[Frontiers in Bioscience E2, 829-840, June 1, 2010]

Expression profile reveals novel prognostic biomarkers in hepatocellular carcinoma

Meiqian Sun1, Gang Wu1, Yao Li1, Xuping Fu1, Yan Huang1, Rong Tang1, Yi Guo1, Minyan Qiu2, Yumin Mao1, Feng Zhao3, Lin Li4, Shengdong Huang3, Xianxian Zhao3, Yi Xie1

1State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, PR China, 2Shanghai BioStar Genechip Inc., Shanghai, PR China, 3Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, PR China, and 4 Department of Radiation Therapy, Affiliated Tumor Hospital of Guangxi Medical University, Guangxi, PR China

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Materials and methods
3.1. Tissue samples and RNA isolation
3.2. cDNA microarrays
3.3. Tissue microarray-based immunohistochemistry
3.4. Statistical analysis
4. Results
4.1. Reproducibility of cDNA microarray
4.2. Identification and validation of differentially expressed genes in HCC
4.3. Identification of a gene expression signature predicting differentiation degree and survival of HCC samples
4.4. Functional analysis of gene Ontology biological process categories and pathways involved in HCC carcinogenesis and tumor progression
4.5. Cytogenetic aberrations analysis
4.6. Validation of MCM2 protein overexpression related to poor-differentiation in HCC
5. Discussion
6. Acknowledgment
7. References

1. ABSTRACT

The purpose of this study was to identify and validate novel prognostic biomarkers in human hepatocellular carcinoma (HCC). We analyzed gene expression profiles not only between 33 HCCs and their corresponding noncancerous liver tissues, but also between 25 HCCs and pooled normal liver tissues using cDNA microarrays containing 12800 genes. Functional analysis of differentially expressed genes involved in HCC carcinogenesis and tumor progression revealed that up-regulated and down-regulated genes are mainly associated with cell cycle and immune response, respectively. We detected two regions of cytogenetic changes only in poorly-differentiated HCCs using the expression data. We identified a 9-gene expression signature, which was able to predict differentiation degree and survival of HCC samples. Among the 9 most discriminatory genes, minichromosome maintenance protein 2 (MCM2), a significantly up-regulated gene involved in cell cycle pathway, was selected for further analysis. Overexpression of MCM2 protein related to poor-differentiation in HCC was validated using tissue microarray-based immunohistochemistry containing 96 HCCs. Our studies show that the 9-gene expression signature may serve as promising prognostic biomarkers involved in hepatocarcinogenesis and tumor progression.