title: Upstream CpG island methylation of the PAX3 gene in human rhabdomyosarcomas.
abstract: BACKGROUND
  Adult tumors can be characterized by hypermethylation of CpG islands associated with 5'-upstream and coding regions of specific genes. This hypermethylation can also be part of the aging process. In contrast, much less is known about gene hypermethylation in childhood cancers, where methylation changes are not part of the aging process but likely represent developmental dysregulation. PAX3 is an important gene in muscle development and muscle-producing neoplasms such as rhabdomyosarcomas.
  
  
  METHODS
  We examined the methylation status of a PAX3 5'-CpG island in rhabdomyosarcoma subtypes and in normal fetal skeletal muscle. PAX3 methylation was analyzed in 15 embryonal rhabdomyosarcomas, 12 alveolar rhabdomyosarcomas, and in six normal skeletal muscle samples, using semi-quantitative PCR analysis of DNA digested with methyl-sensitive restriction enzymes.
  
  
  RESULTS
  The CpG island in the upstream region of the human PAX3 gene was hypermethylated in the majority of ERMS examined (13 of 15 tumors, mean of 52% methylation), whereas most ARMS (9 of 12 tumors) and all normal muscle samples showed relative hypomethylation (both 18% mean methylation). Various CpG sites differ in contribution to overall PAX3 CpG island methylation, with methylation at a HaeII site being inversely correlated with PAX3 expression.
  
  
  CONCLUSIONS
  PAX3 CpG island methylation appears to distinguish embryonal subtype of rhabdomyosarcoma from alveolar, and methylation at certain sites within this CpG island is inversely correlated with PAX3 expression. In addition to exemplifying developmental dysregulation, methylation of PAX3 has potential in the development of an epigenetic profile for the diagnosis of rhabdomyosarcoma.
authors.affiliation: Department of Biochemistry, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA.
authors.forename: Raushan T
authors.initials: RT
authors.lastname: Kurmasheva
authors.forename: Charlotte A
authors.initials: CA
authors.lastname: Peterson
authors.forename: David M
authors.initials: DM
authors.lastname: Parham
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.forename: Rachel E
authors.initials: RE
authors.lastname: McDonald
authors.forename: Craig A
authors.initials: CA
authors.lastname: Cooney
mesh_terms: D002648:Child; D018899:CpG Islands; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D024510:Muscle Development / Q000235:genetics; D018482:Muscle, Skeletal / Q000737:chemistry / Q000196:embryology; D000072041:PAX3 Transcription Factor; D051761:Paired Box Transcription Factors; D012208:Rhabdomyosarcoma / Q000235:genetics* / Q000473:pathology; D018232:Rhabdomyosarcoma, Alveolar / Q000235:genetics / Q000473:pathology; D018233:Rhabdomyosarcoma, Embryonal / Q000235:genetics / Q000473:pathology; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D000072041:PAX3 Transcription Factor; C489409:PAX3 protein, human; D051761:Paired Box Transcription Factors; D014157:Transcription Factors