Background: Osteonecrosis of jaw (ONJ) is a rare but serious medication induced adverse effect, mainly associated with the use of intravenous (IV) bisphosphonates (BPs). Our previous whole-exome sequencing (WES) results identified SIRT1 intronic SNP rs7896005 to be associated with ONJ related to BPs. This SNP is an eQTL for SIRT1 gene and the A allele had higher SIRT1 mRNA expression level in the genotype-Tissue Expression dataset. SIRT1 plays a vital role in bone remodeling by affecting the Wnt signaling pathway and RANK/RANKL/OPG pathway. However, the associated function of the index SNP rs7896005 is still unclear. The purpose of this study is to identify functional SNPs in high linkage disequilibrium (LD) with the index SNP associated with ONJ.
Methods: All SNPs in high LD (r2 >0.8) with the index SNP rs7896005 in European populations were extracted using the rAggr software. These SNPs were then categorized based on their locations such as 5’-upstream region, intronic region, and 3’-downstream region and evaluated for the potential function. In silico tools such as SNP Nexus, ENCODE, Ensembl, miRBase, and Human Splicing Finder were used to predict the potential function of these SNPs. Pyrosequencing assay was used to genotype the potentially functional SNP in 126 cancer patients of European ancestry treated with IV BPs including 60 ONJ cases and 66 controls. Multiple logistic regression was performed to validate the association of this potential functional SNP and ONJ after adjusting for age and gender.
Results: Total of 185 SNPs in high LD with the index SNP were extracted. Based on the result of in silico analysis, we identified SNP rs932658 as the potential functional SNP for this association. This SNP is located in the promoter region of SIRT1 gene, -13bp upstream of SP1 transcription factor binding site and was predicted to affect binding of this transcription factor. The minor allele (A) frequency for rs932658 was 0.31. The LD (r2) between this SNP and the index SNP was 0.94. Similar to the index SNP, the A carrier of rs932658 was associated with lower risk of ONJ with an odds ratio of 0.19 and 95% confidence interval of 0.08-0.42 (p=5.2*10-5).
Conclusions: Using in silico analysis followed by validation analysis, we identified the SIRT1 promoter region SNP rs932658, which is in high LD with the index SNP (rs7896005), as a potential causal SNP for the SIRT1 association with BPs-related ONJ. Additional functional validation is still ongoing.