Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

Table 5 Methylation comparing cancer to paired adjacent samples, and correlation of methylation in invasive breast cancer samples with gene expression

	This study	TCGA database, within study region +/- 100 bp							TCGA database, within study region
	Pyroseq^a	Illum. 450 k: Mean % methylation					Assn. with expr.		Illum. 450 k: Mean % Methylation					Assn. with expr.
Gene	# CpG	# CpG	Adjacent^b (N = 96)	Cancer^c (N = 96)	Diff^d	P-value^e	ρ^f	P-value	# CpG	Adjacent^b (N = 96)	Cancer^c (N = 96)	Diff^d	P-value^e	ρ^f	P-value
Promoter region
BRCA1	11	13	4	4	0	NS	-0.19	0.0000	9	3	4	0	NS	-0.20	0.0000
CD44	8	5	4	9	5	0.0001	-0.18	0.0000	1	6	10	5	0.004	-0.18	0.0000
ESR1	5	2	67	40	-28	0.0000	-0.52	0.0000	2	67	40	-28	0.0000	-0.52	0.0000
GSTM2	8	3	4	16	13	0.0000	-0.13	0.0003	1	2	2	-1	0.0000	-0.13	0.0002
GSTP1	4	2	7	24	17	0.0000	-0.43	0.0000	0	---	---		---	---	---
MAGEA1	6	2	97	77	-21	0.0000	-0.23	0.0000	2	97	77	-20	0.0000	-0.23	0.0000
MSI1	5	2	3	6	3	0.0000	-0.20	0.0000	0	---	---		---	---	---
NFE2L3	14	1	39	48	9	0.0001	-0.55	0.0000	0	---	---		---	---	---
RASSF1	9	2	12	47	35	0.0000	-0.18	0.0000	1	9	49	41	0.0000	-0.16	0.0000
RUNX3	28	1	2	23	21	0.0000	-0.28	0.0000	0	---	---		---	---	---
SIX3	12	4	6	24	18	0.0000	-0.21	0.0000	2	4	26	22	0.0000	-0.20	0.0000
TFF1	5	4	77	46	-31	0.0000	-0.20	0.0000	1	74	47	-27	0.0000	-0.19	0.0000
Upstream of promoter
EN1 ^g	6	2	23	32	8	0.0000	0.12	0.001	0	---	---		---	---	---
PAX3	5	2	6	30	24	0.0000	-0.12	0.004	1	9	29	19	0.0000	-0.10	0.003
PITX2 ^g	10	2	23	38	15	0.0000	0.22	0.0000	0	---	---		---	---	---
SGK1	6	4	9	21	12	0.0000	-0.10	0.003	2	5	17	12	0.0000	-0.11	0.003
Introns
APC ^g	4	11	6	28	22	0.0000	0.13	0.002	3	5	28	23	0.0000	0.12	0.004
EGFR	4	1	9	37	29	0.0000	-0.15	0.0000	1	9	37	29	0.0000	-0.15	0.0000
LHX2 ^g	11	1	17	32	15	0.0000	0.24	0.0000	0	---	---		---	---	---
RFX1	4	0	---	---		---	---	---	0	---	---		---	---	---
SOX9	4	1	5	15	11	0.0000	-0.34	0.0000	0	---	---		---

^aPyrosequencing (Pyroseq) assay coordinates are given in Table 1
^bNon-cancer tissue adjacent to paired breast cancer from 96 patients in the TCGA Illumina Methylation450 database for genome-wide DNA methylation [14]
^cSamples from the invasive component of the breast cancer from patients in the TCGA Methylation450 and expression (expr.; RNA-seq) databases [16, 17]
^dDifference in mean % methylation for cancer minus that for the paired adjacent tissue for the 96 patients with both in the TCGA database
^eFrom a dependent sample Wilcoxon Sign Rank test; P-values > 0.10 are suppressed
^fSpearman correlation coefficient for methylation levels vs expression levels among all the invasive breast cancer samples in the TCGA database
^gThe four underlined genes were the only ones that had a positive association of cancer methylation in non-promoter regions with expression levels of the associated gene

ISSN: 1471-2407