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Cited by 92Osteoarthritis Treatment and MechanismsGenetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

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Klein, Jason C., Keith, Aidan, Rice, Sarah J., Shepherd, Colin, Agarwal, Vikram, Loughlin, John, Shendure, Jay·2019·Nature Communications
DOI 10.1038/s41467-019-10439-yPMC PMC6547687

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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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  • MPRAs have been applied to assess biochemically annotated candidate enhancers, candidate enhancers harbouring variants that potentially mediate eQTLs, and even scans of the entire human genome.

    “MPRAs have been applied to assess biochemically annotated candidate enhancers77,176-178, candidate enhancers harbouring variants that potentially mediate eQTLs179-182, and even scans of the entire human genome108,183.”

    From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [182]

    The Introduction says MPRAs have been used to characterize variants underlying eQTLs, and the Results identify two tested osteoarthritis-associated SNPs as eQTLs. This paper’s own MPRA, however, selected variants associated with osteoarthritis GWAS signals rather than candidate enhancers selected for potentially mediating eQTLs. The cited paper therefore supports the general eQTL application, but not that more specific description of its screen. (LLM, conf=0.81)

    Experimental — accuracy not yet measured

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References 59 · Cited by 92

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Authors
Klein, J. C., Keith, A., Rice, S. J., Shepherd, C., Agarwal, V., Loughlin, J., & Shendure, J.
Affiliations
  • University of Washington (US)
  • Centre for Life (GB)
  • Howard Hughes Medical Institute (US)
Corresponding author
Shendure, Jay
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-06-04
Volume
10
Issue
1
Pages
2434-2434
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-019-10439-y
PMC
PMC6547687
OpenAlex
W2951845986
Cited by
92
References
59
Citations by year
2026: 4 · 2025: 9 · 2024: 14 · 2023: 16 · 2022: 14 · 2021: 14 · 2020: 17 · 2019: 4
FWCI
9.29
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Research Explorer (The University of Manchester) (submittedVersion)
  • Newcastle University ePrints (Newcastle Univesity) (cc-by)
Funders
  • U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (1F30HG009479)
  • Arthritis Research UK (20771)
  • Howard Hughes Medical Institute
Topics
  • Health Sciences › Medicine › Rheumatology › Osteoarthritis Treatment and Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
osteoarthritis, single nucleotide polymorphisms, regulatory action, massively parallel reporter assay, HBP1, Wnt signaling, chondrocytes, osteosarcoma, nuclear protein binding, linkage disequilibrium
MeSH terms
Alleles, Cartilage, Articular, Haplotypes, High Mobility Group Proteins, Humans, Nuclear Proteins, Osteoarthritis, Protein Binding, Repressor Proteins, Linkage Disequilibrium, Chondrocytes, Genetic Predisposition to Disease, Protein Isoforms, Polymorphism, Single Nucleotide, Electrophoretic Mobility Shift Assay, Cell Line, Tumor, Gene Regulatory Networks, Genome-Wide Association Study, Gene Knock-In Techniques, Wnt Signaling Pathway

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