Genome-wide differences in hepatitis C- vs alcoholism-associated hepatocellular carcinoma

Table 1 Clinical data from patients with HCC or controls

Patient1	Sex	Age	Pathology	Etiology2	Tumor grade3	Number of nodules4	Nodule size (cm)	Vascular invasion	Lymphocyte infiltration5
V1	F	71	HCC	HCV	3	2	4; 5	Yes	0
V3	F	67	HCC	HCV	3	1	2.5	No	+++
V4	F	72	HCC	HCV	3	1	4	No	+++
V8	M	66	HCC	HCV	3	1	4	Yes	++
V9	M	65	HCC	HCV	3	2	1.5; 3	No	+
V14	M	63	HCC	HCV	2	1	2	No	0
V15	M	70	HCC	HCV	1	1	3.5	No	+++
V17	M	69	HCC	HCV	3	1	2.5	No	+++
V20	F	73	HCC	HCV	3	1	1.5	Yes	++
V21	M	65	HCC	HCV	2	1	2	No	+
V23	F	68	HCC	HCV	2	2	1; 5.5	Yes	0
V24	M	80	HCC	HCV	1; 3	2	2.5; 3.5	No	0
V25	M	64	HCC	HCV	3	2	2; 5.5	Yes	+++
V26	M	46	HCC	HCV	3	1	2.5	Yes	+
V27	M	55	HCC	HCV	3	2	3; 3.5	Yes	0
V28	M	55	HCC	HCV	2	2	4; 4	No	++
V35	M	53	HCC	HCV	2; nd; nd	3	7; nd; nd	Yes	+
A2	M	68	HCC	ALC	2	1	11	No	0
A5	M	79	HCC	ALC	2	1	6	No	++
A6	M	63	HCC	ALC	2	1	3	No	+
A7	M	49	HCC	ALC	1	1	2	No	0
A10	M	73	HCC	ALC	2	1	5	No	+
A11	M	50	HCC	ALC	2	1	4.5	No	+
A12	M	64	HCC	ALC	1	1	2.5	No	+
A13	M	72	HCC	ALC	3	1	2.5	Yes	++
A16	M	56	HCC	ALC	3	1	8.5	Yes	++
A18	M	70	HCC	ALC	2	1	3.5	No	+
A19	M	70	HCC	ALC	3	1	2.5	No	+++
A22	M	78	HCC	ALC	1	1	1.7	No	+
A29	M	66	HCC	ALC	2	1	7	No	+
A30	M	55	HCC	ALC	2	1	4.5	No	0
A31	M	56	HCC	ALC	2	1	4	Yes	0
A32	F	66	HCC	ALC	3	1	8	No	0
A33	M	55	HCC	ALC	3	1	15	Yes	0
A34	M	69	HCC	ALC	3	1	2.2	Yes	0
C1	M	74	AD6	-
C2	F	45	AD	-
C3	F	68	AD	-
C4	F	43	AD+FNH6	-
C5	F	30	FNH	-

¹V1 to A34, patients with cirrhosis and HCC, A or V refers to the alcoholic or viral etiology. C1 to -5, control patients. Patients V1 to V21 and A2 to A22 were first studied by microarray, and next used as a training set for SVM.

²HCV: Hepatitis C virus infection; ALC: Alcohol abuse; -: None.

³Differentiation grade; nd: Not determined.

⁴In multinodular HCCs, only 1 nodule was studied.

⁵Nodular infiltration; semi-quantitative appraisal done by a trained anatomopathologist (AF).

⁶Histologically normal liver taken away from a benign adenoma (AD) or a focal nodular hyperplasia (FNH).

Table 2 Etiology-dependent frequency of dysregulated transcripts within functionally defined subsets

	HCV patients (n = 10)			Alcoholic patients (n = 12)
			Tumor/cirrhosis1			Tumor/cirrhosis
Subset: Regulation of cell cycle (GO 0000074)2
CCT43	Hs.4215094	1.38 (7)a
ZAK	Hs.444451	1.44 (8)
CUL1	Hs.146806	1.69 (7)
MAPRE1	Hs.472437	1.78 (10)	χ2
CLK1	Hs.433732	1.80 (7)	P < 0.05
CKS2	Hs.83758	1.92 (8)
NME1	Hs.463456	1.97 (9)
CDC37	Hs.160958	2.05 (6)				-
TSC1	Hs.370854	2.60 (6)a
Subset: Transcription factor (GO 0003700)
IRF6	Hs.355827	0.55 (10)b		RUNX1	Hs.149261	0.67 (12)b
FOSL2	Hs.220971	0.58 (10)a		NR3C1	Hs.122926	1.68 (12)b
ETS2	Hs.592158	0.79 (10)b
IRF2	Hs.374097	0.83 (9)
DSCR1	Hs.282326	1.53 (10)
NR4A3	Hs.279522	1.63 (7)a
ZNF397	Hs.84307	1.72 (10)	χ2
HMGA1	Hs.518805	1.75 (9)	P < 0.05
SPIB	Hs.437905	1.77 (10)
NME1	Hs.463456	1.97 (6)a
ATF3	Hs.460	2.22 (6)
MSRB2	Hs.461420	2.32 (6)
DSIPI	Hs.420569	2.51 (7)
IRF3	Hs.75254	2.70 (7)
Subset: Acute phase response (GO 0006953)
CRP5	Hs.76452	0.46 (10)a		AHSG	Hs.324746	0.84 (12)
APCS5	Hs.507080	0.84 (10)a	χ2	ORM1	Hs.567311	1.24 (12)
			P < 0.05	SAA25	Hs.1955	1.84 (11)a
				SAA15	Hs.632144	1.90 (11)a
				CRP5	Hs.76452	2.17 (12)

¹Average ratio of mRNA levels in tumor and cirrhotic tissue in patients with a detectable expression of this mRNA. The number of such patients is indicated in brackets and a significant difference between tumors and paired cirrhotic tissues per etiology is indicated (^aP < 0.05;

^bP < 0.01; Wilcoxon’s non parametric, paired test).

²Subset of mRNAs coding for proteins with a shared function as identified by Gene Ontology (GO) number.

³Dysregulated mRNAs, as defined by an abnormal tumor/cirrhosis ratio found in at least 3 patients of at least one etiology group (total 475 mRNAs; HCV, 301; alcoholism, 174). The dysregulated mRNAs with an ontology-defined function (HCV, 183; alcoholism, 100) were a subset of the 475 mRNAs.

⁴Hs. number as a unique mRNA identifier.

⁵Only 5 of the 23 mRNAs listed in Figure 2B appear herein because the other mRNAs in Figure 2B belonged to functional classes in which the number of mRNAs was not different in alcoholic vs HCV patients.

Table S1 Etiology-dependent location of dysregulated genes on chromosomes

HCV			Alcohol
gene	Hs. Number	chr.	gene	Hs. Number	chr.
Trans. Locus	Hs.597833	2	MAP3K2	Hs.145605	2q14.3
VAMP5	Hs.172684	2p11.2	WDFY1	Hs.642721	2q36.1
KCMF1	Hs.345694	2p11.2
LOC56902	Hs.262858	2p13.3
UGP2	Hs.516217	2p14-p13
CCT4	Hs.421509	2p15
KIAA1387	Hs.516182	2p16.1
MRPL33	Hs.515879	2p21
FNDC4	Hs.27836	2p23.3
FOSL2	Hs.220971	2p23.3
CKAP2L	Hs.434250	2q13
CXCR4	Hs.421986	2q21
ZAK	Hs.444451	2q24.2
LEREPO4	Hs.368598	2q32.2
CLK1	Hs.433732	2q33
MAP2	Hs.368281	2q34-q35
CPS1	Hs.149252	2q35
NHEJ1	Hs.225988	2q35
WDFY1	Hs.642721	2q36.1
AGXT	Hs.144567	2q36-q37
TNRC15	Hs.565319	2q37.1
DGKD	Hs.471675	2q37.1
STK25	Hs.516807	2q37.3
LONRF1	Hs.180178	8p23	PLAT	Hs.491582	8p12
EXOSC4	Hs.632041	8q24.3	CLU	Hs.436657	8p21-p12
TIGD5	Hs.71574	8q24.3	FGL1	Hs.491143	8p22-p21.3
			MCM4	Hs.460184	8q11.2
			FAM92A1	Hs.125038	8q22.1
			EXOSC4	Hs.632041	8q24.3
			TIGD5	Hs.71574	8q24.3
			RPL8	Hs.178551	8q24.3

The genes shown here are those located on the significant chrs in Figure 1. They are referred to by an Hs. number as a unique identifier. Every such gene had an mRNA level that was significantly altered in tumor vs cirrhosis in at least 25% of the patients within at least one etiology.