Mapping the osteoclast methylome and investigating its role in osteoporosis — ASN Events
  1. Schedule
  2. ANZBMS Plenary Posters Session
  3. Mapping the osteoclast methylome and investigating its role in osteoporosis

Mapping the osteoclast methylome and investigating its role in osteoporosis (#104)

Benjamin H Mullin 1 2 3 , John P Kemp 3 , John P Walsh 1 4 , Kun (Kathy) Zhu 1 4 , Scott G Wilson 1 2
  1. Dept. of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
  2. School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
  3. Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
  4. Medical School, University of Western Australia, Crawley, WA, Australia

Genome-wide association studies have identified hundreds of genetic loci associated with osteoporosis risk. Most of these genetic variants are located in intergenic or intronic DNA and are non-coding, suggesting cell type-specific regulatory effects on gene expression may be responsible for the associations. Epigenetic changes, defined as functionally relevant modifications to the genome without alteration of the DNA sequence, such as DNA methylation, are also known to have a major effect on gene expression levels by influencing the binding of regulatory elements.

The aim of this study was to generate the first map of the osteoclast methylome and investigate whether genetic variants associated with osteoporosis-risk alter DNA methylation in osteoclasts. Blood samples were collected from 158 patients undergoing bone mineral density scanning at Sir Charles Gairdner Hospital in Western Australia. These samples were used to culture osteoclast-like cells in-vitro. The genome and methylome of these cells were characterised using Illumina chip array technology. Genetic variants associated with nearby DNA methylation sites were identified using the FastQTL software. Co-localisation analysis of osteoporosis-risk and DNA methylation association signals was performed using coloc2.

After correction for multiple testing, we identified over 124,000 DNA methylation sites significantly associated with at least one genetic variant located within a 500kb window on either side. Most of these variants were located in relatively close proximity to their DNA methylation site (average 97kb) and many were situated within osteoclast regulatory genes. Integrative analysis with genetic association data for estimated bone mineral density (eBMD) identified 29 strongly colocalised DNA methylation / eBMD association signals. Among them, eBMD and methylation association signals located within the SEPT9 gene showed >99.9% posterior probability for colocalisation. The product of the SEPT9 gene, Septin 9, is synthesised during differentiation of human osteoclasts, and deletion of this gene in mice results in increased trabecular bone volume and impaired growth of the femur.

We have generated the first map of the osteoclast methylome and have characterised its relationship with the genetic code. We have used this information to identify DNA methylation sites that may have a role in osteoporosis, including some located in established bone genes.