Identification of candidate genes and chemicals associated with osteoarthritis by transcriptome-wide association study and chemical-gene interaction analysis
Authors' conclusion
Several candidate OA-associated genes and chemicals were identified through TWAS and CGSEA analysis, which expanded our understanding of the relationship between genes, chemicals, and their impact on OA.
Study context
- Population
- Summary-level GWAS data of knee osteoarthritis (OA) and hip OA integrated with GTEx (Version 8) expression weights
- Comparison
- Knee OA (KOA) vs hip OA (HOA)
- Outcome
- OA susceptibility genes and OA-associated chemicals
Methodological detailssingle-tissue and cross-tissue transcriptome-wide association study (TWAS) (FUSION), aggregate Cauchy association test, chemical-related gene set enrichment analysis (CGSEA), validation in human cartilage mRNA expression profiles
- Single-tissue and cross-tissue TWAS (FUSION)
- Aggregate Cauchy association test
- Chemical-related gene set enrichment analysis (CGSEA)
- Validation in human cartilage mRNA expression profiles
Performance
As reported in the abstract
- Unique TWAS genes for KOA, in 7 chromosomes
- 44
- Unique TWAS genes for HOA, in 11 chromosomes
- 93
- KOA TWAS genes with significantly differential expression in cartilage mRNA profiles (e.g. CRHR1, LTBP1, WWP2, LMX1B, PTHLH)
- fourteen
- HOA TWAS genes with significantly differential expression in cartilage mRNA profiles
- four
- OA-associated chemicals identified by CGSEA, incl. quercetin, bisphenol A, cadmium chloride
- Forty-five
Original publication
Identification of candidate genes and chemicals associated with osteoarthritis by transcriptome-wide association study and chemical-gene interaction analysis. Arthritis Res Ther. Published 25 September 2023. doi:10.
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