Blood DNA methylation markers in prospectively identified hepatocellular carcinoma cases and controls from Taiwan

Table 1 Sociodemographic characteristics of hepatocellular carcinoma cases and matched controls

Variable	Cases	%	Controls	%	P
	n = 159		n =312
Age (yr, mean, SD)	52.8 (8.0)		53.1 (7.8)		0.72
BMI (mean, SD)	24.3 (3.6)		24.8 (3.7)		0.13
Gender
Female	77	48	148	47	0.92
Male	82	52	164	53
HBsAg
Negative	65	41	238	76	< 0.0001
Positive	93	59	72	23
Missing	1	< 1	2	< 1
Anti-HCV
Negative	109	69	243	78	< 0.0001
Positive	29	18	15	5
Missing	21	13	54	17
Smoking
Never	97	61	184	59	0.67
Ever	62	39	128	41
Alcohol
Never	130	82	276	89	0.046
Ever	29	18	36	12

HBsAg: Hepatitis B virus surface antigen; BMI: Body mass index; HCV: Hepatitis C virus.

Table 2 Distribution of DNA methylation by hepatocellular carcinoma status

Locus	Gene	HCC cases		Controls		P1
		Mean	SD	Mean	SD
cg00028598	GABRA5	0.92	0.04	0.92	0.07	0.81
cg00108164	ACP1	0.01	0.02	0.00	0.01	0.55
cg00249511	SCT	0.01	0.04	0.01	0.04	0.80
cg00753478	LDHB	0.09	0.08	0.08	0.06	0.12
cg00817367	GRASP	0.01	0.04	0.01	0.01	0.23
cg00939495	DRD5	0.22	0.10	0.22	0.12	0.95
cg01530024	STK32B	0.97	0.08	0.97	0.07	0.79
cg01566592	RIMS2	0.10	0.09	0.09	0.08	0.32
cg01860297	BASP1	0.96	0.03	0.95	0.08	0.49
cg02527669	OBSL1	0.02	0.02	0.03	0.05	0.53
cg02553663	SECTM1	0.03	0.04	0.03	0.03	0.65
cg02710296	C1orf14	0.33	0.11	0.33	0.11	0.92
cg02736548	FAM109B	0.08	0.09	0.08	0.09	0.46
cg03306486	APC2	0.02	0.02	0.01	0.02	0.44
cg03396005	APCDD1	0.92	0.04	0.92	0.06	0.99
cg03621881	BRUNOL6	0.04	0.05	0.03	0.04	0.70
cg04920951	GSTP1	0.01	0.07	0.00	0.02	0.22
cg05328339	PTPRN2	0.89	0.09	0.88	0.10	0.55
cg05661282	ZNF154	0.03	0.05	0.03	0.08	0.75
cg05699035	KCNK2	0.86	0.07	0.86	0.08	0.99
cg05833351	CUGBP2	0.95	0.07	0.95	0.08	0.70
cg05970721	HS3ST2	0.90	0.10	0.91	0.10	0.49
cg06382344	TBR1	0.02	0.03	0.03	0.05	0.13
cg06445348	ILDR2	0.02	0.06	0.01	0.01	0.24
cg06641285	TIMP2	0.02	0.02	0.02	0.05	0.74
cg07061738	SMOC2	0.94	0.08	0.94	0.11	0.75
cg07689503	MTHFD2	0.00	0.00	0.00	0.01	0.27
cg07759394	GLB1L2	0.01	0.03	0.01	0.02	0.44
cg07765706	KCNQ3	0.95	0.03	0.95	0.08	0.12
cg08328777	DUOX1	0.07	0.05	0.07	0.06	0.30
cg08714590	FZD1	0.86	0.12	0.86	0.12	0.43
cg08738570	C1orf70	0.09	0.10	0.09	0.08	0.69
cg09210956	SNTG2	0.67	0.09	0.67	0.12	0.93
cg09433131	KCNB2	0.94	0.06	0.93	0.10	0.43
cg09489445	ZNF788	0.01	0.03	0.01	0.04	0.92
cg09901035	PLEKHG4B	0.87	0.06	0.87	0.08	0.66
cg10272601	WNK2	0.30	0.07	0.28	0.08	0.04
cg10342963	IGF1R	0.81	0.13	0.79	0.15	0.07
cg11349423	OPCML	0.48	0.15	0.48	0.16	0.93
cg11377136	PKDREJ	0.03	0.03	0.03	0.03	0.69
cg11686528	ABR	0.01	0.07	0.01	0.06	0.60
cg12296772	MTMR7	0.07	0.06	0.07	0.07	0.78
cg12610564	SLC39A12	0.98	0.01	0.97	0.07	0.09
cg12680131	TPO	0.80	0.09	0.82	0.11	0.02
cg12852139	MYO10	0.96	0.02	0.95	0.06	0.70
cg13204512	RNF135	0.01	0.06	0.01	0.02	0.23
cg13517866	SMOC2	0.89	0.11	0.89	0.10	0.58
cg13564825	PPP1R14A	0.01	0.05	0.01	0.02	0.98
cg13604246	ANKMY1	0.11	0.08	0.11	0.09	0.68
cg13611121	COL5A1	0.80	0.08	0.80	0.10	0.73
cg13782274	KCNQ2	0.94	0.08	0.93	0.11	0.39
cg13791254	FOXE1	0.02	0.02	0.01	0.03	0.62
cg13879483	USP44	0.08	0.06	0.07	0.07	0.34
cg13895235	PRKAR1B	0.01	0.01	0.01	0.03	0.39
cg14183206	HLA-L	0.24	0.10	0.23	0.09	0.61
cg14486338	KCNS2	0.12	0.07	0.12	0.07	0.53
cg14644001	PRRT1	0.04	0.03	0.04	0.05	0.63
cg14645545	SLC11A1	0.20	0.12	0.19	0.12	0.83
cg14715697	HRNBP3	0.70	0.08	0.71	0.08	0.20
cg14866200	SHISA3	0.02	0.07	0.02	0.06	0.74
cg14988503	CDKL2	0.02	0.03	0.02	0.03	0.85
cg15092343	MSX1	0.07	0.05	0.07	0.04	0.48
cg15167871	TCERG1L	0.92	0.10	0.92	0.11	0.98
cg15549700	AJAP1	0.96	0.05	0.96	0.08	0.53
cg15760257	SARM1	0.01	0.01	0.01	0.05	0.35
cg17264670	RGS17	0.08	0.06	0.08	0.08	0.94
cg17497608	FZD1	0.83	0.11	0.84	0.12	0.43
cg17725364	COL6A3	0.96	0.10	0.96	0.09	0.86
cg18537730	IZUMO1	0.16	0.07	0.16	0.08	0.63
cg19429281	ZNF702P	0.02	0.01	0.02	0.03	0.40
cg19464917	ISL2	0.06	0.04	0.05	0.03	0.17
cg20129213	RIMS2	0.01	0.05	0.01	0.05	0.47
cg20399616	BCAT1	0.05	0.08	0.04	0.08	0.40
cg21385746	LOC150568	0.96	0.10	0.95	0.11	0.80
cg21472506	OTX1	0.01	0.04	0.01	0.04	0.98
cg21790626	ZNF154	0.04	0.04	0.05	0.05	0.32
cg22403469	RIMBP2	0.83	0.05	0.83	0.08	0.63
cg22511877	MYT1L	0.56	0.17	0.60	0.16	0.01
cg22524061	OSR2	0.23	0.09	0.22	0.09	0.48
cg22655988	CRMP1	0.96	0.08	0.96	0.10	0.77
cg22789900	MIXL1	0.00	0.01	0.01	0.04	0.55
cg23004031	MGMT	0.55	0.31	0.58	0.32	0.41
cg23391785	DNM3	0.02	0.06	0.01	0.04	0.28
cg23498518	POM121L12	0.79	0.07	0.80	0.10	0.36
cg23864180	ADARB2	0.90	0.06	0.91	0.07	0.26
cg24274117	C20orf195	0.03	0.07	0.04	0.07	0.52
cg24425838	C2CD4D	0.05	0.08	0.05	0.07	0.98
cg24432073	CDKL2	0.02	0.03	0.02	0.04	0.84
cg24563094	FAM59B	0.10	0.04	0.10	0.05	0.55
cg24602704	ATP10A	0.97	0.02	0.97	0.07	0.46
cg24816460	CDYL	0.03	0.07	0.03	0.07	0.51
cg25480336	ZFP64	0.01	0.02	0.01	0.01	0.16
cg25577023	AMN	0.09	0.09	0.09	0.09	0.82
cg25622366	OTX1	0.02	0.07	0.02	0.05	0.66
cg26010734	EPHX3	0.05	0.05	0.05	0.04	0.43
cg26841013	WNT3A	0.03	0.02	0.03	0.03	0.45

¹P value for student’s t-test.

Table 3 White blood cell DNA methylation and hepatocellular carcinoma risk

Locus		Cases/controls	OR (95%CI)
WNK2 cg10272601	Below median (< 0.279)	56/157	1.0
	Above median (≥ 0.279)	103/155	1.91 (1.27-2.86)
TPO cg12680131	Below median (< 0.836)	102/157	1.0
	Above median (≥ 0.836)	57/155	0.59 (0.39-0.87)
MYT1L cg22511877	Below median (< 0.636)	105/159	1.0
	Above median (≥ 0.636)	54/153	0.50 (0.33-0.77)

Table 4 Multiple variables model for DNA methylation and hepatocellular carcinoma risk

Variable	OR (95%CI)	P
WNK2 cg102726011	2.26 (1.42-3.61)	0.0006
TPO cg126801312	0.55 (0.34-0.87)	0.01
MYT1L cg225118773	0.53 (0.32-0.88)	0.01
HBsAg (positive vs negative)	5.50 (3.34-9.03)	< 0.0001
Alcohol (yes vs no)	2.10 (1.08-4.07)	0.03

¹Above or below the median of 0.279;

²Above or below the median of 0.836;

³Above or below the median of 0.636. HBsAg: Hepatitis B virus surface antigen.