This study aimed to explore the susceptibility genes and the roles played by their variants in osteoporosis. METHODS Blood samples were collected from 45 osteoporosis patients and 30 healthy individuals, and genome-wide association study was performed on array data. The expression levels of the candidate gene in different genotypes were further determined by using quantitative real-time PCR. Moreover, the differentiation capacity of bone marrow mesenchymal stem cells under different genotypes from osteoporosis patients was investigated. RESULTS The most significant variant rs1891632 located in the upstream (918 bp) region of CRB2, which could down-regulate the expression levels of CRB2 in genotype-tissue expression database and played an essential role in the regulation of osteoblastic and osteoclastic differentiation during skeletal development. Another significant variant rs1061657 located within the 3'UTR region of TBX3 gene. We found that the mRNA levels of TBX3 decreased in the bMSCs of old osteoporosis patients. Interestingly, osteoblast differentiation capacity and TBX3 mRNA levels were similar between the young healthy individuals carrying derived and ancestral allele of rs1061657, whereas the differentiation capacity and TBX3 mRNA levels dramatically declined in elderly patients with osteoporosis. CONCLUSIONS The variant rs1061657 might affect the osteogenesis of bMSCs in an age-dependent manner and that TBX3 may be a key susceptibility gene for primary osteoporosis. In conclusion, CRB2 and TBX3 may influence the development of osteoporosis; additionally, rs1891632 and rs1061657, as the key variants first reported to be associated with primary osteoporosis, may potentially contribute to predicting the risk of osteoporosis (especially for older individuals) and may serve as therapeutic targets.
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Affiliation(s)
- Yanjiao Li
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Qi Liu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Qiuye Ma
- Orthopedics, Chongqing Jiulongpo District Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Zhaoxia Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Juan Chen
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - An Yu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Changguo Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Lihua Qiu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Hongsuo Liang
- Joint Surgery Department of the Second People's Hospital of Nanning City, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Min Hu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
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Lafont JE, Moustaghfir S, Durand AL, Mallein-Gerin F. The epigenetic players and the chromatin marks involved in the articular cartilage during osteoarthritis. Front Physiol 2023; 14:1070241. [PMID: 36733912 PMCID: PMC9887161 DOI: 10.3389/fphys.2023.1070241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Epigenetics defines the modifications of the genome that do not involve a change in the nucleotide sequence of DNA. These modifications constitute a mechanism of gene regulation poorly explored in the context of cartilage physiology. They are now intensively studied by the scientific community working on articular cartilage and its related pathology such as osteoarthritis. Indeed, epigenetic regulations can control the expression of crucial gene in the chondrocytes, the only resident cells of cartilage. Some epigenetic changes are considered as a possible cause of the abnormal gene expression and the subsequent alteration of the chondrocyte phenotype (hypertrophy, proliferation, senescence…) as observed in osteoarthritic cartilage. Osteoarthritis is a joint pathology, which results in impaired extracellular matrix homeostasis and leads ultimately to the progressive destruction of cartilage. To date, there is no pharmacological treatment and the exact causes have yet to be defined. Given that the epigenetic modifying enzymes can be controlled by pharmacological inhibitors, it is thus crucial to describe the epigenetic marks that enable the normal expression of extracellular matrix encoding genes, and those associated with the abnormal gene expression such as degradative enzyme or inflammatory cytokines encoding genes. In this review, only the DNA methylation and histone modifications will be detailed with regard to normal and osteoarthritic cartilage. Although frequently referred as epigenetic mechanisms, the regulatory mechanisms involving microRNAs will not be discussed. Altogether, this review will show how this nascent field influences our understanding of the pathogenesis of OA in terms of diagnosis and how controlling the epigenetic marks can help defining epigenetic therapies.
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Izda V, Dunn CM, Prinz E, Schlupp L, Nguyen E, Sturdy C, Jeffries MA. A Pilot Analysis of Genome-Wide DNA Methylation Patterns in Mouse Cartilage Reveals Overlapping Epigenetic Signatures of Aging and Osteoarthritis. ACR Open Rheumatol 2022; 4:1004-1012. [PMID: 36253145 PMCID: PMC9746664 DOI: 10.1002/acr2.11506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/25/2022] [Accepted: 09/25/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Cartilage epigenetic changes are strongly associated with human osteoarthritis (OA). However, the influence of individual environmental OA risk factors on these epigenetic patterns has not been determined; herein we characterize cartilage DNA methylation patterns associated with aging and OA in a mouse model. METHODS Murine knee cartilage DNA was extracted from healthy young (16-week, n = 6), old (82-week, n = 6), and young 4-week post-destabilization of the medial meniscus (DMM) OA (n = 6) C57BL6/J mice. Genome-wide DNA methylation patterns were determined via Illumina BeadChip. Gene set enrichment analysis was performed by Ingenuity Pathway Analysis. The top seven most differentially methylated positions (DMPs) were confirmed by pyrosequencing in an independent animal set. Results were compared to previously published human OA methylation data. RESULTS Aging was associated with 20,940 DMPs, whereas OA was associated with 761 DMPs. Merging these two conditions revealed 279 shared DMPs. All demonstrated similar directionality and magnitude of change (Δβ 1.0% ± 0.2%, mean methylation change ± SEM). Shared DMPs were enriched in OA-associated pathways, including RhoA signaling (P = 1.57 × 10-4 ), protein kinase A signaling (P = 3.38 × 10-4 ), and NFAT signaling (P = 6.14 × 10-4 ). Upstream regulators, including TET3 (P = 6.15 × 10-4 ), immunoglobulin (P = 6.14 × 10-4 ), and TLR7 (P = 7.53 × 10-4 ), were also enriched. Pyrosequencing confirmed six of the seven top DMPs in an independent cohort. CONCLUSION Aging and early OA following DMM surgery induce similar DNA methylation changes within a murine OA model, suggesting that aging may induce pro-OA epigenetic "poising" within articular cartilage. Future research should focus on confirming and expanding these findings to other environmental OA risk factors, including obesity, as well as determining late OA changes in mice.
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Affiliation(s)
- Vladislav Izda
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, and Icahn School of Medicine at Mt. Sinai, New York
| | - Christopher M Dunn
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program and University of Oklahoma Health Sciences Center, Oklahoma City
| | - Emmaline Prinz
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, Oklahoma
| | - Leoni Schlupp
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, Oklahoma
| | - Emily Nguyen
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, Oklahoma
| | - Cassandra Sturdy
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, Oklahoma
| | - Matlock A Jeffries
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program and University of Oklahoma Health Sciences Center, Oklahoma City
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Cai Z, Long T, Zhao Y, Lin R, Wang Y. Epigenetic Regulation in Knee Osteoarthritis. Front Genet 2022; 13:942982. [PMID: 35873487 PMCID: PMC9304589 DOI: 10.3389/fgene.2022.942982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Osteoarthritis (OA) is a complicated disease with both hereditary and environmental causes. Despite an increase in reports of possible OA risk loci, it has become clear that genetics is not the sole cause of osteoarthritis. Epigenetics, which can be triggered by environmental influences and result in transcriptional alterations, may have a role in OA pathogenesis. The majority of recent research on the epigenetics of OA has been focused on DNA methylation, histone modification, and non-coding RNAs. However, this study will explore epigenetic regulation in OA at the present stage. How genetics, environmental variables, and epigenetics interact will be researched, shedding light for future studies. Their possible interaction and control processes open up new avenues for the development of innovative osteoarthritis treatment and diagnostic techniques.
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Affiliation(s)
| | - Teng Long
- *Correspondence: Teng Long, ; You Wang,
| | | | | | - You Wang
- *Correspondence: Teng Long, ; You Wang,
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Izda V, Martin J, Sturdy C, Jeffries MA. DNA methylation and noncoding RNA in OA: Recent findings and methodological advances. OSTEOARTHRITIS AND CARTILAGE OPEN 2022; 3. [PMID: 35360044 PMCID: PMC8966627 DOI: 10.1016/j.ocarto.2021.100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Introduction: Osteoarthritis (OA) is a chronic musculoskeletal disease characterized by progressive loss of joint function. Historically, it has been characterized as a disease caused by mechanical trauma, so-called ‘wear and tear’. Over the past two decades, it has come to be understood as a complex systemic disorder involving gene-environmental interactions. Epigenetic changes have been increasingly implicated. Recent improvements in microarray and next-generation sequencing (NGS) technologies have allowed for ever more complex evaluations of epigenetic aberrations associated with the development and progression of OA. Methods: A systematic review was conducted in the Pubmed database. We curated studies that presented the results of DNA methylation and noncoding RNA research in human OA and OA animal models since 1985. Results: Herein, we discuss recent findings and methodological advancements in OA epigenetics, including a discussion of DNA methylation, including microarray and NGS studies, and noncoding RNAs. Beyond cartilage, we also highlight studies in subchondral bone and peripheral blood mononuclear cells, which highlight widespread and potentially clinically important alterations in epigenetic patterns seen in OA patients. Finally, we discuss epigenetic editing approaches in the context of OA. Conclusions: Although a substantial body of literature has already been published in OA, much is still unknown. Future OA epigenetics studies will no doubt continue to broaden our understanding of underlying pathophysiology and perhaps offer novel diagnostics and/or treatments for human OA.
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Affiliation(s)
- Vladislav Izda
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Jake Martin
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Cassandra Sturdy
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Matlock A. Jeffries
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
- University of Oklahoma Health Sciences Center, Department of Internal Medicine, Division of Rheumatology, Immunology, And Allergy, Oklahoma City, OK, USA
- Corresponding author. Oklahoma Medical Research Foundation, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA.
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Lie MU, Pedersen LM, Heuch I, Winsvold B, Gjerstad J, Hasvik E, Nygaard ØP, Grotle M, Matre D, Zwart JA, Nilsen KB. Low Back Pain With Persistent Radiculopathy; the Clinical Role of Genetic Variants in the Genes SOX5, CCDC26/GSDMC and DCC. Front Genet 2022; 12:757632. [PMID: 35140737 PMCID: PMC8819060 DOI: 10.3389/fgene.2021.757632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/29/2021] [Indexed: 12/28/2022] Open
Abstract
In a recently published genome-wide association study (GWAS) chronic back pain was associated with three loci; SOX5, CCDC26/GSDMC and DCC. This GWAS was based on a heterogeneous sample of back pain disorders, and it is unknown whether these loci are of clinical relevance for low back pain (LBP) with persistent radiculopathy. Thus, we examine if LBP with radiculopathy 12 months after an acute episode of LBP with radiculopathy is associated with the selected single nucleotide polymorphisms (SNPs); SOX5 rs34616559, CCDC26/GSDMC rs7833174 and DCC rs4384683. In this prospective cohort study, subjects admitted to a secondary health care institution due to an acute episode of LBP with radiculopathy, reported back pain, leg pain, and Oswestry Disability Index (ODI), were genotyped and followed up at 12 months (n = 338). Kruskal-Wallis H test showed no association between the SNPs and back pain, leg pain or ODI. In conclusion, LBP with radiculopathy 12 months after an acute episode of LBP with radiculopathy, is not associated with the selected SNPs; SOX5 rs34616559, CCDC26/GSDMC rs7833174 and DCC rs4384683. This absent or weak association suggests that the SNPs previously associated with chronic back pain are not useful as prognostic biomarkers for LBP with persistent radiculopathy.
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Affiliation(s)
- Marie Udnesseter Lie
- Research and Communication Unit for Musculoskeletal Health (FORMI), Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Marie Udnesseter Lie,
| | - Linda Margareth Pedersen
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Physiotherapy, Oslo Metropolitan University, Oslo, Norway
| | - Ingrid Heuch
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
| | - Bendik Winsvold
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Johannes Gjerstad
- Department of Work Psychology and Physiology, National Institute of Occupational Health, Oslo, Norway
- Department of Bioscience, University of Oslo, Oslo, Norway
| | - Eivind Hasvik
- Department of Physical Medicine and Rehabilitation, Østfold Hospital Trust, Grålum, Norway
| | - Øystein Petter Nygaard
- Department of Neurosurgery, St Olavs University Hospital, Trondheim, Norway
- Department of Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- National Advisory Unit on Spinal Surgery, St Olavs Hospital, Trondheim, Norway
| | - Margreth Grotle
- Research and Communication Unit for Musculoskeletal Health (FORMI), Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Physiotherapy, Oslo Metropolitan University, Oslo, Norway
| | - Dagfinn Matre
- Department of Work Psychology and Physiology, National Institute of Occupational Health, Oslo, Norway
| | - John-Anker Zwart
- Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
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Du T, Gao J, Li P, Wang Y, Qi Q, Liu X, Li J, Wang C, Du L. Pyroptosis, metabolism, and tumor immune microenvironment. Clin Transl Med 2021; 11:e492. [PMID: 34459122 PMCID: PMC8329701 DOI: 10.1002/ctm2.492] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
In response to a wide range of stimulations, host cells activate pyroptosis, a kind of inflammatory cell death which is provoked by the cytosolic sensing of danger signals and pathogen infection. In manipulating the cleavage of gasdermins (GSDMs), researchers have found that GSDM proteins serve as the real executors and the deterministic players in fate decisions of pyroptotic cells. Whether inflammatory characteristics induced by pyroptosis could cause damage the host or improve immune activity is largely dependent on the context, timing, and response degree. Here, we systematically review current points involved in regulatory mechanisms and the multidimensional roles of pyroptosis in several metabolic diseases and the tumor microenvironment. Targeting pyroptosis may reveal potential therapeutic avenues.
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Affiliation(s)
- Tiantian Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Jie Gao
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Peilong Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Yunshan Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Qiuchen Qi
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Xiaoyan Liu
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Juan Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Chuanxin Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| | - Lutao Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
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11
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Jiang W, Xia T, Liu C, Li J, Zhang W, Sun C. Remodeling the Epigenetic Landscape of Cancer-Application Potential of Flavonoids in the Prevention and Treatment of Cancer. Front Oncol 2021; 11:705903. [PMID: 34235089 PMCID: PMC8255972 DOI: 10.3389/fonc.2021.705903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics, including DNA methylation, histone modification, and noncoding RNA regulation, are physiological regulatory changes that affect gene expression without modifying the DNA sequence. Although epigenetic disorders are considered a sign of cell carcinogenesis and malignant events that affect tumor progression and drug resistance, in view of the reversible nature of epigenetic modifications, clinicians believe that associated mechanisms can be a key target for cancer prevention and treatment. In contrast, epidemiological and preclinical studies indicated that the epigenome is constantly reprogrammed by intake of natural organic compounds and the environment, suggesting the possibility of utilizing natural compounds to influence epigenetics in cancer therapy. Flavonoids, although not synthesized in the human body, can be consumed daily and are common in medicinal plants, vegetables, fruits, and tea. Recently, numerous reports provided evidence for the regulation of cancer epigenetics by flavonoids. Considering their origin in natural and food sources, few side effects, and remarkable biological activity, the epigenetic antitumor effects of flavonoids warrant further investigation. In this article, we summarized and analyzed the multi-dimensional epigenetic effects of all 6 subtypes of flavonoids (including flavonols, flavones, isoflavones, flavanones, flavanols, and anthocyanidin) in different cancer types. Additionally, our report also provides new insights and a promising direction for future research and development of flavonoids in tumor prevention and treatment via epigenetic modification, in order to realize their potential as cancer therapeutic agents.
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Affiliation(s)
- Weiyi Jiang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tingting Xia
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenfeng Zhang
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
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12
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Rux D, Helbig K, Koyama E, Pacifici M. Hox11 expression characterizes developing zeugopod synovial joints and is coupled to postnatal articular cartilage morphogenesis into functional zones in mice. Dev Biol 2021; 477:49-63. [PMID: 34010606 DOI: 10.1016/j.ydbio.2021.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/07/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
Previous studies on mouse embryo limbs have established that interzone mesenchymal progenitor cells emerging at each prescribed joint site give rise to joint tissues over fetal time. These incipient tissues undergo structural maturation and morphogenesis postnatally, but underlying mechanisms of regulation remain unknown. Hox11 genes dictate overall zeugopod musculoskeletal patterning and skeletal element identities during development. Here we asked where these master regulators are expressed in developing limb joints and whether they are maintained during postnatal zeugopod joint morphogenesis. We found that Hoxa11 was predominantly expressed and restricted to incipient wrist and ankle joints in E13.5 mouse embryos, and became apparent in medial and central regions of knees by E14.5, though remaining continuously dormant in elbow joints. Closer examination revealed that Hoxa11 initially characterized interzone and neighboring cells and was then restricted to nascent articular cartilage, intra joint ligaments and structures such as meniscal horns over prenatal time. Postnatally, articular cartilage progresses from a nondescript cell-rich, matrix-poor tissue to a highly structured, thick, zonal and mechanically competent tissue with chondrocyte columns over time, most evident at sites such as the tibial plateau. Indeed, Hox11 expression (primarily Hoxa11) was intimately coupled to such morphogenetic processes and, in particular, to the topographical rearrangement of chondrocytes into columns within the intermediate and deep zones of tibial plateau that normally endures maximal mechanical loads. Revealingly, these expression patterns were maintained even at 6 months of age. In sum, our data indicate that Hox11 genes remain engaged well beyond embryonic synovial joint patterning and are specifically tied to postnatal articular cartilage morphogenesis into a zonal and resilient tissue. The data demonstrate that Hox11 genes characterize adult, terminally differentiated, articular chondrocytes and maintain region-specificity established in the embryo.
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Affiliation(s)
- Danielle Rux
- Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Kimberly Helbig
- Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eiki Koyama
- Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maurizio Pacifici
- Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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13
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Visconti VV, Cariati I, Fittipaldi S, Iundusi R, Gasbarra E, Tarantino U, Botta A. DNA Methylation Signatures of Bone Metabolism in Osteoporosis and Osteoarthritis Aging-Related Diseases: An Updated Review. Int J Mol Sci 2021; 22:ijms22084244. [PMID: 33921902 PMCID: PMC8072687 DOI: 10.3390/ijms22084244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023] Open
Abstract
DNA methylation is one of the most studied epigenetic mechanisms that play a pivotal role in regulating gene expression. The epigenetic component is strongly involved in aging-bone diseases, such as osteoporosis and osteoarthritis. Both are complex multi-factorial late-onset disorders that represent a globally widespread health problem, highlighting a crucial point of investigations in many scientific studies. In recent years, new findings on the role of DNA methylation in the pathogenesis of aging-bone diseases have emerged. The aim of this systematic review is to update knowledge in the field of DNA methylation associated with osteoporosis and osteoarthritis, focusing on the specific tissues involved in both pathological conditions.
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Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Ida Cariati
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Simona Fittipaldi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
| | - Riccardo Iundusi
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Elena Gasbarra
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Umberto Tarantino
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
- Department of Clinical Science and Translational Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
- Correspondence:
| | - Annalisa Botta
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
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14
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Singh P, Lessard SG, Mukherjee P, Rourke B, Otero M. Changes in DNA methylation accompany changes in gene expression during chondrocyte hypertrophic differentiation in vitro. Ann N Y Acad Sci 2020; 1490:42-56. [PMID: 32978775 DOI: 10.1111/nyas.14494] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/29/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022]
Abstract
During osteoarthritis (OA), articular chondrocytes undergo phenotypic changes that resemble developmental patterns characteristic of growth plate chondrocytes. These phenotypic alterations lead to a hypertrophy-like phenotype characterized by altered production of extracellular matrix constituents and increased collagenase activity, which, in turn, results in cartilage destruction in OA disease. Recent studies have shown that the phenotypic instability and dysregulated gene expression in OA are associated with changes in DNA methylation patterns. Subsequent efforts have aimed to identify changes in DNA methylation with functional impact in OA disease, to potentially uncover therapeutic targets. Here, we paired an in vitro 3D/pellet culture system that mimics chondrocyte hypertrophy with RNA sequencing (RNA-Seq) and enhanced reduced representation of bisulfite sequencing (ERRBS) to identify transcriptomic and epigenomic changes in murine primary articular chondrocytes undergoing hypertrophy-like differentiation. We identified hypertrophy-associated changes in DNA methylation patterns in vitro. Integration of RNA-Seq and ERRBS datasets identified associations between changes in methylation and gene expression. Our integrative analyses showed that hypertrophic differentiation of articular chondrocytes is accompanied by transcriptomic and epigenomic changes in vitro. We believe that our integrative approaches have the potential to uncover new targets for therapeutic intervention.
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Affiliation(s)
- Purva Singh
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Samantha G Lessard
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Piali Mukherjee
- Epigenomics Core Facility, Weill Cornell Medicine, New York, New York
| | - Brennan Rourke
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Miguel Otero
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
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15
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Suntsov V, Jovanovic F, Knezevic E, Candido KD, Knezevic NN. Can Implementation of Genetics and Pharmacogenomics Improve Treatment of Chronic Low Back Pain? Pharmaceutics 2020; 12:pharmaceutics12090894. [PMID: 32967120 PMCID: PMC7558486 DOI: 10.3390/pharmaceutics12090894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Etiology of back pain is multifactorial and not completely understood, and for the majority of people who suffer from chronic low back pain (cLBP), the precise cause cannot be determined. We know that back pain is somewhat heritable, chronic pain more so than acute. The aim of this review is to compile the genes identified by numerous genetic association studies of chronic pain conditions, focusing on cLBP specifically. Higher-order neurologic processes involved in pain maintenance and generation may explain genetic contributions and functional predisposition to formation of cLBP that does not involve spine pathology. Several genes have been identified in genetic association studies of cLBP and roughly, these genes could be grouped into several categories, coding for: receptors, enzymes, cytokines and related molecules, and transcription factors. Treatment of cLBP should be multimodal. In this review, we discuss how an individual's genotype could affect their response to therapy, as well as how genetic polymorphisms in CYP450 and other enzymes are crucial for affecting the metabolic profile of drugs used for the treatment of cLBP. Implementation of gene-focused pharmacotherapy has the potential to deliver select, more efficacious drugs and avoid unnecessary, polypharmacy-related adverse events in many painful conditions, including cLBP.
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Affiliation(s)
- Vladislav Suntsov
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, 836 W. Wellington Ave. Suite 4815, Chicago, IL 60657, USA; (V.S.); (F.J.); (E.K.); (K.D.C.)
| | - Filip Jovanovic
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, 836 W. Wellington Ave. Suite 4815, Chicago, IL 60657, USA; (V.S.); (F.J.); (E.K.); (K.D.C.)
| | - Emilija Knezevic
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, 836 W. Wellington Ave. Suite 4815, Chicago, IL 60657, USA; (V.S.); (F.J.); (E.K.); (K.D.C.)
| | - Kenneth D. Candido
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, 836 W. Wellington Ave. Suite 4815, Chicago, IL 60657, USA; (V.S.); (F.J.); (E.K.); (K.D.C.)
- Department of Anesthesiology, University of Illinois, Chicago, IL 60612, USA
- Department of Surgery, University of Illinois, Chicago, IL 60612, USA
| | - Nebojsa Nick Knezevic
- Department of Anesthesiology, Advocate Illinois Masonic Medical Center, 836 W. Wellington Ave. Suite 4815, Chicago, IL 60657, USA; (V.S.); (F.J.); (E.K.); (K.D.C.)
- Department of Anesthesiology, University of Illinois, Chicago, IL 60612, USA
- Department of Surgery, University of Illinois, Chicago, IL 60612, USA
- Correspondence: ; Tel.: +1-773-296-5619; Fax: +1-773-296-5362
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16
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Wu J, Sun Y, Xiong Z, Liu J, Li H, Liu Y, Li B, Jin T. Association of GSDMC polymorphisms with lumbar disc herniation among Chinese Han population. Int J Immunogenet 2020; 47:546-553. [PMID: 32333499 DOI: 10.1111/iji.12488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/10/2020] [Accepted: 03/22/2020] [Indexed: 02/06/2023]
Abstract
Lumbar disc herniation (LDH) is a relatively common spinal disease, but its pathogenesis is still unknown. Numerous studies have shown that LDH is closely correlated with inflammation, and it has been found to be related to some single nucleotide polymorphisms (SNPs). Our purpose is to explore the correlation between gene polymorphisms of GSDMC and LDH risk, which is of great significance for the study of the pathogenesis of LDH. DNA was extracted from 508 LDH patients and 508 controls. We select SNPs with minor allele frequency >5% in GSDMC gene from 1,000 genome project (http://www.internationalgenome.org/). Then, genotyping was performed using Agena MassARRAY. We used unconditional logistic regression analysis to calculate odds ratios (ORs) and 95% confidence intervals (CIs). The haplotype construction and analysis in GSDMC were applied to detect the association. We identified that rs77681114 in the GSDMC gene was significantly associated with a decreased risk of LDH in the alleles model (OR = 0.81, 95% CI = 0.66-0.99, p = .049) and the log-additive model (OR = 0.81, 95% CI = 0.65-0.99, p = .049) adjusted by age and gender. The haplotype "AG" constructed by rs77681114 and rs4285452 (OR = 1.24, 95% CI = 1.01-1.53, p = .039) was associated with increased risk of LDH. After age and gender stratification, rs77681114 protected LDH risk at age 49 or older in allelic model (p = .010), co-dominant model (p = .006), dominant model (p = .029), recessive model (p = .011) and log-additive model (p = .005). Rs77681114 had protective effect on female LDH risk in both co-dominant models (p = .033) and recessive models (p = .043). These studies indicated that genetic polymorphisms of GSDMC can relatively reduce the risk of LDH.
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Affiliation(s)
- Jiamin Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Yao Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Zichao Xiong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Jianfeng Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Haiyue Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Yuanwei Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China.,Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,School of Basic Medical Sciences, Xizang Minzu University, Xianyang, China
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17
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Huang J, Bai L, Cui B, Wu L, Wang L, An Z, Ruan S, Yu Y, Zhang X, Chen J. Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. Genome Biol 2020; 21:88. [PMID: 32252795 PMCID: PMC7132874 DOI: 10.1186/s13059-020-02001-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenome-wide association studies (EWAS), which seek the association between epigenetic marks and an outcome or exposure, involve multiple hypothesis testing. False discovery rate (FDR) control has been widely used for multiple testing correction. However, traditional FDR control methods do not use auxiliary covariates, and they could be less powerful if the covariates could inform the likelihood of the null hypothesis. Recently, many covariate-adaptive FDR control methods have been developed, but application of these methods to EWAS data has not yet been explored. It is not clear whether these methods can significantly improve detection power, and if so, which covariates are more relevant for EWAS data. RESULTS In this study, we evaluate the performance of five covariate-adaptive FDR control methods with EWAS-related covariates using simulated as well as real EWAS datasets. We develop an omnibus test to assess the informativeness of the covariates. We find that statistical covariates are generally more informative than biological covariates, and the covariates of methylation mean and variance are almost universally informative. In contrast, the informativeness of biological covariates depends on specific datasets. We show that the independent hypothesis weighting (IHW) and covariate adaptive multiple testing (CAMT) method are overall more powerful, especially for sparse signals, and could improve the detection power by a median of 25% and 68% on real datasets, compared to the ST procedure. We further validate the findings in various biological contexts. CONCLUSIONS Covariate-adaptive FDR control methods with informative covariates can significantly increase the detection power for EWAS. For sparse signals, IHW and CAMT are recommended.
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Affiliation(s)
- Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Ling Bai
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Bowen Cui
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Liang Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Liwen Wang
- Department of General Surgery, Rui-Jin Hospital, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Zhiyin An
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Shulin Ruan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yue Yu
- Division of Digital Health Sciences, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Xianyang Zhang
- Department of Statistics, Texas A&M University, Blocker 449D, College Station, TX, 77843, USA.
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
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18
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Zhang X, Ehrlich KC, Yu F, Hu X, Meng XH, Deng HW, Shen H, Ehrlich M. Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15. Epigenetics 2020; 15:728-749. [PMID: 31975641 PMCID: PMC7574382 DOI: 10.1080/15592294.2020.1716491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A major challenge in translating findings from genome-wide association studies (GWAS) to biological mechanisms is pinpointing functional variants because only a very small percentage of variants associated with a given trait actually impact the trait. We used an extensive epigenetics, transcriptomics, and genetics analysis of the TBX15/WARS2 neighbourhood to prioritize this region's best-candidate causal variants for the genetic risk of osteoporosis (estimated bone density, eBMD) and obesity (waist-hip ratio or waist circumference adjusted for body mass index). TBX15 encodes a transcription factor that is important in bone development and adipose biology. Manual curation of 692 GWAS-derived variants gave eight strong candidates for causal SNPs that modulate TBX15 transcription in subcutaneous adipose tissue (SAT) or osteoblasts, which highly and specifically express this gene. None of these SNPs were prioritized by Bayesian fine-mapping. The eight regulatory causal SNPs were in enhancer or promoter chromatin seen preferentially in SAT or osteoblasts at TBX15 intron-1 or upstream. They overlap strongly predicted, allele-specific transcription factor binding sites. Our analysis suggests that these SNPs act independently of two missense SNPs in TBX15. Remarkably, five of the regulatory SNPs were associated with eBMD and obesity and had the same trait-increasing allele for both. We found that WARS2 obesity-related SNPs can be ascribed to high linkage disequilibrium with TBX15 intron-1 SNPs. Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.
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Affiliation(s)
- Xiao Zhang
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA
| | - Kenneth C Ehrlich
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA
| | - Fangtang Yu
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA
| | - Xiaojun Hu
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA.,Department of Orthopedics, People's Hospital of Rongchang District , Chongqing, China
| | - Xiang-He Meng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University , Changsha, Hunan, China
| | - Hong-Wen Deng
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA
| | - Hui Shen
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA
| | - Melanie Ehrlich
- Tulane Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University , New Orleans, LA, USA.,Tulane Cancer Center, Hayward Human Genetics Program, Tulane University Health Sciences , New Orleans, LA, USA
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19
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M Dunn C, Nevitt MC, Lynch JA, Jeffries MA. A pilot study of peripheral blood DNA methylation models as predictors of knee osteoarthritis radiographic progression: data from the Osteoarthritis Initiative (OAI). Sci Rep 2019; 9:16880. [PMID: 31727952 PMCID: PMC6856188 DOI: 10.1038/s41598-019-53298-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/30/2019] [Indexed: 12/20/2022] Open
Abstract
Knee osteoarthritis (OA) is a leading cause of chronic disability worldwide, but no diagnostic or prognostic biomarkers are available. Increasing evidence supports epigenetic dysregulation as a contributor to OA pathogenesis. In this pilot study, we investigated epigenetic patterns in peripheral blood mononuclear cells (PBMCs) as models to predict future radiographic progression in OA patients enrolled in the longitudinal Osteoarthritis Initiative (OAI) study. PBMC DNA was analyzed from baseline OAI visits in 58 future radiographic progressors (joint space narrowing at 24 months, sustained at 48 months) compared to 58 non-progressors. DNA methylation was quantified via Illumina microarrays and beta- and M-values were used to generate linear classification models. Data were randomly split into a 60% development and 40% validation subsets, models developed and tested, and cross-validated in a total of 40 cycles. M-value based models outperformed beta-value based models (ROC-AUC 0.81 ± 0.01 vs. 0.73 ± 0.02, mean ± SEM, comparison p = 0.002), with a mean classification accuracy of 73 ± 1% (mean ± SEM) for M- and 69 ± 1% for beta-based models. Adjusting for covariates did not significantly alter model performance. Our findings suggest that PBMC DNA methylation-based models may be useful as biomarkers of OA progression and warrant additional evaluation in larger patient cohorts.
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Affiliation(s)
- Christopher M Dunn
- University of Oklahoma Health Sciences Center, Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, Oklahoma City, OK, USA
- Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology Program, Oklahoma City, OK, USA
| | | | - John A Lynch
- University of California San Francisco, San Francisco, CA, USA
| | - Matlock A Jeffries
- University of Oklahoma Health Sciences Center, Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, Oklahoma City, OK, USA.
- Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology Program, Oklahoma City, OK, USA.
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20
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Cortés-Pereira E, Fernández-Tajes J, Fernández-Moreno M, Vázquez-Mosquera ME, Relaño S, Ramos-Louro P, Durán-Sotuela A, Dalmao-Fernández A, Oreiro N, Blanco FJ, Rego-Pérez I. Differential Association of Mitochondrial DNA Haplogroups J and H With the Methylation Status of Articular Cartilage: Potential Role in Apoptosis and Metabolic and Developmental Processes. Arthritis Rheumatol 2019; 71:1191-1200. [PMID: 30747498 DOI: 10.1002/art.40857] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/07/2019] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To analyze the influence of mitochondrial genome variation on the DNA methylome of articular cartilage. METHODS DNA methylation profiling was performed using data deposited in the NCBI Gene Expression Omnibus database (accession no. GSE43269). Data were obtained for 14 cartilage samples from subjects with haplogroup J and 20 cartilage samples from subjects with haplogroup H. Subsequent validation was performed in an independent subset of 7 subjects with haplogroup J and 9 with haplogroup H by RNA-seq. Correlated genes were validated by real-time polymerase chain reaction in an independent cohort of 12 subjects with haplogroup J and 12 with haplogroup H. Appropriate analyses were performed using R Bioconductor and qBasePlus software, and gene ontology analysis was conducted using DAVID version 6.8. RESULTS DNA methylation profiling revealed 538 differentially methylated loci, while whole-transcriptome profiling identified 2,384 differentially expressed genes, between cartilage samples from subjects with haplogroup H and those with haplogroup J. Seventeen genes showed an inverse correlation between methylation and expression. In terms of gene ontology, differences in correlations between methylation and expression were also detected between cartilage from subjects with haplogroup H and those with haplogroup J, highlighting a significantly enhanced apoptotic process in cartilage from subjects with haplogroup H (P = 0.007 for methylation and P = 0.019 for expression) and repressed apoptotic process in cartilage from subjects with haplogroup J (P = 0.021 for methylation), as well as a significant enrichment of genes related to metabolic processes (P = 1.93 × 10-4 for methylation and P = 6.79 x 10-4 for expression) and regulation of gene expression (P = 0.012 for methylation) in cartilage from subjects with haplogroup H, and to developmental processes (P = 0.015 for methylation and P = 8.25 x 10-12 for expression) in cartilage from subjects with haplogroup J. CONCLUSION Mitochondrial DNA variation differentially associates with the methylation status of articular cartilage by acting on key mechanisms involved in osteoarthritis, such as apoptosis and metabolic and developmental processes.
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Affiliation(s)
- Estefanía Cortés-Pereira
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | | | | | - María E Vázquez-Mosquera
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Sara Relaño
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Paula Ramos-Louro
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Alejandro Durán-Sotuela
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Andrea Dalmao-Fernández
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Natividad Oreiro
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Francisco J Blanco
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
| | - Ignacio Rego-Pérez
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), and Universidade da Coruña, A Coruña, Spain
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21
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van Meurs JB, Boer CG, Lopez-Delgado L, Riancho JA. Role of Epigenomics in Bone and Cartilage Disease. J Bone Miner Res 2019; 34:215-230. [PMID: 30715766 DOI: 10.1002/jbmr.3662] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]
Abstract
Phenotypic variation in skeletal traits and diseases is the product of genetic and environmental factors. Epigenetic mechanisms include information-containing factors, other than DNA sequence, that cause stable changes in gene expression and are maintained during cell divisions. They represent a link between environmental influences, genome features, and the resulting phenotype. The main epigenetic factors are DNA methylation, posttranslational changes of histones, and higher-order chromatin structure. Sometimes non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are also included in the broad term of epigenetic factors. There is rapidly expanding experimental evidence for a role of epigenetic factors in the differentiation of bone cells and the pathogenesis of skeletal disorders, such as osteoporosis and osteoarthritis. However, different from genetic factors, epigenetic signatures are cell- and tissue-specific and can change with time. Thus, elucidating their role has particular difficulties, especially in human studies. Nevertheless, epigenomewide association studies are beginning to disclose some disease-specific patterns that help to understand skeletal cell biology and may lead to development of new epigenetic-based biomarkers, as well as new drug targets useful for treating diffuse and localized disorders. Here we provide an overview and update of recent advances on the role of epigenomics in bone and cartilage diseases. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Lopez-Delgado
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Jose A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
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22
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Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. Sci Rep 2018; 8:15499. [PMID: 30341348 PMCID: PMC6195601 DOI: 10.1038/s41598-018-33779-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022] Open
Abstract
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.
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23
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Suri P, Palmer MR, Tsepilov YA, Freidin MB, Boer CG, Yau MS, Evans DS, Gelemanovic A, Bartz TM, Nethander M, Arbeeva L, Karssen L, Neogi T, Campbell A, Mellstrom D, Ohlsson C, Marshall LM, Orwoll E, Uitterlinden A, Rotter JI, Lauc G, Psaty BM, Karlsson MK, Lane NE, Jarvik GP, Polasek O, Hochberg M, Jordan JM, Van Meurs JBJ, Jackson R, Nielson CM, Mitchell BD, Smith BH, Hayward C, Smith NL, Aulchenko YS, Williams FMK. Genome-wide meta-analysis of 158,000 individuals of European ancestry identifies three loci associated with chronic back pain. PLoS Genet 2018; 14:e1007601. [PMID: 30261039 PMCID: PMC6159857 DOI: 10.1371/journal.pgen.1007601] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/02/2018] [Indexed: 01/07/2023] Open
Abstract
Back pain is the #1 cause of years lived with disability worldwide, yet surprisingly little is known regarding the biology underlying this symptom. We conducted a genome-wide association study (GWAS) meta-analysis of chronic back pain (CBP). Adults of European ancestry were included from 15 cohorts in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, and from the UK Biobank interim data release. CBP cases were defined as those reporting back pain present for ≥3-6 months; non-cases were included as comparisons ("controls"). Each cohort conducted genotyping using commercially available arrays followed by imputation. GWAS used logistic regression models with additive genetic effects, adjusting for age, sex, study-specific covariates, and population substructure. The threshold for genome-wide significance in the fixed-effect inverse-variance weighted meta-analysis was p<5×10(-8). Suggestive (p<5×10(-7)) and genome-wide significant (p<5×10(-8)) variants were carried forward for replication or further investigation in the remaining UK Biobank participants not included in the discovery sample. The discovery sample comprised 158,025 individuals, including 29,531 CBP cases. A genome-wide significant association was found for the intronic variant rs12310519 in SOX5 (OR 1.08, p = 7.2×10(-10)). This was subsequently replicated in 283,752 UK Biobank participants not included in the discovery sample, including 50,915 cases (OR 1.06, p = 5.3×10(-11)), and exceeded genome-wide significance in joint meta-analysis (OR 1.07, p = 4.5×10(-19)). We found suggestive associations at three other loci in the discovery sample, two of which exceeded genome-wide significance in joint meta-analysis: an intergenic variant, rs7833174, located between CCDC26 and GSDMC (OR 1.05, p = 4.4×10(-13)), and an intronic variant, rs4384683, in DCC (OR 0.97, p = 2.4×10(-10)). In this first reported meta-analysis of GWAS for CBP, we identified and replicated a genetic locus associated with CBP (SOX5). We also identified 2 other loci that reached genome-wide significance in a 2-stage joint meta-analysis (CCDC26/GSDMC and DCC).
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Affiliation(s)
- Pradeep Suri
- Seattle Epidemiologic Research and Information Center (ERIC), Department of Veterans Affairs Office of Research and Development, Seattle, Washington, United States of America
- Division of Rehabilitation Care Services, VA Puget Sound Health Care System, Seattle, Washington, United States of America
- Department of Rehabilitation Medicine, University of Washington, Seattle, Washington, United States of America
| | - Melody R. Palmer
- Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Yakov A. Tsepilov
- Polyomica, ‘s-Hertogenbosch, the Netherlands
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics SD RAS, Novosibirsk, Russia
| | - Maxim B. Freidin
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Cindy G. Boer
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Michelle S. Yau
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, United States of America
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Andrea Gelemanovic
- Department of Public Health, University of Split Medical School, Split, Croatia
| | - Traci M. Bartz
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Maria Nethander
- Department of Medicine, University of Göteborg, Göteborg, Sweden
| | - Liubov Arbeeva
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Tuhina Neogi
- Clinical Epidemiology Unit, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Mellstrom
- Geriatric Medicine, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Sweden
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Göteborg, Sweden
| | - Lynn M. Marshall
- Department of Orthopedics and Rehabilitation, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Eric Orwoll
- Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, United States of America
- Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Gordan Lauc
- Genos Ltd, Osijek, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Health Services, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, United States of America
| | - Magnus K. Karlsson
- Department of Orthopedics, Skane University Hospital, Lund University, Malmö, Sweden
| | - Nancy E. Lane
- Departments of Medicine and Rheumatology, University of California Davis, Sacramento, California, United States of America
| | - Gail P. Jarvik
- Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Ozren Polasek
- Department of Public Health, University of Split Medical School, Split, Croatia
- Hospital “Sveti Ivan”, Zagreb, Croatia
| | - Marc Hochberg
- Departments of Medicine and Epidemiology, University of Maryland, Baltimore, Maryland, United States of America
| | - Joanne M. Jordan
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Rebecca Jackson
- Department of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Carrie M. Nielson
- School of Public Health, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Braxton D. Mitchell
- Departments of Medicine and Epidemiology, University of Maryland, Baltimore, Maryland, United States of America
- Geriatric Research, Education and Clinical Center, Veterans Affairs Medical Center, Baltimore, Maryland, United States of America
| | - Blair H. Smith
- Division of Population Health Sciences, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, United Kingdom
| | - Nicholas L. Smith
- Seattle Epidemiologic Research and Information Center (ERIC), Department of Veterans Affairs Office of Research and Development, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, United States of America
| | | | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
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24
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Singh P, Marcu KB, Goldring MB, Otero M. Phenotypic instability of chondrocytes in osteoarthritis: on a path to hypertrophy. Ann N Y Acad Sci 2018; 1442:17-34. [PMID: 30008181 DOI: 10.1111/nyas.13930] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 12/24/2022]
Abstract
Articular chondrocytes are quiescent, fully differentiated cells responsible for the homeostasis of adult articular cartilage by maintaining cellular survival functions and the fine-tuned balance between anabolic and catabolic functions. This balance requires phenotypic stability that is lost in osteoarthritis (OA), a disease that affects and involves all joint tissues and especially impacts articular cartilage structural integrity. In OA, articular chondrocytes respond to the accumulation of injurious biochemical and biomechanical insults by shifting toward a degradative and hypertrophy-like state, involving abnormal matrix production and increased aggrecanase and collagenase activities. Hypertrophy is a necessary, transient developmental stage in growth plate chondrocytes that culminates in bone formation; in OA, however, chondrocyte hypertrophy is catastrophic and it is believed to initiate and perpetuate a cascade of events that ultimately result in permanent cartilage damage. Emphasizing changes in DNA methylation status and alterations in NF-κB signaling in OA, this review summarizes the data from the literature highlighting the loss of phenotypic stability and the hypertrophic differentiation of OA chondrocytes as central contributing factors to OA pathogenesis.
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Affiliation(s)
- Purva Singh
- HSS Research Institute, Hospital for Special Surgery, New York, New York
| | - Kenneth B Marcu
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York
| | - Mary B Goldring
- HSS Research Institute, Hospital for Special Surgery, New York, New York.,Department of Cell and Developmental Biology, Weill Cornell Medical College and Weill Cornell Graduate School of Medical Sciences, New York, New York
| | - Miguel Otero
- HSS Research Institute, Hospital for Special Surgery, New York, New York
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25
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Abstract
PURPOSE OF REVIEW 'Omics' technologies developed for the massive analysis of the major biologically relevant molecules (genes, proteins, metabolites) have been applied to the study of osteoarthritis (OA) for more than a decade. RECENT FINDINGS 'Omics' studies have undoubtedly contributed to increase the knowledge on pathogenic processes related with OA and have provided hundreds to thousands of molecules that might have a putative biomarker utility for this disease. SUMMARY This review describes the most recent 'omics' studies in OA research, their conclusions, and discuss those remaining challenges. Still many validation studies must be performed in large and well-characterized cohorts for the translation of the findings from 'omics' strategies to clinical applications. The development of tools for the intelligent integration of 'omics' data with clinical and imaging information is also mandatory to take full profit of the work that has been already performed.
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Abstract
PURPOSE OF REVIEW Epigenomics has emerged as a key player in our rapidly evolving understanding of osteoarthritis. Historical studies implicated epigenetic alterations, particularly DNA methylation, in OA pathogenesis; however, recent technological advances have resulted in numerous epigenome-wide studies examining in detail epigenetic modifications in OA. The purpose of this article is to introduce basic concepts in epigenetics and their recent applications to the study of osteoarthritis development and progression. RECENT FINDINGS Epigenetics describes three major phenomena: DNA modification via methylation, histone sidechain modifications, and short noncoding RNA sequences which work in concert to regulate gene transcription in a heritable fashion. Cartilage has been the most widely studied tissue in OA, and differential methylation of genes involved in inflammation, cell cycle, TGFβ, and HOX genes have been confirmed several times. Bone studies suggest similar findings, and the intriguing possibility of epigenetic changes in subchondral bone during many OA processes. Multiple studies have demonstrated the involvement of certain noncoding RNAs, particularly miR-140, in OA development via modulation of key catabolic factors. Although much work has been done, much is still unknown. Future epigenomic studies will no doubt continue to widen our understanding of extraarticular tissues and OA pathogenesis, and studies in animal models may offer glimpses into epigenome alterations in the earliest stages of OA.
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Peffers MJ, Balaskas P, Smagul A. Osteoarthritis year in review 2017: genetics and epigenetics. Osteoarthritis Cartilage 2018; 26:304-311. [PMID: 28989115 PMCID: PMC6292677 DOI: 10.1016/j.joca.2017.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The purpose of this review is to describe highlights from original research publications related to osteoarthritis (OA), epigenetics and genomics with the intention of recognising significant advances. DESIGN To identify relevant papers a Pubmed literature search was conducted for articles published between April 2016 and April 2017 using the search terms 'osteoarthritis' together with 'genetics', 'genomics', 'epigenetics', 'microRNA', 'lncRNA', 'DNA methylation' and 'histone modification'. RESULTS The search term OA generated almost 4000 references. Publications using the combination of descriptors OA and genetics provided the most references (82 references). However this was reduced compared to the same period in the previous year; 8.1-2.1% (expressed as a percentage of the total publications combining the terms OA and genetics). Publications combining the terms OA with genomics (29 references), epigenetics (16 references), long non-coding RNA (lncRNA) (11 references; including the identification of novel lncRNAs in OA), DNA methylation (21 references), histone modification (3 references) and microRNA (miR) (79 references) were reviewed. Potential OA therapeutics such as histone deacetylase (HDAC) inhibitors have been identified. A number of non-coding RNAs may also provide targets for future treatments. CONCLUSION There continues to be a year on year increase in publications researching miRs in OA (expressed as a percentage of the total publications), with a doubling over the last 4 years. An overview on the last year's progress within the fields of epigenetics and genomics with respect to OA will be given.
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Affiliation(s)
- M J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - P Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - A Smagul
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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28
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Abstract
PURPOSE OF REVIEW Bone remodeling is a diverse field of study with many direct clinical applications; past studies have implicated epigenetic alterations as key factors of both normal bone tissue development and function and diseases of pathologic bone remodeling. The purpose of this article is to review the most important recent advances that link epigenetic changes to the bone remodeling field. RECENT FINDINGS Epigenetics describes three major phenomena: DNA modification via methylation, histone side chain modifications, and short non-coding RNA sequences which work in concert to regulate gene transcription in a heritable fashion. Recent findings include the role of DNA methylation changes of Wnt, RANK/RANKL, and other key signaling pathways, epigenetic regulation of osteoblast and osteoclast differentiation, and others. Although much work has been done, much is still unknown. Future epigenome-wide studies should focus on extending the tissue coverage, integrating multiple epigenetic analyses with transcriptome data, and working to uncover epigenetic changes linked with early events in aberrant bone remodeling.
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Affiliation(s)
- Ali Husain
- Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Matlock A Jeffries
- Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology Program, 825 NE 13th St., Laboratory MC400, Oklahoma City, OK, USA.
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