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Saville L, Wu L, Habtewold J, Cheng Y, Gollen B, Mitchell L, Stuart-Edwards M, Haight T, Mohajerani M, Zovoilis A. NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs. Genome Biol 2024; 25:233. [PMID: 39198865 PMCID: PMC11351768 DOI: 10.1186/s13059-024-03375-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression. Here, we present NERD-seq, which enables detection of multiple non-coding RNAs, excluded by the standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq expands representation of frequently modified non-coding RNAs, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, and rRFs. NERD-seq represents an RNA-seq approach to simultaneously study mRNA and ncRNA epitranscriptomes in brain tissues and beyond.
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Affiliation(s)
- Luke Saville
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Li Wu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
| | - Jemaneh Habtewold
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
| | - Yubo Cheng
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Babita Gollen
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Liam Mitchell
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Matthew Stuart-Edwards
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Travis Haight
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Majid Mohajerani
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada
| | - Athanasios Zovoilis
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.
- Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.
- Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.
- Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
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Zhou X, Shen K, Cao S, Li P, Xiao J, Dong J, Cheng Q, Hu L, Xu Z, Yang L. Polymorphism rs2327430 in TCF21 predicts the risk and prognosis of gastric cancer by affecting the binding between TFAP2A and TCF21. Cancer Cell Int 2024; 24:159. [PMID: 38714991 PMCID: PMC11075239 DOI: 10.1186/s12935-024-03343-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Single nuclear polymorphisms (SNPs) have been published to be correlated with multiple diseases. Transcription Factor 21 (TCF21) is a critical transcription factor involved in various types of cancers. However, the association of TCF21 genetic polymorphisms with gastric cancer (GC) susceptibility and prognosis remains unclear. METHODS A case-control study comprising 890 patients diagnosed with GC and an equal number of cancer-free controls was conducted. After rigorous statistical analysis, molecular experiments were carried out to elucidate the functional significance of the SNPs in the context of GC. RESULTS TCF21 rs2327430 (OR = 0.78, P = 0.026) provides protection against GC, while rs4896011 (OR = 1.39, P = 0.005) exhibit significant associations with GC risk. Furthermore, patients with the (TC + CC) genotype of rs2327430 demonstrate a relatively favorable prognosis (OR = 0.47, P = 0.012). Mechanistically, chromatin immunoprecipitation assay and luciferase reporter assay revealed that the C allele of rs2327430 disrupts the binding of Transcription Factor AP-2 Alpha (TFAP2A) to the promoter region of TCF21, resulting in increased expression of TCF21 and inhibition of malignant behaviors in GC cells. CONCLUSION Our findings highlight the significant role of TCF21 SNPs in both the risk and prognosis of GC and provide valuable insights into the underlying molecular mechanisms. Specifically, the disruptive effect of rs2327430 on TCF21 expression and its ability to modulate malignant cell behaviors suggest that rs2327430 may serve as a potential predictive marker for GC risk and prognosis.
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Affiliation(s)
- Xinyi Zhou
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Kuan Shen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Shuqing Cao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Pengyu Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Jian Xiao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Jiacheng Dong
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Quan Cheng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Li Hu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China.
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Tyurin A, Akhiiarova K, Minniakhmetov I, Mokrysheva N, Khusainova R. The Genetic Markers of Knee Osteoarthritis in Women from Russia. Biomedicines 2024; 12:782. [PMID: 38672138 PMCID: PMC11048526 DOI: 10.3390/biomedicines12040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Osteoarthritis is a chronic progressive joint disease that clinically debuts at the stage of pronounced morphologic changes, which makes treatment difficult. In this regard, an important task is the study of genetic markers of the disease, which have not been definitively established, due to the clinical and ethnic heterogeneity of the studied populations. To find the genetic markers for the development of knee osteoarthritis (OA) in women from the Volga-Ural region of Russia, we conducted research in two stages using different genotyping methods, such as the restriction fragment length polymorphism (RFLP) measurement, TaqMan technology and competitive allele-specific PCR-KASPTM. In the first stage, we studied polymorphic variants of candidate genes (ACAN, ADAMTS5, CHST11, SOX9, COL1A1) for OA development. The association of the *27 allele of the VNTR locus of the ACAN gene was identified (OR = 1.6). In the second stage, we replicated the GWAS results (ASTN2, ALDH1A2, DVWA, CHST11, GNL3, NCOA3, FILIP/SENP1, MCF2L, GLT8D, DOT1L) for knee OA studies. The association of the *T allele of the rs7639618 locus of the DVWA gene was detected (OR = 1.54). Thus, the VNTR locus of ACAN and the rs7639618 locus of DVWA are risk factors for knee OA in women from the Volga-Ural region of Russia.
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Affiliation(s)
- Anton Tyurin
- Internal Medicine Department, Bashkir State Medical University, 450008 Ufa, Russia;
| | - Karina Akhiiarova
- Internal Medicine Department, Bashkir State Medical University, 450008 Ufa, Russia;
| | - Ildar Minniakhmetov
- Endocrinology Research Centre, Dmitriya Ulianova Street, 11, 117036 Moscow, Russia; (I.M.); (N.M.); (R.K.)
| | - Natalia Mokrysheva
- Endocrinology Research Centre, Dmitriya Ulianova Street, 11, 117036 Moscow, Russia; (I.M.); (N.M.); (R.K.)
| | - Rita Khusainova
- Endocrinology Research Centre, Dmitriya Ulianova Street, 11, 117036 Moscow, Russia; (I.M.); (N.M.); (R.K.)
- Medical Genetics Department, Bashkir State Medical University, 450008 Ufa, Russia
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Antontseva EV, Degtyareva AO, Korbolina EE, Damarov IS, Merkulova TI. Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis. Vavilovskii Zhurnal Genet Selektsii 2023; 27:662-675. [PMID: 37965371 PMCID: PMC10641029 DOI: 10.18699/vjgb-23-77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 11/16/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of variation in the human genome. The vast majority of SNPs identified in the human genome do not have any effect on the phenotype; however, some can lead to changes in the function of a gene or the level of its expression. Most SNPs associated with certain traits or pathologies are mapped to regulatory regions of the genome and affect gene expression by changing transcription factor binding sites. In recent decades, substantial effort has been invested in searching for such regulatory SNPs (rSNPs) and understanding the mechanisms by which they lead to phenotypic differences, primarily to individual differences in susceptibility to diseases and in sensitivity to drugs. The development of the NGS (next-generation sequencing) technology has contributed not only to the identification of a huge number of SNPs and to the search for their association (genome-wide association studies, GWASs) with certain diseases or phenotypic manifestations, but also to the development of more productive approaches to their functional annotation. It should be noted that the presence of an association does not allow one to identify a functional, truly disease-associated DNA sequence variant among multiple marker SNPs that are detected due to linkage disequilibrium. Moreover, determination of associations of genetic variants with a disease does not provide information about the functionality of these variants, which is necessary to elucidate the molecular mechanisms of the development of pathology and to design effective methods for its treatment and prevention. In this regard, the functional analysis of SNPs annotated in the GWAS catalog, both at the genome-wide level and at the level of individual SNPs, became especially relevant in recent years. A genome-wide search for potential rSNPs is possible without any prior knowledge of their association with a trait. Thus, mapping expression quantitative trait loci (eQTLs) makes it possible to identify an SNP for which - among transcriptomes of homozygotes and heterozygotes for its various alleles - there are differences in the expression level of certain genes, which can be located at various distances from the SNP. To predict rSNPs, approaches based on searches for allele-specific events in RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, MPRA, and other data are also used. Nonetheless, for a more complete functional annotation of such rSNPs, it is necessary to establish their association with a trait, in particular, with a predisposition to a certain pathology or sensitivity to drugs. Thus, approaches to finding SNPs important for the development of a trait can be categorized into two groups: (1) starting from data on an association of SNPs with a certain trait, (2) starting from the determination of allele-specific changes at the molecular level (in a transcriptome or regulome). Only comprehensive use of strategically different approaches can considerably enrich our knowledge about the role of genetic determinants in the molecular mechanisms of trait formation, including predisposition to multifactorial diseases.
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Affiliation(s)
- E V Antontseva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A O Degtyareva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E E Korbolina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I S Damarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T I Merkulova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Young DA, Barter MJ, Soul J. Osteoarthritis year in review: genetics, genomics, epigenetics. Osteoarthritis Cartilage 2022; 30:216-225. [PMID: 34774787 PMCID: PMC8811265 DOI: 10.1016/j.joca.2021.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In this review, we have highlighted the advances over the past year in genetics, genomics and epigenetics in the field of osteoarthritis (OA). METHODS A literature search of PubMed was performed using the criteria: "osteoarthritis" and one of the following terms "genetic(s), genomic(s), epigenetic(s), polymorphism, noncoding ribonucleic acid (RNA), microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing (RNA-seq), single cell sequencing, transcriptomics, or deoxyribonucleic acid (DNA) methylation between April 01, 2020 and April 30, 2021. RESULTS In total we identified 765 unique publications, which eventually reduced to 380 of relevance to the field as judged by two assessors. Many of these studies included multiple search terms. We summarised advances relating to genetics, functional genetics, genomics and epigenetics, focusing on our personal key papers during the year. CONCLUSIONS This year few studies have identified new genetic variants contributing to OA susceptibility, but a focus has been on refining risk loci or their functional validation. The use of new technologies together with investigating the cross-talk between multiple tissue types, greater sample sizes and/or better patient classification (OA subtypes) will continue to increase our knowledge of disease mechanisms and progress towards understanding and treating OA.
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Affiliation(s)
- D A Young
- Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK.
| | - M J Barter
- Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - J Soul
- Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
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Yan S, Nie H, Bu G, Yuan W, Wang S. The effect of common variants in GDF5 gene on the susceptibility to chronic postsurgical pain. J Orthop Surg Res 2021; 16:420. [PMID: 34210342 PMCID: PMC8247225 DOI: 10.1186/s13018-021-02549-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The growth differentiation factor 5 (GDF5) gene regulates the growth of neuronal axons and dendrites and plays a role in the inflammatory response and tissue damage. The gene may also be associated with chronic postsurgical pain. This study aimed to reveal the relationship between SNPs in the GDF5 gene and orthopedic chronic postsurgical pain in Han Chinese population based on a case-control study. Methods We genotyped 8 SNPs within GDF5 gene in 1048 surgical patients with chronic postsurgical pain as the case group and 2062 surgical patients who were pain free as the control group. SNP and haplotypic analyses were performed, and stratified analyses were conducted to determine the correlations between significant SNPs and clinical characteristics. Results Only rs143384 in the 5′UTR of GDF5 was identified as significantly associated with increased susceptibility to chronic postsurgical pain, and the risk of A allele carriers was increased approximately 1.35-fold compared with that of G allele carriers. Haplotypes AGG and GGG in the LD block rs143384-rs224335-rs739329 also showed similar association patterns. Furthermore, we found that rs143384 was significantly correlated with chronic postsurgical pain in the subgroup aged ≤ 61 years, subgroup with a BMI ≤ 26, subgroup with no-smoking or no pain history, and subgroup with a drinking history. Conclusion Our study provided supportive evidence that genetic variations in the GDF5 gene are potential genetic factors that can increase the risk of chronic postsurgical pain in the Han Chinese population, but further research is necessary to elucidate the underlying mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-021-02549-5.
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Affiliation(s)
- Shaoyao Yan
- Department of Pain, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, Shaanxi, China
| | - Huiyong Nie
- Department of Pain, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, Shaanxi, China
| | - Gang Bu
- Department of Pain, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, Shaanxi, China
| | - Weili Yuan
- Department of Pain, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, Shaanxi, China
| | - Suoliang Wang
- Department of Pain, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, Shaanxi, China.
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Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. Int J Mol Sci 2021; 22:6454. [PMID: 34208629 PMCID: PMC8235176 DOI: 10.3390/ijms22126454] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Then, we brief the recent comprehensive examples of rSNPs studied from the discovery of the changes in the TFBS sequence as a result of a nucleotide substitution to identification of its effect on the target gene expression and, eventually, to phenotype. We also describe state-of-the-art genome-wide approaches to identification of regulatory variants, including both making molecular sense of genome-wide association studies (GWAS) and the alternative approaches the primary goal of which is to determine the functionality of genetic variants. Among these approaches, special attention is paid to expression quantitative trait loci (eQTLs) analysis and the search for allele-specific events in RNA-seq (ASE events) as well as in ChIP-seq, DNase-seq, and ATAC-seq (ASB events) data.
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Affiliation(s)
- Arina O. Degtyareva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Elena V. Antontseva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Tatiana I. Merkulova
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Rice SJ, Roberts JB, Tselepi M, Brumwell A, Falk J, Steven C, Loughlin J. Genetic and Epigenetic Fine-Tuning of TGFB1 Expression Within the Human Osteoarthritic Joint. Arthritis Rheumatol 2021; 73:1866-1877. [PMID: 33760378 DOI: 10.1002/art.41736] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Osteoarthritis (OA) is an age-related disease characterized by articular cartilage degeneration. It is largely heritable, and genetic screening has identified single-nucleotide polymorphisms (SNPs) marking genomic risk loci. One such locus is marked by the G>A SNP rs75621460, downstream of TGFB1. This gene encodes transforming growth factor β1, the correct expression of which is essential for cartilage maintenance. This study investigated the regulatory activity of rs75621460 to characterize its impact on TGFB1 expression in disease-relevant patient samples (n = 319) and in Tc28a2 immortalized chondrocytes. METHODS Articular cartilage samples from human patients were genotyped, and DNA methylation levels were quantified using pyrosequencing. Gene reporter and electrophoretic mobility shift assays were used to determine differential nuclear protein binding to the region. The functional impact of DNA methylation on TGFB1 expression was tested using targeted epigenome editing. RESULTS The analyses showed that SNP rs75621460 was located within a TGFB1 enhancer region, and the OA risk allele A altered transcription factor binding, with decreased enhancer activity. Protein complexes binding to A (but not G) induced DNA methylation at flanking CG dinucleotides. Strong correlations between patient DNA methylation levels and TGFB1 expression were observed, with directly opposing effects in the cartilage and the synovium at this locus. This demonstrated biologic pleiotropy in the impact of the SNP within different tissues of the articulating joint. CONCLUSION The OA risk SNP rs75621460 impacts TGFB1 expression by modulating the function of a gene enhancer. We propose a mechanism by which the SNP impacts enhancer function, providing novel biologic insight into one mechanism of OA genetic risk, which may facilitate the development of future pharmacologic therapies.
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Affiliation(s)
- Sarah J Rice
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - Jack B Roberts
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - Maria Tselepi
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - Abby Brumwell
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - Julia Falk
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - Charlotte Steven
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
| | - John Loughlin
- Newcastle University and International Centre for Life, Newcastle-upon-Tyne, UK
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Sun K, Guo J, Yao X, Guo Z, Guo F. Growth differentiation factor 5 in cartilage and osteoarthritis: A possible therapeutic candidate. Cell Prolif 2021; 54:e12998. [PMID: 33522652 PMCID: PMC7941218 DOI: 10.1111/cpr.12998] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Growth differentiation factor 5 (GDF-5) is essential for cartilage development and homeostasis. The expression and function of GDF-5 are highly associated with the pathogenesis of osteoarthritis (OA). OA, characterized by progressive degeneration of joint, particularly in cartilage, causes severe social burden. However, there is no effective approach to reverse the progression of this disease. Over the past decades, extensive studies have demonstrated the protective effects of GDF-5 against cartilage degeneration and defects. Here, we summarize the current literature describing the role of GDF-5 in development of cartilage and joints, and the association between the GDF-5 gene polymorphisms and OA susceptibility. We also shed light on the protective effects of GDF-5 against OA in terms of direct GDF-5 supplementation and modulation of the GDF-5-related signalling. Finally, we discuss the current limitations in the application of GDF-5 for the clinical treatment of OA. This review provides a comprehensive insight into the role of GDF-5 in cartilage and emphasizes GDF-5 as a potential therapeutic candidate in OA.
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Affiliation(s)
- Kai Sun
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Jiachao Guo
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Xudong Yao
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Zhou Guo
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Fengjing Guo
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
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11
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Wang T, Zhang J, Liao J, Zhang F, Zhou G. Donor genetic backgrounds contribute to the functional heterogeneity of stem cells and clinical outcomes. Stem Cells Transl Med 2020; 9:1495-1499. [PMID: 32830917 PMCID: PMC7695629 DOI: 10.1002/sctm.20-0155] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/21/2020] [Accepted: 07/19/2020] [Indexed: 12/11/2022] Open
Abstract
Stable and sustainable stem cell sources for stem cell‐based therapies are scarce and a key bottleneck for clinical applications. The regenerative potential of stem cells is usually attributed to several allogeneic or even autologous donor‐related factors. Genetic background and epigenetic variations in different individuals may significantly affect the functional heterogeneity of stem cells. Particularly, single‐nucleotide polymorphisms (SNPs) have been implicated in diseases with monogenetic or multifactorial and complex genetic etiologies. However, the possible effects of individual SNPs on donor stem cells remain far from fully elucidated. In this Perspective, we will discuss the roles played by donor genetic traits in the functional heterogeneity of induced pluripotent stem cells, mesenchymal stem cells, and hematopoietic stem cells and their implications for regenerative medicine and therapy.
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Affiliation(s)
- Ting Wang
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China
| | - Juan Zhang
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, People's Republic of China
| | - Jinqi Liao
- Lungene Scientific Ltd., Shenzhen, People's Republic of China
| | - Fan Zhang
- Department of Endocrinology and Metabolic Diseases, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, People's Republic of China
| | - Guangqian Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China
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12
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Anti-Inflammatory and Chondroprotective Effects of Vanillic Acid and Epimedin C in Human Osteoarthritic Chondrocytes. Biomolecules 2020; 10:biom10060932. [PMID: 32575510 PMCID: PMC7356262 DOI: 10.3390/biom10060932] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 01/15/2023] Open
Abstract
In osteoarthritis (OA), inhibition of excessively expressed pro-inflammatory cytokines in the OA joint and increasing the anabolism for cartilage regeneration are necessary. In this ex-vivo study, we used an inflammatory model of human OA chondrocytes microtissues, consisting of treatment with cytokines (interleukin 1β (IL-1β)/tumor necrosis factor α (TNF-α)) with or without supplementation of six herbal compounds with previously identified chondroprotective effect. The compounds were assessed for their capacity to modulate the key catabolic and anabolic factors using several molecular analyses. We selectively investigated the mechanism of action of the two most potent compounds Vanillic acid (VA) and Epimedin C (Epi C). After identification of the anti-inflammatory and anabolic properties of VA and Epi C, the Ingenuity Pathway Analysis showed that in both treatment groups, osteoarthritic signaling pathways were inhibited. In the treatment group with VA, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling was inhibited by attenuation of the nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha (IκBα) phosphorylation. Epi C showed a significant anabolic effect by increasing the expression of collagenous and non-collagenous matrix proteins. In conclusion, VA, through inhibition of phosphorylation in NF-κB signaling pathway and Epi C, by increasing the expression of extracellular matrix components, showed significant anti-inflammatory and anabolic properties and might be potentially used in combination to treat or prevent joint OA.
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13
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Mohasseb DMF, Saba EKA, Saad NLM, Sarofeem ADH. Genetic Association Between Growth Differentiation Factor 5 Single Nucleotide Polymorphism and Primary Knee Osteoarthritis in a Group of Egyptian Patients: A Pilot Study. Mediterr J Rheumatol 2019; 30:114-122. [PMID: 32185351 PMCID: PMC7045969 DOI: 10.31138/mjr.30.2.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022] Open
Abstract
Aim This study aimed to determine the genetic association between Growth Differentiation Factor 5 (GDF5) gene (rs143383 T/C) single nucleotide polymorphism (SNP) and primary knee osteoarthritis (OA) in a group of Egyptian patients. Patients and Methods The study included 47 patients with primary knee OA and 40 apparently healthy control subjects. The disease was assessed using Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score and Health Assessment Questionnaire (HAQ). Radiological assessment was done by Kellgren-Laurence (K/L) grading system. The genetic association of the SNP with primary knee OA was assessed by restriction fragment length polymorphism - polymerase chain reaction (RFLP-PCR). Results The mean total WOMAC index was significantly higher in patients with TT genotype as compared to patients with CC and CT genotypes (P<0.001). Similarly, the HAQ score was significantly higher among patients with TT genotype when compared to patients with CT and CC genotypes (P<0.001). There was a statistically significant association between different GDF5 genotypes and K/L radiological grading of knee OA among the studied patients (P=0.029). No statistically significant association was detected on comparing the frequency distribution of GDF5 alleles and genotypes frequencies of the SNP in patients and healthy controls. Conclusion There is a possible genetic association between GDF5 (rs143383) SNP and severity of primary knee OA, which might facilitate the detection of patients with high risk for disease progression. The present study did not detect an association between the SNP and development of primary knee OA.
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Affiliation(s)
- Dia Mohamed Fahmy Mohasseb
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Alexandria University, Egypt
| | - Emmanuel Kamal Aziz Saba
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Alexandria University, Egypt
| | | | - Amira Dimas Hanna Sarofeem
- Physical Medicine, Rheumatology and Rehabilitation Department, Ministry of Health, Alexandria Governorate, Egypt
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14
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Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun 2019; 10:2434. [PMID: 31164647 PMCID: PMC6547687 DOI: 10.1038/s41467-019-10439-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Aidan Keith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Rice
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Colin Shepherd
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - John Loughlin
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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15
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Hodgkinson T, Shen B, Diwan A, Hoyland JA, Richardson SM. Therapeutic potential of growth differentiation factors in the treatment of degenerative disc diseases. JOR Spine 2019; 2:e1045. [PMID: 31463459 PMCID: PMC6686806 DOI: 10.1002/jsp2.1045] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/16/2019] [Accepted: 02/04/2019] [Indexed: 02/06/2023] Open
Abstract
Intervertebral disc (IVD) degeneration is a major contributing factor to chronic low back pain and disability, leading to imbalance between anabolic and catabolic processes, altered extracellular matrix composition, loss of tissue hydration, inflammation, and impaired mechanical functionality. Current treatments aim to manage symptoms rather than treat underlying pathology. Therefore, IVD degeneration is a target for regenerative medicine strategies. Research has focused on understanding the molecular process of degeneration and the identification of various factors that may have the ability to halt and even reverse the degenerative process. One such family of growth factors, the growth differentiation factor (GDF) family, have shown particular promise for disc regeneration in in vitro and in vivo models of IVD degeneration. This review outlines our current understanding of IVD degeneration, and in this context, aims to discuss recent advancements in the use of GDF family members as anabolic factors for disc regeneration. An increasing body of evidence indicates that GDF family members are central to IVD homeostatic processes and are able to upregulate healthy nucleus pulposus cell marker genes in degenerative cells, induce mesenchymal stem cells to differentiate into nucleus pulposus cells and even act as chemotactic signals mobilizing resident cell populations during disc injury repair. The understanding of GDF signaling and its interplay with inflammatory and catabolic processes may be critical for the future development of effective IVD regeneration therapies.
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Affiliation(s)
- Tom Hodgkinson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchester Academic Health Sciences CentreManchesterUK
- Centre for the Cellular Microenvironment, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Bojiang Shen
- St. George Clinical SchoolUniversity of New South WalesSydneyNew South WalesAustralia
| | - Ashish Diwan
- St. George Clinical SchoolUniversity of New South WalesSydneyNew South WalesAustralia
| | - Judith A. Hoyland
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchester Academic Health Sciences CentreManchesterUK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation TrustManchester Academic Health Sciences CentreManchesterUK
| | - Stephen M. Richardson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchester Academic Health Sciences CentreManchesterUK
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16
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Interaction between GDF5 gene polymorphisms and environment factors increased the risk of knee osteoarthritis: a case-control study. Biosci Rep 2019; 39:BSR20182423. [PMID: 30777926 PMCID: PMC6390126 DOI: 10.1042/bsr20182423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/06/2019] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
Using a case–control design, we assessed the association between single nucleotide polymorphisms (SNPs) of growth and differentiation factor 5 (GDF5)/rs143383 gene and interaction with environments and knee osteoarthritis (KOA). We recruited 288 KOA patients from the First Clinical College, Henan University of Chinese Medicine between June 2017 and May 2018. There was significant difference in genotype distribution between case group and control group (χ2 = 22.661, P=0.000). The minor C allele was significantly higher in the case group than that in the control group (20.5 vs 8.1%, P=0.000, odds ratio (OR) = 1.62, 95% confidence interval (CI): 1.29–2.03). Significant differences were also observed in other gene models. For age, all models show significant differences (P<0.05) for those whose age was more than 60 years, and no significant difference was observed for those under 60 years. For non-smoking group, there were significant differences between case group and control group, and for smoker, significance level was found in TT compared with CC and allele gene models. Patients with drinking and Bbody mass index (MI )≥ 24 also showed significant relationship between rs143383 and osteoarthritis (OA) under the following models: TT vs CC (P=0.000, P=0.018), TT/CT vs CC (P=0.043), TT vs CT/CC (P=0.000, P=0.009), and T vs C (P=0.024, P=0.000). Other gene models indicated no significance (P>0.05). Our results revealed a possible genetic association between GDF5 and KOA, and the TT genotype of rs143383 increased the risk of KOA in Chinese Han population. The interaction between GDF5 gene and drinking, smoking, and obesity further increased the risk of KOA.
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17
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Skarp S, Kämäräinen OP, Wei GH, Jakkula E, Kiviranta I, Kröger H, Auvinen J, Lehenkari P, Ala-Kokko L, Männikkö M. Whole exome sequencing in Finnish families identifies new candidate genes for osteoarthritis. PLoS One 2018; 13:e0203313. [PMID: 30157244 PMCID: PMC6114922 DOI: 10.1371/journal.pone.0203313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Osteoarthritis (OA) is the most common degenerative joint disease and one of the major causes of disability worldwide. It is a multifactorial disorder with a significant genetic component. The heritability of OA has been estimated to be 60% for hip OA and 39% for knee OA. Genetic factors behind OA are still largely unknown. Studying families with strong history of OA, facilitates examining the co-segregation of genetic variation and OA. The aim of this study was to identify new, rare genetic factors and novel candidate genes for OA. METHODS Eight patients from three Finnish families with hip and knee OA were studied using whole exome sequencing. We focused on rare exonic variants with predicted pathogenicity and variants located in active promoter or strong enhancer regions. Expression of identified candidate genes were studied in bone and cartilage tissues and the observed variants were investigated using bioinformatic analyses. RESULTS Two rare variants co-segregated with OA in two families. In Family 8 a missense variant (c.628C>G, p.Arg210Gly) was observed in the OLIG3 gene that encodes a transcription factor known to be associated with rheumatoid arthritis and inflammatory polyarthritis. The Arg210Gly variant was estimated to be pathogenic by Polyphen-2 and Mutation taster and the locus is conserved among mammals. In Family 12 the observed variant (c.-127G>T) was located in the transcription start site of the FIP1L1 gene. FIP1L1 participates in the regulation of polyadenylation. The c.-127G>T is located in the transcription start site and may alter the DNA-binding of transcription factors. Both, OLIG3 and FIP1L1 were observed in human bone and cartilage. CONCLUSION The identified variants revealed novel candidate genes for OA. OLIG3 and FIP1L1 have specific roles in transcription and may effect expression of other genes. Identified variants in these genes may thus have a role in the regulatory events leading to OA.
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Affiliation(s)
- Sini Skarp
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- * E-mail:
| | | | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Eveliina Jakkula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ilkka Kiviranta
- Department of Orthopaedics and Traumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Orthopaedics and Traumatology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Heikki Kröger
- Department of Orthopaedics and Traumatology, Kuopio University Hospital and Kuopio Musculoskeletal Research Unit, University of Eastern Finland, Kuopio, Finland
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Petri Lehenkari
- Department of Anatomy and Cell biology and Surgery Clinic, Medical Research Center, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Leena Ala-Kokko
- Connective Tissue Gene Tests, Allentown, PA, United States of America
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Northern Finland Birth Cohort, Faculty of Medicine, University of Oulu, Oulu, Finland
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18
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Shepherd C, Zhu D, Skelton AJ, Combe J, Threadgold H, Zhu L, Vincent TL, Stuart P, Reynard LN, Loughlin J. Functional Characterization of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies rs12915901 as a Key Target Variant. Arthritis Rheumatol 2018; 70:1577-1587. [PMID: 29732726 PMCID: PMC6175168 DOI: 10.1002/art.40545] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To identify the functional single-nucleotide polymorphisms (SNPs) and mechanisms conferring increased risk of hand osteoarthritis (OA) at the ALDH1A2 locus, which is a retinoic acid regulatory gene. METHODS Tissue samples from 247 patients with knee, hip, or hand OA who had undergone joint surgery were included. RNA-sequencing analysis was used to investigate differential expression of ALDH1A2 and other retinoic acid signaling pathway genes in cartilage. Expression of ALDH1A2 in joint tissues obtained from multiple sites was quantified using quantitative reverse transcription-polymerase chain reaction. Allelic expression imbalance (AEI) was measured by pyrosequencing. The consequences of ALDH1A2 depletion by RNA interference were assessed in primary human chondrocytes. In silico and in vitro analyses were used to pinpoint which, among 62 highly correlated SNPs, could account for the association at the locus. RESULTS ALDH1A2 expression was observed across multiple joint tissue samples, including osteochondral tissue from the hand. The expression of ALDH1A2 and of several retinoic acid signaling genes was different in diseased cartilage compared to non-diseased cartilage, with ALDH1A2 showing lower levels in OA cartilage. Experimental depletion of ALDH1A2 resulted in changes in the expression levels of a number of chondrogenic markers, including SOX9. In addition, reduced expression of the OA risk-conferring allele was witnessed in a number of joint tissues, with the strongest effect in cartilage. The intronic SNP rs12915901 recapitulated the AEI observed in patient tissues, while the Ets transcription factors were identified as potential mediators of this effect. CONCLUSION The ALDH1A2 locus seems to increase the risk of hand OA through decreased expression of ALDH1A2 in joint tissues, with the effect dependent on rs12915901. These findings indicate a mechanism that may now be targeted to modulate OA risk.
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Affiliation(s)
| | - Dongxing Zhu
- Newcastle University, Newcastle upon Tyne, UK, and Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, and Guangzhou Medical University, Guangzhou, China
| | | | | | | | - Linyi Zhu
- Arthritis Research UK Centre for OA Pathogenesis, University of Oxford, Oxford, UK
| | - Tonia L Vincent
- Arthritis Research UK Centre for OA Pathogenesis, University of Oxford, Oxford, UK
| | - Paul Stuart
- Newcastle University Teaching Hospitals NHS Trust, Freeman Hospital, Newcastle upon Tyne, UK
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19
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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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20
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Wang Z, Li Y, Wang Y, Wang X, Zhang J, Tian J. Association between GDF5 single nucleotide polymorphism rs143383 and lumbar disc degeneration. Exp Ther Med 2018; 16:1900-1904. [PMID: 30186416 PMCID: PMC6122412 DOI: 10.3892/etm.2018.6382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/21/2018] [Indexed: 01/02/2023] Open
Abstract
The association between growth differentiation factor 5 (GDF5), single nucleotide polymorphism (SNP) rs143383 and lumbar disc degeneration (LDD) was investigated. A total of 210 patients with LDD (observation group) and 320 patients without lumbar diseases (control group) diagnosed in Shanghai General Hospital of Nanjing Medical University from August 2013 to March 2017 were randomly selected. Then, deoxyribonucleic acid (DNA) was extracted from the blood of each patient, and Taq-man fluorescent quantitative polymerase chain reaction (qPCR) technique was used to detect rs143383 in GFD5 gene. The frequency of different genotypes in observation group and control group was counted, and the associations between different SNP genotypes and the incidence of LDD were analyzed. Good genotyping results were found in both LDD patient group and control group. There were no significant differences in distribution frequency of TT and TC genotypes at site rs143383 between LDD patient group and control group (P>0.05), but the distribution frequency of CC genotype at site rs143383 in LDD patient group had a statistically significant difference from that in control group (P<0.05). In dominant models, odds ratio (OR) of (TC+CC/TT) was 1.195 (P=0.532). In recessive models, OR of (CC/TT+TC) was 4.333 (P=0.028). In co-dominant models, ORs of (TC/TT) and (CC/TT) were 0.967 and 4.43, respectively (P=0.99). The differences in 3 genotypes showed no statistical significance among different pathological grades (Grade I to V) (χ2=1.034, P=0.998), and there was no statistically significant difference in T and C (χ2=0.012, P=0.999). Pathological grades in dominant models, recessive models and over dominant models were analyzed, and no statistically significant difference was found (P>0.05). In conclusion, CC mutant type at rs143383 in GDF5 gene has a strong association with the incidence of LDD, and a high prevalence risk, but it has no evident correlation with pathological grades.
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Affiliation(s)
- Zhen Wang
- Clinical Medical College, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, P.R. China.,Department of Orthopedics, The Third People's Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Yuqian Li
- Department of Orthopedics, The Third People's Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Yunhao Wang
- Shanghai Jiao Tong University School of Medicine, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai 200080, P.R. China
| | - Xiaodong Wang
- Department of Orthopedics, The Third People's Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Jianhua Zhang
- Department of Orthopedics, The Third People's Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Jiwei Tian
- Department of Orthopedics, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, P.R. China
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Li H, Zhang X, Cao Y, Hu S, Peng F, Zhou J, Li J. Association between EN1 rs4144782 and susceptibility of knee osteoarthritis: A case-control study. Oncotarget 2018; 8:36650-36657. [PMID: 28430581 PMCID: PMC5482684 DOI: 10.18632/oncotarget.16842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/10/2017] [Indexed: 11/25/2022] Open
Abstract
Osteoarthritis (OA) is a complex disease that affects the whole joint, resulting from the combined influence of biomechanical factors and genetic factors. The heritable component for primary OA accounts for about 60% of variation in population liability to the disease. So far, genome-wide association studies (GWAS) and candidate gene studies have established many OA-related loci. However, these findings account for only a rather small fraction of the genetic component. To further reveal the genetic architecture of OA, we conducted this case-control study to explore the association of locus EN1 rs4144782 and knee OA susceptibility in a Chinese population. EN1 rs4144782 was significantly associated with increased risk of knee OA (OR=1.26; 95% CI: 1.05-1.50, P value=0.012). In dominant model, compared with carriers of GG genotype, those with AG or AA genotype have an 1.44-fold increased risk of OA (OR: 1.44; 95% CI: 1.10-1.88; P value=0.008). Subgroup analyses didn't change the results materially. This should be the first association study of EN1 locus on risk of OA, and our finding suggested that the EN1 rs4144782 might contribute to the susceptibility of knee OA.
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Affiliation(s)
- Haohuan Li
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaolong Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yiping Cao
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Department of Physiology, Jianghan University, Wuhan Medical College, Wuhan, 430056, China
| | - Fei Peng
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jianlin Zhou
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jianping Li
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, 430060, China
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Cibrián Uhalte E, Wilkinson JM, Southam L, Zeggini E. Pathways to understanding the genomic aetiology of osteoarthritis. Hum Mol Genet 2018; 26:R193-R201. [PMID: 28977450 PMCID: PMC5886472 DOI: 10.1093/hmg/ddx302] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
Osteoarthritis is a common, complex disease with no curative therapy. In this review, we summarize current knowledge on disease aetiopathogenesis and outline genetics and genomics approaches that are helping catalyse a much-needed improved understanding of the biological underpinning of disease development and progression.
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Affiliation(s)
- Elena Cibrián Uhalte
- Human Genetics and Cellular Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Jeremy Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Lorraine Southam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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Lu R, Mucaki EJ, Rogan PK. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs. Nucleic Acids Res 2017; 45:e27. [PMID: 27899659 PMCID: PMC5389469 DOI: 10.1093/nar/gkw1036] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes.
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Affiliation(s)
- Ruipeng Lu
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada
| | - Peter K Rogan
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada.,Department of Oncology, Western University, London, Ontario, N6A 4L6, Canada.,Cytognomix Inc., London, Ontario, N5X 3X5, Canada
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Abstract
Rheumatic diseases follow a characteristic anatomical pattern of joint and organ involvement. This Review explores three interconnected mechanisms that might be involved in the predilection of specific joints for developing specific forms of arthritis: site-specific local cell types that drive disease; systemic triggers that affect local cell types; and site-specific exogenous factors, such as focal mechanical stress, that activate cells locally. The embryonic development of limbs and joints is also relevant to the propensity of certain joints to develop arthritis. Additionally, location-specific homeostasis and disease occurs in skin and blood vessels, thereby extending the concept of site-specificity in human diseases beyond rheumatology. Acknowledging the importance of site-specific parameters increases the complexity of current disease paradigms and brings us closer to understanding why particular disease processes manifest at a particular location.
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Abd Elazeem MI, Abdelaleem EA, Mohamed RA. Genetic influence of growth and differentiation factor 5 gene polymorphism (+104T/C) on the development of knee osteoarthritis and its association with disease severity. Eur J Rheumatol 2017. [PMID: 28638680 DOI: 10.5152/eurjrheum.2017.160093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE The growth and differentiation factor 5 (GDF5) gene is recognized for its role in the development, repair, and maintenance of cartilage and bone. The present case-control study was conducted to detect the genetic association between GDF5 (+104T/C) single-nucleotide polymorphism (SNP) and primary knee osteoarthritis (KOA), as well as the possible association of SNP with the severity of KOA. MATERIAL AND METHODS The study included 50 patients with primary KOA and 50 healthy control subjects. The severity of the disease was assessed by using the Kellgren-Laurence (K-L) grading system and aided by the Western Ontario & McMaster Universities Osteoarthritis Index (WOMAC) score, visual analog scale (VAS) score, and tenderness score. The genetic association of the SNP with primary KOA was assessed by means of the TaqMan® allelic discrimination technique. RESULTS The radiological assessment of patients according to the K-L grading system revealed a statistically significant association between the wild-type (TT) genotype and disease severity in both the right and left knees (p=0.049). The frequency distribution of patients with VAS score ≤6 was significantly higher in patients carrying the TT genotype (p=0.005) as compared to the CT and CC genotypes. The mean WOMAC score was significantly higher in patients carrying the TT genotype as compared to patients carrying the CC and CT genotypes (p=0.017). No statistically significant association was detected on comparing the frequency distribution of allele and genotype frequencies of the SNP in patients and healthy controls. CONCLUSION The results of the current study revealed a possible genetic association between GDF5 (+104T/C) SNP and the severity of KOA, which might be of benefit for the detection of patients with a high risk for disease progression. The present study did not detect an association between the SNP and development of KOA.
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Affiliation(s)
- Mervat I Abd Elazeem
- Department of Rheumatology and Rehabilitation, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
| | - Enas Abolkheir Abdelaleem
- Department of Rheumatology and Rehabilitation, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
| | - Rabab A Mohamed
- Department of Clinical and Chemical Pathology, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
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Haro E, Watson BA, Feenstra JM, Tegeler L, Pira CU, Mohan S, Oberg KC. Lmx1b-targeted cis-regulatory modules involved in limb dorsalization. Development 2017; 144:2009-2020. [DOI: 10.1242/dev.146332] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/17/2017] [Indexed: 12/28/2022]
Abstract
Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b at E12.5 followed by next generation sequencing (ChIP-seq). Nearly 84% (n=617) of the Lmx1b-bound genomic intervals (LBIs) identified overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs). In addition, 73 LBIs mapped to known CRMs active during limb development. We compared Lmx1b-bound PCRMs to genes differentially expressed by Lmx1b and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontologic analysis suggests that Lmx1b targets extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of a PCRM associated with joint-related Gdf5 that provides a mechanism for Lmx1b-mediated joint modification and a PCRM associated with Lmx1b that suggests a role in autoregulation. This is the first report to describe genome-wide Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.
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Affiliation(s)
- Endika Haro
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
| | - Billy A. Watson
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
| | - Jennifer M. Feenstra
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
| | - Luke Tegeler
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
| | - Charmaine U. Pira
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
| | - Subburaman Mohan
- Musculoskeletal Disease Center, Loma Linda VA HealthCare System, Loma Linda, CA, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA
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Warner SC, Valdes AM. Genetic association studies in osteoarthritis: is it fairytale? Curr Opin Rheumatol 2017; 29:103-109. [DOI: 10.1097/bor.0000000000000352] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Reynard LN, Ratnayake M, Santibanez-Koref M, Loughlin J. Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11-A Bioinformatics and Molecular Study. PLoS One 2016; 11:e0159024. [PMID: 27391021 PMCID: PMC4938163 DOI: 10.1371/journal.pone.0159024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023] Open
Abstract
The single nucleotide polymorphism (SNP) rs835487 is associated with hip osteoarthritis (OA) at the genome-wide significance level and is located within CHST11, which codes for carbohydrate sulfotransferase 11. This enzyme post-translationally modifies proteoglycan prior to its deposition in the cartilage extracellular matrix. Using bioinformatics and experimental analyses, our aims were to characterise the rs835487 association signal and to identify the causal functional variant/s. Database searches revealed that rs835487 resides within a linkage disequilibrium (LD) block of only 2.7 kb and is in LD (r2 ≥ 0.8) with six other SNPs. These are all located within intron 2 of CHST11, in a region that has predicted enhancer activity and which shows a high degree of conservation in primates. Luciferase reporter assays revealed that of the seven SNPs, rs835487 and rs835488, which have a pairwise r2 of 0.962, are the top functional candidates; the haplotype composed of the OA-risk conferring G allele of rs835487 and the corresponding T allele of rs835488 (the G-T haplotype) demonstrated significantly different enhancer activity relative to the haplotype composed of the non-risk A allele of rs835487 and the corresponding C allele of rs835488 (the A-C haplotype) (p < 0.001). Electrophoretic mobility shift assays and supershifts identified several transcription factors that bind more strongly to the risk-conferring G and T alleles of the two SNPs, including SP1, SP3, YY1 and SUB1. CHST11 was found to be upregulated in OA versus non-OA cartilage (p < 0.001) and was expressed dynamically during chondrogenesis. Its expression in adult cartilage did not however correlate with rs835487 genotype. Our data demonstrate that the OA susceptibility is mediated by differential protein binding to the alleles of rs835487 and rs835488, which are located within an enhancer whose target may be CHST11 during chondrogenesis or an alternative gene.
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Affiliation(s)
- Louise N. Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| | - Madhushika Ratnayake
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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Li W, Zheng NZ, Yuan Q, Xu K, Yang F, Gu L, Zheng GY, Luo GJ, Fan C, Ji GJ, Zhang B, Cao H, Tian XL. NFAT5-mediated CACNA1C expression is critical for cardiac electrophysiological development and maturation. J Mol Med (Berl) 2016; 94:993-1002. [PMID: 27368804 DOI: 10.1007/s00109-016-1444-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/18/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023]
Abstract
UNLABELLED Entry of calcium into cardiomyocyte via L-type calcium channel (LTCC) is fundamental to cardiac contraction. CACNA1C, a type of LTCC and a hallmark of a matured ventricular myocyte, is developmentally regulated. Here, we identified 138 potential transcription factors by a comparative genomic study on 5-kb promoter regions of CACNA1C gene across eight vertebrate species, and showed that six factors were developmentally regulated with the expression of Cacna1c in mouse P19cl6 in vitro cardiomyocyte differentiation model. We further demonstrated that the nuclear factor of activated T cells 5 (Nfat5) bound to a consensus sequence TGGAAGCGTTC and activated the transcription of Cacna1c. The siRNA-mediated knockdown of Nfat5 suppressed the expression of Cacna1c and decreased L-type calcium current in mouse neonatal cardiomyocytes. Furthermore, morpholino-mediated knockdown of nfat5 in zebrafish prohibited the expression of cacna1c and resulted in a non-contractile ventricle, while over-expression of either cacna1c or nfat5 rescued this impaired phenotype. Thus, NFAT5-mediated expression of CACNA1C is evolutionarily conserved and critical for cardiac electrophysiological development and maturation of cardiomyocyte. KEY MESSAGE Nfat5 binds to a consensus sequence TGGAAGCGTTC in the promoter of Cacna1c. Nfat5 activates the transcription of Cacna1c. Nfat5 knockdown suppresses Cacna1c expression, decreases L-type calcium current, and results in non-beating ventricle. NFAT5-mediated expression of CACNA1C is evolutionarily conserved. NFAT5-mediated CACNA1C expression is critical for cardiac electrophysiological development and maturation.
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Affiliation(s)
- Wei Li
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Nai-Zhong Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Qi Yuan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Ke Xu
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Fan Yang
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Lei Gu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Gu-Yan Zheng
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Guo-Jie Luo
- School of Electronics Engineering and Computer Science, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Chun Fan
- Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Guang-Ju Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing, 100871, China
| | - Huiqing Cao
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China.
| | - Xiao-Li Tian
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, 5 Yiheyuan Road, Beijing, 100871, China.
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Zhao L, Chang Q, Huang T, Huang C. Prospective cohort study of the risk factors for stress fractures in Chinese male infantry recruits. J Int Med Res 2016; 44:787-95. [PMID: 27207942 PMCID: PMC5536631 DOI: 10.1177/0300060516639751] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/28/2016] [Indexed: 11/15/2022] Open
Abstract
Objective To determine potential risk factors that could predict stress fractures over an 8-week basic military training in Chinese male infantry recruits. Methods Recruits from three infantry units enrolled in this prospective study. At baseline, demographic data, personal history of stress fractures, mean duration of weekly exercise and smoking history were recorded on questionnaires and blood samples taken for analysis of bone turnover biomarkers and genetic factors. Results Of the 1516 male recruits who volunteered to participate in the study, 1398 recruits provided data for analysis. In total, 189 stress fracture cases were observed (incidence rate: 13.5%) during the 8-week training period. Recruits with stress fractures had a significantly higher incidence of prior fracture history and lower exercise level prior to enrolment compared with those without stress fractures. A significant difference in both allelic frequency and genotypic distribution of the growth differentiation factor 5 (GDF5) gene rs143383 polymorphism was observed between recruits with and without stress fractures. However, no difference in serum bone turnover biomarkers was detected between groups. Conclusion This prospective, cohort study indicates that fracture history, lower exercise level and GDF5 rs143383 may be predictive risk factors for stress fractures in Chinese male infantry recruits.
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Affiliation(s)
- Lin Zhao
- Institute of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shannxi, China
| | - Qi Chang
- Institute of Training Related Medical Sciences, the 150th Hospital of Chinese PLA, Luoyang, Henan, China
| | - Tao Huang
- Institute of Training Related Medical Sciences, the 150th Hospital of Chinese PLA, Luoyang, Henan, China
| | - Changlin Huang
- Institute of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shannxi, China
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Reynard LN. Analysis of genetics and DNA methylation in osteoarthritis: What have we learnt about the disease? Semin Cell Dev Biol 2016; 62:57-66. [PMID: 27130636 DOI: 10.1016/j.semcdb.2016.04.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/25/2016] [Indexed: 01/30/2023]
Abstract
Osteoarthritis (OA) is a chronic musculoskeletal disease characterised by the destruction of articular cartilage, synovial inflammation and bone remodelling. Disease aetiology is complex and highly heritable, with genetic variation estimated to contribute to 50% of OA occurrence. Epigenetic alterations, including DNA methylation changes, have also been implicated in OA pathophysiology. This review examines what genetic and DNA methylation studies have taught us about the genes and pathways involved in OA pathology. The influence of DNA methylation on the molecular mechanisms underlying OA genetic risk and the consequence of this interaction on disease susceptibility and penetrance are also discussed.
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Affiliation(s)
- Louise N Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, NE2 4HH, UK.
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Gee F, Rushton MD, Loughlin J, Reynard LN. Correlation of the osteoarthritis susceptibility variants that map to chromosome 20q13 with an expression quantitative trait locus operating on NCOA3 and with functional variation at the polymorphism rs116855380. Arthritis Rheumatol 2016. [PMID: 26211391 PMCID: PMC4832313 DOI: 10.1002/art.39278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Objective To functionally characterize the osteoarthritis (OA) susceptibility variants that map to a region of high linkage disequilibrium (LD) on chromosome 20q13 marked by the single‐nucleotide polymorphism (SNP) rs6094710 and encompassing NCOA3 and SULF2. Methods Nucleic acids were extracted from the cartilage of OA patients. Overall and allelic expression of NCOA3 and SULF2 were measured by quantitative reverse transcription–polymerase chain reaction and pyrosequencing, respectively. The functional effect of SNPs within the 20q13 locus was assessed in vitro using luciferase reporter constructs and electrophoretic mobility shift assays (EMSAs). The in vivo effect of nuclear receptor coactivator 3 (NCOA3) protein depletion on primary human OA articular cartilage chondrocytes was assessed using RNA interference. Results Expression of NCOA3 correlated with the genotype at rs6094710 (P = 0.006), and the gene demonstrated allelic expression imbalance (AEI) in individuals heterozygous for the SNP (mean AEI 1.21; P < 0.0001). In both instances, expression of the OA‐associated allele was reduced. In addition, there was reduced enhancer activity of the OA‐associated allele of rs116855380, a SNP in perfect LD with rs6094710 in luciferase assays (P < 0.001). EMSAs demonstrated a protein complex binding with reduced affinity to this allele. Depletion of NCOA3 led to significant changes (all P < 0.05) in the expression of genes involved in cartilage homeostasis. Conclusion NCOA3 is subject to a cis‐acting expression quantitative trait locus in articular cartilage, which correlates with the OA association signal and with the OA‐associated allele of the functional SNP rs116855380, a SNP that is located only 10.3 kb upstream of NCOA3. These findings elucidate the effect of the association of the 20q13 region on OA cartilage and provide compelling evidence of a potentially causal candidate SNP.
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Affiliation(s)
- Fiona Gee
- Newcastle University, Newcastle upon Tyne, UK
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Abstract
Purpose of review Powerful association studies have identified a number of genetic signals that can be confidently judged as associated with osteoarthritis. Efforts have continued to discover new loci, whilst functional studies are being applied to assess which genes are the likely targets of the risk-conferring alleles. The study of epigenetics has highlighted an interaction between osteoarthritis genetics and DNA methylation. This review will summarize some of the recent key studies in osteoarthritis genetics, including functional and epigenetic analyses. Recent findings Several novel osteoarthritis susceptibility loci have been reported recently, including the regulatory genes NCOA3 and ALDH1A2. Functional analyses of these genes and of others reported previously support earlier suggestions that osteoarthritis susceptibility is principally mediated by modulations to gene expression. DNA methylation analyses provide additional insights into the osteoarthritis disease process, at both a genome-wide level and when investigating direct interactions with risk-conferring alleles. Summary Osteoarthritis genetic risk predominantly acts by modulating gene expression, an effect typically mediated via transcriptional regulation. Effects on various pathways have been detected, including cell differentiation and cartilage homeostasis. The continued identification of risk loci, their functional study, and the unification of genetic and epigenetic analyses will be key themes in the future.
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Rushton MD, Reynard LN, Young DA, Shepherd C, Aubourg G, Gee F, Darlay R, Deehan D, Cordell HJ, Loughlin J. Methylation quantitative trait locus analysis of osteoarthritis links epigenetics with genetic risk. Hum Mol Genet 2015; 24:7432-44. [PMID: 26464490 PMCID: PMC4664171 DOI: 10.1093/hmg/ddv433] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/09/2015] [Indexed: 01/11/2023] Open
Abstract
Osteoarthritis (OA) is a common, painful and debilitating disease of articulating joints resulting from the age-associated loss of cartilage. Well-powered genetic studies have identified a number of DNA polymorphisms that are associated with OA susceptibility. Like most complex trait loci, these OA loci are thought to influence disease susceptibility through the regulation of gene expression, so-called expression quantitative loci, or eQTLs. One mechanism through which eQTLs act is epigenetic, by modulating DNA methylation. In such cases, there are quantitative differences in DNA methylation between the two alleles of the causal polymorphism, with the association signal referred to as a methylation quantitative trait locus, or meQTL. In this study, we aimed to investigate whether the OA susceptibility loci identified to date are functioning as meQTLs by integrating genotype data with whole genome methylation data of cartilage DNA. We investigated potential genotype-methylation correlations within a 1.0-1.5 Mb region surrounding each of 16 OA-associated single-nucleotide polymorphisms (SNPs) in 99 cartilage samples and identified four that function as meQTLs. Three of these replicated in an additional cohort of up to 62 OA patients. These observations suggest that OA susceptibility loci regulate the level of DNA methylation in cis and provide a mechanistic explanation as to how these loci impact upon OA susceptibility, further increasing our understanding of the role of genetics and epigenetics in this common disease.
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Affiliation(s)
| | - Louise N Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine and
| | - David A Young
- Musculoskeletal Research Group, Institute of Cellular Medicine and
| | - Colin Shepherd
- Musculoskeletal Research Group, Institute of Cellular Medicine and
| | | | - Fiona Gee
- Musculoskeletal Research Group, Institute of Cellular Medicine and
| | - Rebecca Darlay
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK and
| | - David Deehan
- Musculoskeletal Research Group, Institute of Cellular Medicine and, Freeman Hospital, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Heather J Cordell
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK and
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine and,
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Ramos YFM, Meulenbelt I. Implementation of Functional Genomics for Bench-to-Bedside Transition in Osteoarthritis. Curr Rheumatol Rep 2015; 17:53. [DOI: 10.1007/s11926-015-0528-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Zhang R, Yao J, Xu P, Ji B, Luck JV, Chin B, Lu S, Kelsoe JR, Ma J. A comprehensive meta-analysis of association between genetic variants of GDF5 and osteoarthritis of the knee, hip and hand. Inflamm Res 2015; 64:405-14. [DOI: 10.1007/s00011-015-0818-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022] Open
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Emerging targets in osteoarthritis therapy. Curr Opin Pharmacol 2015; 22:51-63. [PMID: 25863583 DOI: 10.1016/j.coph.2015.03.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 02/08/2023]
Abstract
Osteoarthritis (OA) is a destructive joint disease in which the initiation may be attributed to direct injury and mechanical disruption of joint tissues, but the progressive changes are dependent on active cell-mediated processes that can be observed or inferred during the generally long time-course of the disease. Based on clinical observations and experimental studies, it is now recognized a that it is possible for individual patients to exhibit common sets of symptoms and structural abnormalities due to distinct pathophysiological pathways that act independently or in combination. Recent research that has focused on the underlying mechanisms involving biochemical cross talk among the cartilage, synovium, bone, and other joint tissues within a background of poorly characterized genetic factors will be addressed in this review.
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Xiao JL, Meng JH, Gan YH, Zhou CY, Ma XC. Association of GDF5, SMAD3 and RUNX2 polymorphisms with temporomandibular joint osteoarthritis in female Han Chinese. J Oral Rehabil 2015; 42:529-36. [PMID: 25757091 DOI: 10.1111/joor.12286] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2015] [Indexed: 01/06/2023]
Affiliation(s)
- J.-L. Xiao
- Department of Oral and Maxillofacial Surgery; Peking University School and Hospital of Stomatology; Beijing China
| | - J.-H. Meng
- Department of Oral and Maxillofacial Surgery; Peking University School and Hospital of Stomatology; Beijing China
| | - Y.-H. Gan
- Center for Temporomandibular Joint Disorder and Orofacial Pain; Peking University School and Hospital of Stomatology; Beijing China
| | - C.-Y. Zhou
- Department of Biochemistry and Molecular Biology; Peking University School of Basic Medical Sciences; Beijing China
| | - X.-C. Ma
- Center for Temporomandibular Joint Disorder and Orofacial Pain; Peking University School and Hospital of Stomatology; Beijing China
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Huang Q. Genetic study of complex diseases in the post-GWAS era. J Genet Genomics 2015; 42:87-98. [PMID: 25819085 DOI: 10.1016/j.jgg.2015.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWASs) have identified thousands of genes and genetic variants (mainly SNPs) that contribute to complex diseases in humans. Functional characterization and mechanistic elucidation of these SNPs and genes action are the next major challenge. It has been well established that SNPs altering the amino acids of protein-coding genes can drastically impact protein function, and play an important role in molecular pathogenesis. Functions of regulatory SNPs can be complex and elusive, and involve gene expression regulation through the effect on RNA splicing, transcription factor binding, DNA methylation and miRNA recruitment. In the present review, we summarize the recent progress in our understanding of functional consequences of GWAS-associated non-coding regulatory SNPs, and discuss the application of systems genetics and network biology in the interpretation of GWAS findings.
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Affiliation(s)
- Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan 430079, China.
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Rodriguez-Fontenla C, Gonzalez A. Genética de la artrosis. ACTA ACUST UNITED AC 2015; 11:33-40. [DOI: 10.1016/j.reuma.2014.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/06/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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Tsezou A. Osteoarthritis year in review 2014: genetics and genomics. Osteoarthritis Cartilage 2014; 22:2017-24. [PMID: 25456297 DOI: 10.1016/j.joca.2014.07.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 02/02/2023]
Abstract
Recent developments in genetics/genomics of osteoarthritis (OA) are discussed to improve our understanding of OA pathophysiology. The discovery of a novel variant near the NCOA3 (nuclear receptor coactivator 3) gene associated with hip OA and the regulation of GDF5 gene by four transcription factors via the OA susceptibility locus rs143383 are among important findings in OA genetics. Several microarray-based gene expression studies were published for different tissues of the joint. In OA synovium elevation of collagens and cross-linking enzymes (COL1A1, COL5A1, PLOD2, LOX and TIMP1) responsive to TGF-β was found as well as differential expression pattern between different areas of the osteoarthritic synovial membrane. In OA peripheral blood the role of apoptotic genes was highlighted, while whole genome expression profiling in OA subchondral bone and cartilage revealed common genes in cartilage and bone to be involved in OA development. In epigenetics, several microRNAs (miRNAs) were found to regulate genes' expression in chondrocytes, among which miR-125, miR-127b miR-21, miR-148a and their use as potential drug targets was highlighted. Future studies must focus on the integration of genetics, genomics and epigenetics for the identification of signaling pathways and regulatory networks responsible for OA development.
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Affiliation(s)
- A Tsezou
- University of Thessaly, Faculty of Medicine, Dept. Biology, 41110 Larissa, Greece
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Reynard LN, Bui C, Syddall CM, Loughlin J. CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383. Hum Genet 2014; 133:1059-73. [PMID: 24861163 PMCID: PMC4099533 DOI: 10.1007/s00439-014-1447-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/12/2014] [Indexed: 01/25/2023]
Abstract
GDF5 encodes an extracellular signalling molecule that is essential for normal skeletal development. The rs144383 C to T SNP located in the 5'UTR of this gene is functional and has a pleiotropic effect on the musculoskeletal system, being a risk factor for knee-osteoarthritis (OA), congenital hip dysplasia, lumbar disc degeneration and Achilles tendon pathology. rs143383 exerts a joint-wide effect on GDF5 expression, with expression of the OA-associated T allele being significantly reduced relative to the C allele, termed allelic expression imbalance. We have previously reported that the GDF5 locus is subject to DNA methylation and that allelic imbalance of rs143383 is mediated by SP1, SP3 and DEAF1 transcriptional repressors. In this study, we have assayed GDF5 methylation in normal and osteoarthritic cartilage, and investigated the effect of methylation on the allelic imbalance of rs143383. We observed demethylation of the GDF5 5'UTR in OA knee cartilage relative to both OA (p = 0.009) and non-OA (p = 0.001) hip cartilage, with the most significant demethylation observed at the highly conserved +37 CpG site located 4 bp upstream of rs143383. Methylation modulates the level and direction of allelic imbalance of rs143383, with methylation of the +37 CpG dinucleotide within the SP1/SP3 binding site having an allele-specific effect on SP1 and SP3 binding. Furthermore, methylation attenuated the repressive effects of SP1, SP3 and DEAF1 on GDF5 promoter activity. This data suggest that the differential methylation of the +37 CpG site between osteoarthritic hip and knee cartilage may be responsible for the knee-specific effect of rs143383 on OA susceptibility.
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Affiliation(s)
- Louise N Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, 4th Floor Catherine Cookson Building, The Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK,
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Swindell WR, Stuart PE, Sarkar MK, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era. BMC Med Genomics 2014; 7:27. [PMID: 24885462 PMCID: PMC4060870 DOI: 10.1186/1755-8794-7-27] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 05/16/2014] [Indexed: 12/20/2022] Open
Abstract
Background Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings. Methods We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding. Results Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4. Conclusions These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA.
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Gruber HE, Hoelscher GL, Ingram JA, Bethea S, Hanley EN. Growth and differentiation factor-5 (GDF-5) in the human intervertebral annulus cells and its modulation by IL-1ß and TNF-α in vitro. Exp Mol Pathol 2014; 96:225-9. [DOI: 10.1016/j.yexmp.2014.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 02/17/2014] [Indexed: 10/25/2022]
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Insights from human genetic studies into the pathways involved in osteoarthritis. Nat Rev Rheumatol 2013; 9:573-83. [DOI: 10.1038/nrrheum.2013.121] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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