Table 2.
List of 35 cross-species conserved early HCC signature genes with qRT-PCR and independent human/rat early HCC validations overlaid
| Gene Symbol1 | Description | Chromosomal Loci | P-value | qRT-PCR | Independent Validation Datasets. | |||
|---|---|---|---|---|---|---|---|---|
| Human | Rat | |||||||
| Chiang et al. | Boyault et al. | Liao et al. | Liu et al. | |||||
| VIM* | vimentin | 10p13 | 1.49E-16 | DEa | NS | NS | NS | DEc |
| DCN | decorin | 12q21.33 | 2.86E-15 | DEb | DEc | DEc | DEc | DEc |
| EIF4EBP1* | eukaryotic translation initiation factor 4E binding protein 1 | 8p12 | 8.91E-15 | NA | DEc | NS | NS | NS |
| AQP1 | aquaporin 1 (channel-forming integral protein, 28 kDa) | 7p14 | 1.15E-14 | NA | NS | DEd | NS | NS |
| IMPA2 | inositol(myo)-1(or 4)-monophosphatase 2 | 18p11.2 | 7.74E-14 | NA | NS | DEd | NS | NS |
| FBN1 | fibrillin 1 | 15q21.1 | 1.75E-12 | NA | NS | NS | NS | NS |
| DCK* | deoxycytidine kinase | 4q13.3-q21.1 | 4.22E-11 | NA | DEc | DEc | NS | |
| GJA1* | gap junction protein, alpha 1,43kDa (connexin 43) | 6q21-q23.2 | 5.08E-11 | DEa | NS | DEc | DEd | DEc |
| SP100* | SP100 nuclear antigen | 2q37.1 | 6.95E-11 | DEa | DEc | NS | NS | NS |
| SGCB* | sarcoglycan, beta (43kDa dystrophin-associated glycoprotein) | 4q12 | 3.18E-10 | NA | DEc | NS | NS | NS |
| FGFR2* | fibroblast growth factor receptor 2 | 10q26 | 1.15E-09 | NA | NS | NS | DEd | NS |
| ABCC9 | ATP-binding cassette, sub-family C (CFTR/MRP), member 9 | 12p12.1 | 1.75E-09 | NA | DEc | NS | DEc | NS |
| MMP2* | matrix metallopeptidase 2 | 16q13-q21 | 1.22E-08 | DEa | DEd | DEc | NS | NS |
| LGALS3BP* | lectin, galactoside-binding, soluble, 3 binding protein | 17q25 | 4.29E-08 | DEa | DEd | NS | NS | DEc |
| GSTA1* | glutathione S-transferase A1 | 6p12.1 | 5.16E-08 | NA | NS | NS | NS | NS |
| NAT8 | N-acetyltransferase 8 | 2p13.1-p12 | 3.20E-07 | NA | DEc | DEd | DEd | NS |
| HMGB2* | high-mobility group box 2 | 4q31 | 3.34E-07 | NA | DEc | DEd | DEd | NS |
| EXPH5 | exophilin 5 | 11q22.3 | 6.15E-07 | NA | DEc | NS | NS | NS |
| COL1A1* | collagen, type I, alpha 1 | 17q21.3-q22.1 | 7.62E-07 | DEa | DEd | NS | NS | DEc |
| POLRMT | polymerase (RNA) mitochondrial (DNA directed) | 19p13.3 | 7.95E-07 | NA | DEc | NS | DEc | NS |
| AGPAT2 | 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) |
9q34.3 | 1.04E-06 | NA | DEc | DEc | DEd | NS |
| CTBP2* | C-terminal binding protein 2 | 10q26.13 | 1.09E-06 | NA | NS | NS | DEd | NS |
| PROM1 | prominin 1 | 4p15.32 | 2.49E-06 | NA | DEc | DEd | NS | NS |
| HPX* | hemopexin | 11p15.5-p15.4 | 3.00E-06 | NA | DEc | DEc | NS | NS |
| HEPH | hephaestin | Xq11-q12 | 3.15E-06 | NA | NS | NS | DEc | |
| HLA-DQA1* | major histocompatibility complex, class II, DQ alpha 1 | 6p21.3 | 2.68E-05 | NA | DEd | DEd | NS | NS |
| COL5A2 | collagen, type V, alpha 2 | 2q14-q32 | 3.88E-05 | NA | DEd | NS | DEd | DEc |
| BIRC3 | baculoviral IAP repeat-containing 3 | 11q22 | 6.19E-05 | NA | DEd | NS | NS | NS |
| DPP4 | dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) |
2q24.3 | 0.00034 | DEa | DEc | NS | DEd | NS |
| AGL* | amylo-1, 6-glucosidase, 4-alpha-glucanotransferase | 1p21 | 0.000426 | NA | DEc | DEc | DEc | NS |
| PDZK1IP1 | PDZK1 interacting protein 1 | 1p33 | 0.001118 | NA | DEc | DEd | NS | NS |
| SRPX | sushi-repeat-containing protein, X-linked | Xp21.1 | 0.001189 | NA | DEc | DEc | DEd | NS |
| IL13RA1 | interleukin 13 receptor, alpha 1 | Xq24 | 0.004051 | NA | DEc | NS | DEc | NS |
| IGFBP3 | insulin-like growth factor binding protein 3 | 7p13-p12 | 0.006904 | DEa | DEc | DEc | DEc | DEc |
| PLN* | phospholamban | 6q22.1 | 0.028062 | NA | NS | NS | NS | NS |
1 Genes with asterisk are also located in the chromosomal CNA regions.
NA indicates genes for which qRT-PCR data are not available.
aValidation was performed using whole blood of human early HCC patients (p < 0.05)
bValidation was performed on rat early HCC tissues (p < 0.05); five additional rat genes that are not listed in Table 2 are also confirmed (Figure 6).
cDifferentially expressed (p < 0.02 and fold change (FC) > 1.8); NS: Not significant
dDifferentially expressed: FC > 1.8, but not statistically significant (p > 0.05)