An epigenome-wide view of osteoarthritis in primary tissues

Kreitmaier, Peter; Suderman, Matthew; Southam, Lorraine; Almeida, Rodrigo Coutinho de; Hatzikotoulas, Konstantinos; Meulenbelt, Ingrid; Steinberg, Julia; Relton, Caroline; Wilkinson, J. Mark; Zeggini, Eleftheria

doi:10.1016/j.ajhg.2022.05.010

Cited by 20 publications

(33 citation statements)

References 61 publications

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“…To establish if any of the variants in the credible set were also chondrocyte molecular quantitative trait loci (QTLs), we queried the largest available chondrocyte functional genomics datasets. We looked for expression QTLs (eQTLs), protein QTLs (pQTLs), differential protein abundance,39 differential expression40 and methylation QTLs (methQTLs) 41. These functional datasets were generated in chondrocytes from approximately 100 individuals with knee osteoarthritis undergoing joint replacement.…”

Section: Methodsmentioning

confidence: 99%

Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Bittner,

Shi,

Zhao

et al. 2024

Ann Rheum Dis

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ObjectivesOsteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organisation in three-dimensional (3D) space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner. Here, we generate the first whole genome chromosome conformation analysis (Hi-C) map of primary osteoarthritis chondrocytes and identify novel candidate effector genes for the disease.MethodsPrimary chondrocytes collected from 8 patients with knee osteoarthritis underwent Hi-C analysis to link chromosomal structure to genomic sequence. The identified loops were then combined with osteoarthritis GWAS results and epigenomic data from primary knee osteoarthritis chondrocytes to identify variants involved in gene regulation via enhancer-promoter interactions.ResultsWe identified 345 genetic variants residing within chromatin loop anchors that are associated with 77 osteoarthritis GWAS signals. Ten of these variants reside directly in enhancer regions of 10 newly described active enhancer-promoter loops, identified with multiomics analysis of publicly available chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data from primary knee chondrocyte cells, pointing to two new candidate effector genesSPRY4andPAPPA (pregnancy-associated plasma protein A)as well as further support for the geneSLC44A2known to be involved in osteoarthritis. For example, PAPPA is directly associated with the turnover of insulin-like growth factor 1 (IGF-1) proteins, and IGF-1 is an important factor in the repair of damaged chondrocytes.ConclusionsWe have constructed the first Hi-C map of primary human chondrocytes and have made it available as a resource for the scientific community. By integrating 3D genomics with large-scale genetic association and epigenetic data, we identify novel candidate effector genes for osteoarthritis, which enhance our understanding of disease and can serve as putative high-value novel drug targets.

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Section: Methodsmentioning

confidence: 99%

Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Bittner,

Shi,

Zhao

et al. 2024

Ann Rheum Dis

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“…When this is known for a locus/pathway, intelligent timing of a pharmacological intervention can then be undertaken, and those which act in later life can be prioritised. Investigations that directly compare multiple joint tissues have also recently proven insightful into the molecular basis of the disease 8,57 . Such studies undertaken throughout the life course will be vital to further elucidate the tissue-specific gene regulatory networks contributing to disease, paving the way for therapeutic intervention.…”

Section: Discussionmentioning

confidence: 99%

“…OA is a global leading cause of disability amongst older adults, hallmarked by the degradation of articular cartilage in the joints, most commonly the hip or knee. Studies of the aged cartilage methylome have revealed distinct epigenomic signatures between disease states 8,9 , and between joint sites themselves 10,11 , increasing our understanding of the joint specificity of disease. OA is multifactorial, with genetic risk factors contributing to ∼30% of the lifetime risk of developing knee OA.…”

Section: Introductionmentioning

confidence: 99%

Epigenetic mechanisms of osteoarthritis risk in human skeletal development

McDonnell,

Orr,

Barter

et al. 2024

Preprint

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The epigenome, including the methylation of cytosine bases at CG dinucleotides, is intrinsically linked to transcriptional regulation. The tight regulation of gene expression during skeletal development is essential, with ~1/500 individuals born with skeletal abnormalities. Furthermore, increasing evidence is emerging to link age-associated complex genetic musculoskeletal diseases, including osteoarthritis (OA), to developmental factors including joint shape. Multiple studies have shown a functional role for DNA methylation in the genetic mechanisms of OA risk using articular cartilage samples taken from aged patients. Despite this, our knowledge of temporal changes to the methylome during human cartilage development has been limited. We quantified DNA methylation at ~700,000 individual CpGs across the epigenome of developing human articular cartilage in 72 samples ranging from 7-21 post-conception weeks, a time period that includes cavitation of the developing knee joint. We identified significant changes in 8% of all CpGs, and >9400 developmental differentially methylated regions (dDMRs). The largest hypermethylated dDMRs mapped to transcriptional regulators of early skeletal patterning including MEIS1 and IRX1. Conversely, the largest hypomethylated dDMRs mapped to genes encoding extracellular matrix proteins including SPON2 and TNXB and were enriched in chondrocyte enhancers. Significant correlations were identified between the expression of these genes and methylation within the hypomethylated dDMRs. We further identified 811 CpGs at which significant dimorphism was present between the male and female samples, with the majority (68%) being hypermethylated in female samples. Following imputation, we captured the genotype of these samples at >5 million variants and performed epigenome-wide methylation quantitative trait locus (mQTL) analysis. Colocalization analysis identified 26 loci at which genetic variants exhibited shared impacts upon methylation and OA genetic risk. This included loci which have been previously reported to harbour OA-mQTLs (including GDF5 and ALDH1A2), yet the majority (73%) were novel (including those mapping to CHST3, FGF1 and TEAD1). To our knowledge, this is the first extensive study of DNA methylation across human articular cartilage development. We identify considerable methylomic plasticity within the development of knee cartilage and report active epigenomic mediators of OA risk operating in prenatal joint tissues.

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“…In 2022 Kreitmaier and colleagues published a genome-wide methylation array and genotype array analysis of DNA extracted from the cartilage of OA patients [41]. They also reported the mQTL at cg26736200, using SNP rs61611907 (pairwise r 2 of 0.68 with rs34195470 in European ancestry cohorts).…”

Section: Discussionmentioning

confidence: 99%

“…They also reported the mQTL at cg26736200, using SNP rs61611907 (pairwise r 2 of 0.68 with rs34195470 in European ancestry cohorts). They applied Mendelian randomization to identify CpGs from the methylation array that have a potential causal role in OA and identi ed cg26736200 as one such site [41]. Our analysis of TFs that are predicted to bind at the DMR identi ed hypoxia-inducible factor-1a (HIF1A) as binding across CpG7 and CpG8/cg26736200.…”

Section: Discussionmentioning

confidence: 99%

Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence

Roberts,

Boldvig,

Aubourg

et al. 2024

Preprint

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Background Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism rs34195470 and which maps to functional candidates WWP2 and microRNA-140 (miR-140). Methods Nucleic acids were extracted from adult OA (arthroplasty) and foetal cartilage. Samples were genotyped and DNA methylation (DNAm) quantified by pyrosequencing at 16 CpG dinucleotides located within a putative enhancer. CpGs were tested for transcriptional regulatory effects using a chondrocyte cell line and reporter gene assay. DNAm was altered using epigenetic editing, with the impact on gene expression determined using RT-qPCR. In silico analysis complemented laboratory experiments. Results rs34195470 genotype associates with differential methylation of the CpGs, forming a methylation quantitative trait locus (mQTL). The mQTL is more pronounced in adult versus foetal cartilage. The differential methylation acts as a transcriptional regulatory intermediate between risk allele and level of WWP2 expression by targeting the full-length and N-terminal transcript isoforms of the gene. Conclusions As far as we are aware, this is the first experimental demonstration of an OA association signal targeting specific transcript isoforms of a gene. WWP2 encodes a ubiquitin ligase, with its isoforms encoding proteins with varying substrate specificities, including for components of the TGFb signaling pathway. Future analysis should focus on the substrates regulated by the WWP2 isoforms that are the targets of the genetic risk.

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An epigenome-wide view of osteoarthritis in primary tissues

Cited by 20 publications

References 61 publications

Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Epigenetic mechanisms of osteoarthritis risk in human skeletal development

Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence

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