Dataset: Transcription profiling by array of human hepatocellular carcinomas with hepatitis C virus etiology
To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an...
To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set. Strikingly, this locus overlapped with copy gains in 4 of 371 lung adenocarcinomas. Overexpression of VEGFA via 6p21 gain suggested a cell-nonautonomous mechanism of oncogene activation. Hierarchical clustering of gene expression among 91 tumors identified 5 classes, including 'Wnt-CTNNB1', 'proliferation' and 'nterferon-related' gene classes. We also discovered a novel class defined by polysomy of chromosome 7, gains of which were associated with early tumor recurrence after resection. These findings reveal key alterations in HCC pathogenesis and implicate potential therapeutic targets. Experiment Overall Design: 91 hepatocellular carcinomas were obtained at the time of surgical resection or orthotopic transplantation.
- Species:
- human
- Samples:
- 91
- Source:
- E-GEOD-9843
- Updated:
- Dec.12, 2014
- Registered:
- Sep.22, 2014
Factors:
(via ArrayExpress)
| Sample | CLINICAL_INFORMATION | HISTOLOGY | GENOTYPE |
|---|---|---|---|
| GSE9843GSM248688 | Inflammation | pAkt not available, pIGFR1 not available, CTNNB1 not available, pRPS6 not available | CTNNB1 mutation: not available, TP53 mutation: negative |
| GSE9843GSM248689 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: 256G>GT | R249R/S |
| GSE9843GSM248690 | Polysomy chr7 | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248691 | Unannotated | pAkt negative, pIGFR1 positive, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 233A>AG,p.D32D/G, TP53 mutation: negative |
| GSE9843GSM248692 | Unannotated | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 239G>GA,p.G34G/E, TP53 mutation: negative |
| GSE9843GSM248693 | Unannotated | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 239G>GT,p.G34G/V, TP53 mutation: negative |
| GSE9843GSM248694 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248695 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 259A>AG,p.T41T/A, TP53 mutation: negative |
| GSE9843GSM248696 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248697 | Proliferation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248698 | Unannotated | pAkt not available, pIGFR1 not available, CTNNB1 not available, pRPS6 not available | CTNNB1 mutation: not available, TP53 mutation: negative |
| GSE9843GSM248699 | Polysomy chr7 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 233A>AG,p.D32D/G, TP53 mutation: negative |
| GSE9843GSM248700 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248701 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248702 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: 236C>CT | S33S/F, TP53 mutation: 256G>GT | R249R/S |
| GSE9843GSM248703 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248704 | Polysomy chr7 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 271T>TG,p.S45S/A, TP53 mutation: negative |
| GSE9843GSM248705 | Unannotated | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248706 | CTNNB1 | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 232G>GA | D32D/N, TP53 mutation: negative |
| GSE9843GSM248707 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 247T>TG | S37S/A, TP53 mutation: negative |
| GSE9843GSM248708 | CTNNB1 | pAkt not available, pIGFR1 not available, CTNNB1 not available, pRPS6 not available | CTNNB1 mutation: not available, TP53 mutation: negative |
| GSE9843GSM248709 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248710 | CTNNB1 | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 248C>CG | S37S/C, TP53 mutation: negative |
| GSE9843GSM248711 | Polysomy chr7 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248712 | Proliferation | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248713 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248714 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248715 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: 284G>GT | D259D/Y |
| GSE9843GSM248694 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248717 | Proliferation | pAkt negative, pIGFR1 positive, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: 236C>CG | S33S/C, TP53 mutation: negative |
| GSE9843GSM248718 | Unannotated | pAkt not available, pIGFR1 not available, CTNNB1 not available, pRPS6 not available | CTNNB1 mutation: not available, TP53 mutation: not available |
| GSE9843GSM248719 | Unannotated | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248720 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 247T>TG | S37S/A, TP53 mutation: negative |
| GSE9843GSM248694 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248722 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: not available |
| GSE9843GSM248723 | Proliferation | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: 440G>GA | C176C/Y |
| GSE9843GSM248724 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248713 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248726 | CTNNB1 | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: 248C>CT | S37S/F, TP53 mutation: negative |
| GSE9843GSM248727 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: 344A>AC | Q144Q/P |
| GSE9843GSM248728 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248709 | Unannotated | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248730 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: not available, TP53 mutation: not available |
| GSE9843GSM248731 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: 271T>TG,p.S45S/A, TP53 mutation: negative |
| GSE9843GSM248732 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248733 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 233A>AT | D32D/V, TP53 mutation: negative |
| GSE9843GSM248734 | Polysomy chr7 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 233A>AG,p.D32D/G, TP53 mutation: negative |
| GSE9843GSM248735 | Unannotated | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248736 | Polysomy chr7 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: 236C>CT,p.S33S/F, TP53 mutation: negative |
| GSE9843GSM248732 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248738 | Polysomy chr7 | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: 366A>AG,Y205Y/C |
| GSE9843GSM248739 | CTNNB1 | pAkt not available, pIGFR1 not available, CTNNB1 not available, pRPS6 not available | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248740 | Inflammation | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: 366A>AG,Y205Y/C |
| GSE9843GSM248732 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248732 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248743 | Polysomy chr7 | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 232G>GA,p.D32D/N, TP53 mutation: negative |
| GSE9843GSM248744 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 235T>TC | S33S/P, TP53 mutation: negative |
| GSE9843GSM248745 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248746 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248747 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: 232G>GT | D32D/Y, TP53 mutation: negative |
| GSE9843GSM248748 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation:195G>GT | E271E/X |
| GSE9843GSM248749 | CTNNB1 | pAkt positive, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: 248C>CT | S37S/F, TP53 mutation: negative |
| GSE9843GSM248750 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: 386G>GT | R158R/L |
| GSE9843GSM248751 | CTNNB1 | pAkt positive, pIGFR1 positive, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248752 | Inflammation | pAkt negative, pIGFR1 not available, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: not available, TP53 mutation: not available |
| GSE9843GSM248753 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation:249_250het_insGAATC |
| GSE9843GSM248754 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248712 | Proliferation | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248696 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248757 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: not available |
| GSE9843GSM248758 | Polysomy chr7 | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: 364C>CA | P151P/T |
| GSE9843GSM248759 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: 234_245het_delCTCTGGAATCCA, TP53 mutation: negative |
| GSE9843GSM248760 | Inflammation | pAkt positive, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248712 | Proliferation | pAkt negative, pIGFR1 positive, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248697 | Proliferation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248728 | Proliferation | pAkt positive, pIGFR1 positive, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248764 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: 232G>GA | D32D/N, TP53 mutation: negative |
| GSE9843GSM248732 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 positive, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248696 | Inflammation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248767 | CTNNB1 | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 248C>CG | S37S/C, TP53 mutation: negative |
| GSE9843GSM248768 | Proliferation | pAkt negative, pIGFR1 not available, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: not available, TP53 mutation: not available |
| GSE9843GSM248769 | Inflammation | pAkt negative, pIGFR1 not available, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248770 | Inflammation | pAkt positive, pIGFR1 not available, CTNNB1 positive, pRPS6 not available | CTNNB1 mutation: not available, TP53 mutation: negative |
| GSE9843GSM248771 | Inflammation | pAkt negative, pIGFR1 not available, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248697 | Proliferation | pAkt negative, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248771 | Inflammation | pAkt negative, pIGFR1 not available, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248774 | CTNNB1 | pAkt negative, pIGFR1 not available, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: 239G>GT | G34G/V, TP53 mutation: negative |
| GSE9843GSM248775 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 negative | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248776 | Proliferation | pAkt negative, pIGFR1 not available, CTNNB1 positive, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248777 | Proliferation | pAkt not available, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |
| GSE9843GSM248701 | Proliferation | pAkt positive, pIGFR1 negative, CTNNB1 negative, pRPS6 positive | CTNNB1 mutation: negative, TP53 mutation: negative |