Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use

Table 4 Differentially methylated loci (p < 1 × 10⁻⁴): ever smokers vs. never smokers (BE, LGD, HGD/EAC combined)

Probe ID	Gene	Average β ever smoker	Average β never smoker (overall change)	p value	Probe location	Relation to island	Relative expression BE vs. normal^	Relative expression EAC vs. normal^	Cancer associated?
cg05951860	CTTNBP2	0.49	0.15 (↓)	5.80E-07	Body	Island	NS	NS	Y
cg15310873	C20orf85	0.74	0.60 (↓)	5.06E-06	Body	Island	NS	3.34*	N
cg23039279	PROK2	0.48	0.21 (↓)	1.92E-05	5′UTR; 1st exon	Island	NS	1.90*	Y
cg16024318	SLC6A7	0.39	0.20 (↓)	2.68E-05	5′UTR; 1st exon	Island	1.31*	1.17*	Y
cg20285514	GNG4	0.52	0.19 (↓)	2.82E-05	TSS200; 5′UTR	Island	NS	NS	Y
cg07657743	WNT7A	0.56	0.22 (↓)	3.93E-05	Body	Island	NS	NS	N
cg19169023	TYRO3	0.74	0.57 (↓)	4.24E-05	Body	Shore	NS	NS	N
cg25757598	RALYL	0.51	0.25 (↓)	4.59E-05	5′UTR; 1st exon	Island	1.16*	2.30*	N
cg14196840	CTTNBP2	0.37	0.11 (↓)	5.08E-05	Body	Island	NS	NS	Y
cg04842146	RALYL	0.46	0.15 (↓)	5.55E-05	TSS1500	Shore	1.16*	2.30*	Y
cg20620272	C3orf50	0.42	0.16 (↓)	5.77E-05	Body	Island	NS	NS	N
cg09374774	FAM78A	0.19	0.43 (↑)	5.80E-05	TSS200	Island	NS	1.04*	N
cg18016194	RALYL	0.50	0.29 (↓)	7.17E-05	5′UTR; 1st exon	Island	1.16*	2.30*	N
cg27603796	CTTNBP2	0.47	0.21 (↓)	7.21E-05	Body	Shore	NS	NS	Y
cg00818822	RFX2	0.90	0.80 (↓)	8.05E-05	Body	Island	1.24*	6.23*	N
cg10879116	LPAR3	0.51	0.26 (↓)	8.54E-05	5′UTR	Island	NS	NS	Y
cg11981631	ABCC8	0.59	0.30 (↓)	9.36E-05	Body	Island	1.38*	1.11–1.70*	Y
cg06600429	GABRB2	0.32	0.55 (↑)	9.75E-05	TSS1500	Shore	NS	NS	Y

5′UTR = 5′ untranslated region; TSS200/TSS1500 = 200/1500 bp’s upstream from transcription start site; Shore = DNA sequence up to 2 kb from CpG island; NS = not significant; ^ = relative gene expression data obtained from www.oncomine.org; *p ≤ 0.05; (↑)/(↓) = increase/decrease in methylation never smokers vs. smokers

ISSN: 1868-7083