Genomic-wide analysis of lymphatic metastasis-associated genes in human hepatocellular carcinoma

Table 1 Clincal data of patients with hepatocellular carcinoma

Case	Sex	Age	Hepatitis virus	Differentiated grade	TNM score
1	M	54	HBV	WD	T1N0M0
2	M	60	HCV	WD	T1N0M0
3	F	61	HBV	WD	T2N0M0
4	M	62	HBV	WD	T2N0M0
5	M	58	HBV	WD	T1N0M0
6	F	56	HCV	MD	T3N0M0
7	F	44	HBV	WD	T2N0M0
8	M	49	HCV	WD	T1N0M0
9	M	58	HBV	WD	T2N0M0
10	M	67	HCV	PD	T3N0M0
11	M	69	HBV	WD	T2N0M0
12	F	63	HCV	WD	T1N0M0
13	M	48	HCV	MD	T2N0M0
14	F	63	HBV	WD	T1N0M0
15	M	49	HCV	MD	T1N0M0
16	F	51	HBV	PD	T3N1M0
17	M	65	HCV	MD	T3N1M0
18	F	58	HBV	PD	T4N1M1
19	M	60	HBV	MD	T2N1M0
20	F	56	HCV	PD	T3N1M1
21	M	42	HCV	PD	T3N1M0
22	M	55	HBV	PD	T4N1M1
23	M	66	HBV	MD	T3N1M0
24	F	70	HCV	WD	T2N1M0
25	M	58	HBV	PD	T4N1M1
26	M	53	HCV	PD	T3N1M0
27	M	61	HBV	PD	T4N1M0
28	F	65	HBV	MD	T3N1M0
29	M	59	HCV	MD	T3N1M1
30	M	50	HBV	PD	T3N1M0
31	F	63	HCV	PD	T4N1M1
32	M	66	HCV	PD	T3N1M0

M: Male; F: Female; HBV: Hepatitis B virus infection; HCV: Hepatitis C virus infection; WD: Well differentiated HCC; MD: Moderately differentiated HCC; PD: Poorly differentiated HCC.

Table 2 Up-regulated genes correlated with lymphatic metastasis

Gene name	Symbola	Accessionb	Fold changec	pN1:pN0d
Cell adhesion proteins
CD58 antigen, (lymphocyte function-assocoated antigens)	CD58	NM_001779	7.75	2.28
Integrin αM	ITGAM	NM_000632	5.04	2.06
Integrin β5	ITGB5	NM_002213	3.98	1.87
Opioid-binding protein/cell adhesion molecule-like	OPCML	NM_002545
Cell membrane receptor
CD86 antigen, (CD28 antigen ligand 2, B7-2 antigen)	CD86	NM_006889	6.76	2.33
v-jun sarcoma virus 17 oncogene homolog (avian)	JUN	NM_002228	7.43	2.27
Met proto-oncogene (hepatocyte growth factor receptor)	MET	NM_000245	10.11	3.46
EphA2	EPHA2	NM_004431	8.26	2.13
Epidermal growth factor receptor [avian erythroblastic leukemia viral (v-erb-b) oncogene homolog]	EGFR	NM_005228	8.35	2.62
Cell death regulator
BCL2/adenovirus E1B 19kDa interacing protein 3	BNIP3	NM_004052	3.88	2.29
Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	SEMA4D	NM_006378	5.71	3.64
Intracellular signaling
Rho GDP dissociation inhibitor γ	ARHGDIG	NM_001175	5.37	1.97
Ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3)	RAC3	AK054993	4.63	2.07
Insulin-like growth factor binding protein 3	IGFBP3	M35878	5.39	2.15
Coagulation factor II (thrombin) receptor	F2R	NM_001992	6.17	2.43
Growth/differentiation factor
Vascular endothelial growth factor C	VEGFC	NM_005429	5.68	2.47
Cell cycle regulator
Cyclin D1 (PRAD1: parathyroid adenomatosis 1)	CCND1	NM_053056	11.56	4.31
Cyclin-dependent kinase 4	CDK4	NM_000075	8.73	3.59
Others
Tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)	TIMP3	NM_000362	3.95	1.89
Ubiquitin-conjugating enzyme E2A (RAD6 homolog)	UBE2A	NM_003336	4.38	1.95
v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1	YES1	NM_005433	5.66	2.37
P450(cytochrome) oxidoreductase	POR	AF258341	4.74	1.99
Matrix metalloproteinase 13	MMP13	NM_00247	5.67	2.45
Matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)	MMP2	NM_004530	7.13	3.36

^aSymbol in LocusLink database;

^bGeneBank accession number;

^cFold change, ratio of mean expression values in lymph node metastasis cases (cancer cells vs non-cancerous cells);

^dpN1:pN0, ratio of mean expression values (lymph node positive cases to lymph node negative cases).

Table 3 Down-regulated genes correlated with lymphatic metastasis

Gene name	Symbola	Accessionb	Fold changec	pN1:pN0d
Cell adhesion proteins
Desmoplakin (DPI, DPII)	DSP	NM_004415	-14.22	0.24
Protocadherin gamma subfamily C, 3	PCDHGC3	NM_002588	-7.88	0.41
Integrin, beta 4	ITGB4	NM_000213	-13.39	0.26
Integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	ITGA3	NM_002204	-6.24	0.38
Catenin (cadherin-associated protein), alpha 1 (102kD)	CTNNA1	NM_001903	-8.53	0.37
Cadherin 1, type 1, E-cadherin (epithelial)	CDH1	NM_004360	-15.85	0.25
Cell cycle regulator
Cell division cycle 25B	CDC25B	NM_021784	-6.90	0.46
Cyclin-dependent kinase 5	CDK5	NM_004935	-5.51	0.48
Cyclin D2	CCND2	NM_001759	-6.29	0.43
Microtubule-associated protein, RP/EB family, member 1	MAPRE1	NM_012325	-13.16	0.29
Protein phosphatase 1D	PPM1D	NM_003620	-11.77	0.39
Ataxia telangiectasia and Rad3 related	ATR	NM_001184	-7.86	0.41
Protein phosphatase 2, regulatory subunit B (B56), alpha isoform	PPP2R5A	NM_006243	-3.89	0.49
Intracellular signaling
Mitogen-activated protein kinase 14	MAPK14	NM_001315	-5.67	0.43
Mitogen-activated protein kinase 7	MAPK7	NM_002749	-7.15	0.39
Mitogen-activated protein kinase 4	MAPK4	NM_002747	-3.83	0.32
Small inducible cytokine B subfamily (Cys-X-Cys motif), member 13 (B-cell chemoattractant)	SCYB13	NM_006419	-4.58	0.46
Signal transducer and activator of transcription 5B	STAT5B	NM_012448	-8.13	0.37
Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1	SERPINB1	NM_030666	-4.47	0.48
Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2	SERPINB2	NM_002575	-5.72	0.41
SH3-domain binding protein 2	SH3BP2	AB000462	-3.29	0.52
G protein-coupled receptor kinase 6	GPRK6	NM_002082	-14.12	0.29
GTP-binding protein ragB	RAGB	NM_016656	-6.77	0.46
Protein tyrosine phosphatase, receptor type, F	PTPRF	NM_002840	-7.21	0.34
Cell membrane receptor
EphB6	EPHB6	NM_004445	-12.88	0.38
Kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4)	KAI1	NM_002231	-2.24	0.67
Small inducible cytokine subfamily A (Cys-Cys), member 25	SCYA25	NM_005624	-3.76	0.72
Monoglyceride lipase	MGLL	NM_007283	-4.66	0.43
Interferon (alpha, beta and omega) receptor 1	IFNAR1	NM_000629	-2.39	0.81
Insulin-like growth factor binding protein 6	IGFBP6	NM_002178	-3.53	0.62
Metabolic enzyme
Serine protease inhibitor, Kunitz type, 2	SPINT2	NM_021102	-5.44	0.46
Protein phosphatase 2, regulatory subunit B (B56), alpha isoform	PPP2R5A	NM_006243	-7.12	0.37
Protein tyrosine phosphatase, non-receptor type 2	PTPN2	NM_002828	-19.73	0.23
Deoxyribonuclease I-like 3	DNASE1L3	NM_004944	-8.23	0.29
Cathepsin L	CTSL	NM_001912	-4.39	0.37
Cell death regulator
Caspase 3, apoptosis-related cysteine protease	CASP3	NM_004346	-14.57	0.29
Programmed cell death 10	PDCD10	NM_007217	-7.19	0.36
DNA damage response
Ataxia telangiectasia and Rad3 related	ATR	NM_001184	-4.78	0.48
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)	XRCC5	NM_021141	-2.59	0.73
Mouse double min 2	MDM2	NM_002392	-6.37	0.51
Growth/differentiation factor
Bone morphogenetic protein 5	BMP5	NM_021073	-2.78	0.53
Keratin 4	KRT4	NM_002272	-3.12	0.62
Keratin 13	KRT13	NM_002274	-4.24	0.48
Connective tissue growth factor	CTGF	NM_001901	-5.51	0.42
Others
Heat shock 70kDa protein 4	HSPA4	AB023420	-3.19	0.56
Retinoid X receptor, α	RXRA	NM_002957	-2.89	0.77
Ubiquitin-activating enzyme E1-like	UBE1L	NM_003335	-2.95	0.53
Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	SLC25A5	NM_001152	-6.18	0.46

^aSymbol in LocusLink database;

^bGeneBank accession number;

^cFold change, ratio of mean expression values in lymph node metastasis cases (cancer cells vs non-cancerous cells);

^dpN1:pN0, ratio of mean expression values (lymph node positive cases to lymph node negative cases).