The osteoporosis susceptibility SNP rs188303909 at 2q14.2 regulates EN1 expression by modulating DNA methylation and E2F6 binding

• Published in: Journal of molecular medicine (Berlin, Germany) Germany), 2024-02, Vol.102 (2), p.273-284
• Main Authors: Wang, Ya, Huang, Xinyao, Zhang, Qiongdan, Cheng, Chen, Qin, Zixuan, Lu, Li, Huang, Qingyang
• Format: Article
• Language: English
• Subjects: Biomedical and Life Sciences; Biomedicine; Bone density; Bone growth; Chromosome 2; CpG islands; DNA methylation; Genome-wide association studies; Genomes; Homeobox; Human Genetics; Internal Medicine; Molecular Medicine; Original Article; Osteogenesis; Osteoporosis; Precision medicine; Single-nucleotide polymorphism; Susceptibility; Therapeutic targets; Transcription factors
• ISSN: 0946-2716; 1432-1440
• DOI: 10.1007/s00109-023-02412-6

EN1 encodes a homeodomain-containing transcription factor and is a determinant of bone density and fracture. Previous powerful genome-wide association studies (GWASs) have identified multiple single-nucleotide polymorphisms (SNPs) near EN1 at 2q14.2 locus for osteoporosis, but the causal SNPs and functional mechanisms underlying these associations are poorly understood. The target genes regulated by the transcription factor EN1 are also unclear. In this study, we identified rs188303909, a functional CpG-SNP, as a causal SNP for osteoporosis at 2q14.2 through the integration of functional and epigenomic analyses. Functional experiments demonstrated that unmethylated rs188303909 acted as a strong allele-specific distal enhancer to regulate EN1 expression by modifying the binding of transcription factor E2F6, but rs188303909 methylation attenuated the active effect of E2F6 on EN1 expression. Importantly, transcription factor EN1 could differentially bind osteoporosis GWAS lead SNPs rs4869739-T and rs4355801-G to upregulate CCDC170 and COLEC10 expression, thus promoting bone formation. Our study provided a mechanistic insight into expression regulation of the osteoporosis susceptibility gene EN1 , which could be a potential therapeutic target for osteoporosis precision medicine. Key messages CpG-SNP rs188303909 is a causal SNP at the osteoporosis susceptibility locus 2q14.2. Rs188303909 distally regulates  EN1  expression by modulating DNA methylation and E2F6 binding. EN1 upregulates  CCDC170 and COLEC10  expression through osteoporosis GWAS lead SNPs rs4869739 and rs4355801.