Genome-wide Analysis of DNA Methylation Identifies a Novel Locus Associated with Bone Mineral Density

J.A. Morris1,2, P.-C. Tsai3, F. Gao4, V. Forgetta2, Y. Xia4, W. Yuan3, C.M. Greenwood1,2,5,6, E. Grundberg1, T.D. Spector3, J. Wang4, J.T. Bell3, J.B. Richards1,2,3,6

1. Department of Human Genetics, McGill University, Montreal, Canada; 2. Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada; 3. Department of Twin Research & Genetic Epidemiology, King’s College London, London, United Kingdom; 4. BGI-Shenzhen, Shenzhen, China; 5. Department of Oncology, McGill University, Montreal, Canada; 6. Department of Epidemiology, Biostatistics, & Occupational Health, McGill University, Montreal, Canada

Osteoporosis is a common, complex disease characterized by increased bone fragility, often resulting in fracture. Bone mineral density (BMD) is measured to diagnose osteoporosis and estimate fracture risk. Studying the genetic determinants of BMD has lead to novel disease pathophysiology insights. We sought to study epigenetic associations with BMD, as DNA methylation levels are known to influence or be secondary to disease phenotypes. To assess epigenetic associations with BMD, we undertook a genome-wide association study of DNA methylation levels. Methylation levels were estimated using methylated DNA immunoprecipitation sequencing to identify differentially methylated regions (DMRs) associated with BMD measured at the forearm, femoral neck, and lumbar spine in the TwinsUK cohort, in 890, 1,518, and 1,397 twins, respectively. A DMR on chromosome 6q21 was found to be significantly associated with forearm BMD (P-value = 5.3×10-9). The DMR was intergenic and located within 3-dimensional proximity to the PRDM1 and ATG5 genes. Previous studies in mice support both PRDM1 and ATG5 as key regulators of osteoclast differentiation and autophagy, respectively. FANTOM5 data provides supportive evidence that a proximal enhancer RNA could be a differentially methylated regulatory element. The proximal enhancer RNA has been reported as significantly overrepresented solely in monocytes, which are osteoclast precursor cells. Further work is underway to identify an association between genetic variation and BMD within this locus. This study represents the most comprehensive genome-wide analysis to date of the role of methylation in BMD. Future studies will refine the definitive role of epigenetic mediated effects at this osteoclast locus.