title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas.
abstract: Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1-4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2'-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (>0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted P < 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
authors.affiliation: a Centre for Rare Diseases and Personalized Medicine; School of Clinical and Experimental Medicine ; University of Birmingham ; Birmingham , UK.
authors.forename: A
authors.initials: A
authors.lastname: Alholle
authors.forename: A T
authors.initials: AT
authors.lastname: Brini
authors.forename: J
authors.initials: J
authors.lastname: Bauer
authors.forename: S
authors.initials: S
authors.lastname: Gharanei
authors.forename: S
authors.initials: S
authors.lastname: Niada
authors.forename: A
authors.initials: A
authors.lastname: Slater
authors.forename: D
authors.initials: D
authors.lastname: Gentle
authors.forename: E R
authors.initials: ER
authors.lastname: Maher
authors.forename: L
authors.initials: L
authors.lastname: Jeys
authors.forename: R
authors.initials: R
authors.lastname: Grimer
authors.forename: V P
authors.initials: VP
authors.lastname: Sumathi
authors.forename: F
authors.initials: F
authors.lastname: Latif
mesh_terms: D000328:Adult; D000368:Aged; D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D001859:Bone Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D002817:Chordoma / Q000235:genetics*; D019175:DNA Methylation; D000077209:Decitabine; D005260:Female; D015870:Gene Expression / Q000187:drug effects; D016678:Genome; D006801:Humans; D008297:Male; D008875:Middle Aged; D012008:Recurrence
chemical_list: D000964:Antimetabolites, Antineoplastic; D000077209:Decitabine; D001374:Azacitidine
keywords: DNA Methylation; HumanMethylation450 BeadChips; chordomas; non-recurrent; recurrent