Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

Figures & data

Figure 1. Unsupervised hierarchical cluster analysis of the 1000 most variable probes between chordoma samples and nucleus pulposus samples.

Figure 2. Genomic context of CpG methylation. (A) Differentially methylated probes in relation to gene. (B) Differentially methylated probes in relation to CGI context. (C) Sub-location of differentially hypermethylated probes in relation to gene. (D) Functional distribution of hypermethylated probes in relation to CGI.

Table 1. Differentially methylated genes between recurrent and non-recurrent chordoma samples

UCSC_REF GENE_NAME	ID	Chromosome	CGI.Relation	Average β-value in recurrence	Average β-value in non-recurrence	Average β-value difference between recurrence and non-recurrence	P-value	Average in controls	UCSC_REF GENE_ACCESSION	Relation to Gene	UCSC_CPG_ISLANDS_NAME
FAM181B	cg19320476	chr11	Island	0.439897	0.235521	0.204376	0.022539	0.046153	NM_175885	1stExon	chr11:82443435–82444976
NPR3	cg17630392	chr5	Island	0.47289	0.261363	0.204376	0.000756	0.079265	NM_000908	1stExon	chr5:32709910–32714450
RAI1	cg10140454	chr17	Island	0.783044	0.549829	0.204376	0.00584	0.372009	NM_030665	5'UTR	chr17:17625605–17628500
SLC16A5	cg09300114	chr17	Island	0.700374	0.474643	0.204376	0.00878	0.127086	NM_004695	5'UTR	chr17:73083866–73084495
ZNF397OS;ZNF397OS	cg16657538	chr18	Island	0.493249	0.215783	0.204376	0.002872	0.051907	NM_001166012;NM_001112734	5'UTR;5'UTR	chr18:32847284–32848130
KANK2;KANK2	cg07888912	chr19	North Shore	0.58871	0.344717	0.204376	0.000285	0.081067	NM_001136191;NM_015493	5'UTR;TSS1500	chr19:11307495–11308276
RAB32	cg23267550	chr6	North Shore	0.566886	0.35041	0.204376	0.004754	0.216715	NM_006834	TSS1500	chr6:146864481–146865426
PON3	cg08520743	chr7	Island	0.564437	0.344416	0.204376	0.001623	0.052802	NM_000940	TSS200	chr7:95025559–95026122
PON3	cg08828819	chr7	Island	0.603982	0.393397	0.204376	0.005161	0.051629	NM_000940	TSS200	chr7:95025559–95026122

Figure 3. Expression and methylation analysis in ES cell lines. Expression and methylation results for 3 selected genes in chordoma cell lines (PON3, SLC16A5, and NPR3; GAPDH as control). (A) Expression analysis using RT-PCR in 2 chordoma cell lines are shown for each gene with (-) indicating the samples without 5-azaDC treatment and (+) indicating the samples after 5-azaDC treatment. (B) COBRA results for the selected genes in cell lines. Undigested (U) samples were loaded next to the BstU1 digested samples (D). Two chordoma cell lines are shown for each gene and the positive control (Positive C) is in vitro methylated DNA. (*) indicates that the cell line is methylated. β-values from the HumanMethylation450 BeadChip array for UCH-1 cell line is also shown under each digest.

Figure 4. COBRA analysis for selected genes in chordoma samples. (A) Results of COBRA analysis for 5 genes (RAB32, FAM181B, SLC16A5, NPR3, and PON3) selected from differentially methylated gene list between recurrent and non-recurrent chordoma samples. (B) Results of COBRA analysis for 2 genes (COL11A2 and TUBB6) from differentially methylated probe list. (C) Results of COBRA analysis for 2 genes (FGR and PSKH2) selected from cancer-specific hypermethylated probe list. COBRA results are shown for chordoma samples with in vitro methylated DNA as positive control (Positive C). The digested samples (D) are loaded next to the undigested samples (U). (*) indicates methylated samples. β-value from the HumanMethylation450 BeadChip array for each selected sample is shown.