Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range...

Area of Science:

• Genetics
• Molecular Biology
• Bone Metabolism

Background:

• Osteoporosis diagnosis relies on bone mineral density (BMD).
• Genome-wide association studies (GWASs) identified SNPs near RANKL associated with osteoporosis.
• The regulatory mechanism of these SNPs on RANKL remains unclear.

Purpose of the Study:

• To investigate the functional role of GWAS-identified SNPs in regulating RANKL expression.
• To elucidate the molecular mechanisms by which these SNPs contribute to osteoporosis pathogenesis.
• To identify potential therapeutic targets for osteoporosis.

Main Methods:

• Integrative analyses of expression quantitative trait locus (eQTL), high-throughput chromosome conformation capture (Hi-C), and epigenetic data.
• Functional assays including dual-luciferase reporter assays and CRISPR/Cas9 genome editing.
• Identification of transcription factor binding to regulatory SNPs.

Main Results:

• Six SNPs were significantly correlated with RANKL expression.
• Co-localization analysis indicated shared causal variants between eQTLs and BMD-GWAS.
• SNPs rs9533090, rs9594738, rs8001611, rs9533094, and rs9533095 are in a super-enhancer region regulating RANKL via long-range interaction.
• rs9533090 demonstrated allele-specific enhancer activity, recruiting NFIC to increase RANKL expression.
• CRISPR/Cas9-mediated deletion of the rs9533090 region reduced RANKL expression.

Conclusions:

• The study provides a method to identify regulatory noncoding SNPs affecting target gene expression.
• Specific SNPs, particularly rs9533090, distally regulate RANKL expression, contributing to osteoporosis.
• These findings highlight potential therapeutic targets for precision medicine in osteoporosis.