ArticleArthritis & rheumatology (Hoboken, N.J.)2019
Annotating Transcriptional Effects of Genetic Variants in Disease-Relevant Tissue: Transcriptome-Wide Allelic Imbalance in Osteoarthritic Cartilage.
Article in Arthritis & rheumatology (Hoboken, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 2 syntheses or guidelines pooled it, 45 citations in OpenAlex.
- Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture.BMC genomics · 2025Pooled it
- Allelic expression imbalance in articular cartilage and subchondral bone refined genome-wide association signals in osteoarthritis.Rheumatology (Oxford, England) · 2023Pooled it
- From mechanism to medicine: The progress and potential of epigenetics in osteoarthritis.Osteoarthritis and cartilage open · 2025Review
- Response splicing quantitative trait loci in primary human chondrocytes identify putative osteoarthritis risk genes.Nature communications · 2025Article
- Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease.Current rheumatology reports · 2024Review
- Risk and Resilience Variants in the Retinoic Acid Metabolic and Developmental Pathways Associated with Risk of FASD Outcomes.Biomolecules · 2024Article
- Thyroid hormone induces ossification and terminal maturation in a preserved OA cartilage biomimetic model.Arthritis research & therapy · 2024Article
- Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence.Arthritis research & therapy · 2024Article
- Genetic risk of osteoarthritis operates during human skeletogenesis.Human molecular genetics · 2023Article
- Mediation of the Same Epigenetic and Transcriptional Effect by Independent Osteoarthritis Risk-Conferring Alleles on a Shared Target Gene, COLGALT2.Arthritis & rheumatology (Hoboken, N.J.) · 2023Article
- Genetics of osteoarthritis.Osteoarthritis and cartilage · 2022Review
- CRLF1 and CLCF1 in Development, Health and Disease.International journal of molecular sciences · 2022Review
- Article
- Elucidating mechano-pathology of osteoarthritis: transcriptome-wide differences in mechanically stressed aged human cartilage explants.Arthritis research & therapy · 2021Article
- Association between miRNA Target Sites and Incidence of Primary Osteoarthritis in Women from Volga-Ural Region of Russia: A Case-Control Study.Diagnostics (Basel, Switzerland) · 2021Article
- Genetic Variants and Protein Alterations of Selenium- and T-2 Toxin-Responsive Genes Are Associated With Chondrocytic Damage in Endemic Osteoarthropathy.Frontiers in genetics · 2021Article
- Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC.Osteoarthritis and cartilage · 2020Article
- A single cell transcriptional atlas of early synovial joint development.Development (Cambridge, England) · 2020Article
- Interplay between genetics and epigenetics in osteoarthritis.Nature reviews. Rheumatology · 2020Review
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
Abstract
objectiveMultiple single-nucleotide polymorphisms (SNPs) conferring susceptibility to osteoarthritis (OA) mark imbalanced expression of positional genes in articular cartilage, reflected by unequally expressed alleles among heterozygotes (allelic imbalance [AI]). We undertook this study to explore the articular cartilage transcriptome from OA patients for AI events to identify putative disease-driving genetic variation.
methodsAI was assessed in 42 preserved and 5 lesioned OA cartilage samples (from the Research Arthritis and Articular Cartilage study) for which RNA sequencing data were available. The count fraction of the alternative alleles among the alternative and reference alleles together (φ) was determined for heterozygous individuals. A meta-analysis was performed to generate a meta-φ and P value for each SNP with a false discovery rate (FDR) correction for multiple comparisons. To further validate AI events, we explored them as a function of multiple additional OA features.
resultsWe observed a total of 2,070 SNPs that consistently marked AI of 1,031 unique genes in articular cartilage. Of these genes, 49 were found to be significantly differentially expressed (fold change <0.5 or >2, FDR <0.05) between preserved and paired lesioned cartilage, and 18 had previously been reported to confer susceptibility to OA and/or related phenotypes. Moreover, we identified notable highly significant AI SNPs in the CRLF1, WWP2, and RPS3 genes that were related to multiple OA features.
conclusionWe present a framework and resulting data set for researchers in the OA research field to probe for disease-relevant genetic variation that affects gene expression in pivotal disease-affected tissue. This likely includes putative novel compelling OA risk genes such as CRLF1, WWP2, and RPS3.
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