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 b-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.

Identification of Predictive DNA Methylation Biomarkers for Chemotherapy Response in Colorectal Cancer

“…In our study, we identified hypermethylation of PON3. This is in line with the study by Alholle et al (2015) , where PON3 was hypermethylated in recurrent chordomas compared to the primary tumor. DDX43, also known as helicase antigen (HAGE), is responsible for cell proliferation and has a high expression level in cancer compared to normal ( Abdel-Fatah et al, 2014 ).…”

“…Our results showed that recurrent CRC exhibit increased methylation levels compared to non-recurrent group. Similar patterns have been observed in chordomas where higher methylation level were observed in recurrent chordomas compared to non-recurrent ( Alholle et al, 2015 ).…”

Paraoxonase 3 is involved in the multi-drug resistance of esophageal cancer

“…PON3 gene has a high expression level in cancer tissues of the lung, liver and colon [ 11 ]. Previous studies also showed that PON3 is hypermethylated in colorectal cancer [ 9 ] and chordomas [ 21 ]. Notably, the genome-wide DNA methylation analysis identified that several genes, including PON3, are aberrantly methylated in the high-grade non-muscle invasive bladder cancer [ 22 ].…”

Epigenetic deregulations in chordoma

“…showed that a high portion of methylated MGMT promoter was present in recurring clival chordoma, whereas its promoter was always unmethylated in clival chordoma without recurrence ; that study helped predict clinical post‐operative outcomes of chordoma. In a recent investigation, DNA methylation profiling revealed that 8819 loci (2.9%) were differentially methylated in chordoma, among which 5868 probes (66.5%) were hypomethylated and 2,951 (33.5%) were hypermethylated . In addition, 104 probes (104/2951) demonstrated cancer‐specific hypermethylation in chordoma.…”