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Molecular Cancer
Published in: Molecular Cancer 1/2010

Open Access 01-12-2010 | Research

Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

Authors: Dilek Colak, Muhammad A Chishti, Al-Bandary Al-Bakheet, Ahmed Al-Qahtani, Mohamed M Shoukri, Malcolm H Goyns, Pinar T Ozand, John Quackenbush, Ben H Park, Namik Kaya

Published in: Molecular Cancer | Issue 1/2010

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Abstract

Background

Hepatocellular carcinoma (HCC) is the third-leading cause of cancer-related deaths worldwide. It is often diagnosed at an advanced stage, and hence typically has a poor prognosis. To identify distinct molecular mechanisms for early HCC we developed a rat model of liver regeneration post-hepatectomy, as well as liver cells undergoing malignant transformation and compared them to normal liver using a microarray approach. Subsequently, we performed cross-species comparative analysis coupled with copy number alterations (CNA) of independent early human HCC microarray studies to facilitate the identification of critical regulatory modules conserved across species.

Results

We identified 35 signature genes conserved across species, and shared among different types of early human HCCs. Over 70% of signature genes were cancer-related, and more than 50% of the conserved genes were mapped to human genomic CNA regions. Functional annotation revealed genes already implicated in HCC, as well as novel genes which were not previously reported in liver tumors. A subset of differentially expressed genes was validated using quantitative RT-PCR. Concordance was also confirmed for a significant number of genes and pathways in five independent validation microarray datasets. Our results indicated alterations in a number of cancer related pathways, including p53, p38 MAPK, ERK/MAPK, PI3K/AKT, and TGF-β signaling pathways, and potential critical regulatory role of MYC, ERBB2, HNF4A, and SMAD3 for early HCC transformation.

Conclusions

The integrative analysis of transcriptional deregulation, genomic CNA and comparative cross species analysis brings new insights into the molecular profile of early hepatoma formation. This approach may lead to robust biomarkers for the detection of early human HCC.
Appendix
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Metadata
Title
Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old
Authors
Dilek Colak
Muhammad A Chishti
Al-Bandary Al-Bakheet
Ahmed Al-Qahtani
Mohamed M Shoukri
Malcolm H Goyns
Pinar T Ozand
John Quackenbush
Ben H Park
Namik Kaya
Publication date
01-12-2010
Publisher
BioMed Central
Published in
Molecular Cancer / Issue 1/2010
Electronic ISSN: 1476-4598
DOI
https://doi.org/10.1186/1476-4598-9-146

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