title: Genome-wide DNA methylation study of hip and knee cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis.
abstract: BACKGROUND
  Evidence suggests that epigenetics plays a role in osteoarthrits (OA). The aim of the study was to describe the genome wide DNA methylation changes in hip and knee OA and identify novel genes and pathways involved in OA by comparing the DNA methylome of the hip and knee osteoarthritic cartilage tissues with those of OA-free individuals.
  
  
  METHODS
  Cartilage samples were collected from hip or knee joint replacement patients either due to primary OA or hip fractures as controls. DNA was extracted from the collected cartilage and assayed by Illumina Infinium HumanMethylation450 BeadChip array, which allows for the analysis of >480,000 CpG sites. Student T-test was conducted for each CpG site and those sites with at least 10 % methylation difference and a p value <0.0005 were defined as differentially methylated regions (DMRs) for OA. A sub-analysis was also done for hip and knee OA separately. DAVID v6.7 was used for the functional annotation clustering of the DMR genes. Clustering analysis was done using multiple dimensional scaling and hierarchical clustering methods.
  
  
  RESULTS
  The study included 5 patients with hip OA, 6 patients with knee OA and 7 hip cartilage samples from OA-free individuals. The comparisons of hip, knee and combined hip/knee OA patients with controls resulted in 26, 72, and 103 DMRs, respectively. The comparison between hip and knee OA revealed 67 DMRs. The overall number of the sites after considering the overlaps was 239, among which 151 sites were annotated to 145 genes. One-fifth of these genes were reported in previous studies. The functional annotation clustering of the identified genes revealed clusters significantly enriched in skeletal system morphogenesis and development. The analysis revealed significant difference among OA and OA-free cartilage, but less different between hip OA and knee OA.
  
  
  CONCLUSIONS
  We found that a number of CpG sites and genes across the genome were differentially methylated in OA patients, a remarkable portion of which seem to be involved in potential etiologic mechanisms of OA. Genes involved in skeletal developmental pathways and embryonic organ morphogenesis may be a potential area for further OA studies.
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. erfanae@mun.ca.
authors.forename: Erfan
authors.initials: E
authors.lastname: Aref-Eshghi
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. yuhua.zhang@med.mun.ca.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. ming.liu@med.mun.ca.
authors.forename: Ming
authors.initials: M
authors.lastname: Liu
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. peh318@mun.ca.
authors.forename: Patricia E
authors.initials: PE
authors.lastname: Harper
authors.affiliation: Division of Orthopedics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. gmartin@munmed.ca.
authors.forename: Glynn
authors.initials: G
authors.lastname: Martin
authors.affiliation: Division of Orthopedics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. andrewfurey@hotmail.com.
authors.forename: Andrew
authors.initials: A
authors.lastname: Furey
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. rcgreen@mun.ca.
authors.forename: Roger
authors.initials: R
authors.lastname: Green
authors.affiliation: Disicpline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. gsun@mun.ca.
authors.forename: Guang
authors.initials: G
authors.lastname: Sun
authors.affiliation: Disicpline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. prahman@mun.ca.
authors.forename: Proton
authors.initials: P
authors.lastname: Rahman
authors.affiliation: Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. guangju.zhai@med.mun.ca.|Department of Twin Research & Genetic Epidemiology, King's College London, London, UK. guangju.zhai@med.mun.ca.
authors.forename: Guangju
authors.initials: G
authors.lastname: Zhai
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D002358:Cartilage, Articular / Q000378:metabolism; D019175:DNA Methylation; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D009024:Morphogenesis; D015207:Osteoarthritis, Hip / Q000209:etiology* / Q000378:metabolism; D020370:Osteoarthritis, Knee / Q000209:etiology* / Q000378:metabolism; D012863:Skeleton / Q000196:embryology