title: Genome-wide profiling of bone reveals differentially methylated regions in osteoporosis and osteoarthritis.
abstract: OBJECTIVE
  To determine genome-wide methylation profiles of bone from patients with hip osteoarthritis (OA) and those with osteoporotic (OP) hip fractures.
  
  
  METHODS
  Trabecular bone pieces were obtained from the central part of the femoral head of 27 patients with hip fractures and 26 patients with hip OA. DNA was isolated, and methylation was explored with Illumina methylation arrays. RNA was extracted, pooled, and deep-sequenced to obtain the whole transcriptome. Differentially methylated regions were identified, and connections between genes with differentially methylated regions were explored by pathway and text-mining analyses.
  
  
  RESULTS
  After quality control, methylation of 23,367 CpG sites (13,463 genes) was analyzed. There was a genome-wide inverse relationship between methylation and gene expression in both patient groups. Comparison of OP and OA bones revealed 241 CpG sites, located in 228 genes, with significant differences in methylation (false discovery rate<0.05). Of them, 217 were less methylated in OP than in OA. The absolute methylation differences were >5% in 128 CpG sites and >10% in 45 CpG sites. The differentially methylated genes were enriched for association with bone traits in the genome-wide association study catalog. Pathway analysis and text-mining analysis with Gene Relationships Across Implicated Loci software revealed enrichment in genes participating in glycoprotein metabolism or cell differentiation, and particularly in the homeobox superfamily of transcription factors.
  
  
  CONCLUSIONS
  Genome-wide methylation profiling of bone samples revealed differentially methylated regions in OP and OA. These regions were enriched in genes associated with cell differentiation and skeletal embryogenesis, such as those in the homeobox superfamily, suggesting the existence of a developmental component in the predisposition to these disorders.
authors.affiliation: Departamento de Medicina Interna, Hospital U. M. Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, University of Cantabria, and RETICEF, Santander, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Delgado-Calle
authors.forename: Agustín F
authors.initials: AF
authors.lastname: Fernández
authors.forename: Jesús
authors.initials: J
authors.lastname: Sainz
authors.forename: María T
authors.initials: MT
authors.lastname: Zarrabeitia
authors.forename: Carolina
authors.initials: C
authors.lastname: Sañudo
authors.forename: Raúl
authors.initials: R
authors.lastname: García-Renedo
authors.forename: María I
authors.initials: MI
authors.lastname: Pérez-Núñez
authors.forename: Carmen
authors.initials: C
authors.lastname: García-Ibarbia
authors.forename: Mario F
authors.initials: MF
authors.lastname: Fraga
authors.forename: José A
authors.initials: JA
authors.lastname: Riancho
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D001842:Bone and Bones / Q000378:metabolism*; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D015207:Osteoarthritis, Hip / Q000235:genetics* / Q000378:metabolism; D010024:Osteoporosis / Q000235:genetics* / Q000378:metabolism; D058866:Osteoporotic Fractures / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA