The variability in the prognosis of individuals with hepatocellular carcinoma (HCC) suggests that HCC may comprise several distinct biological phenotypes. These phenotypes may result from activation of different oncogenic pathways during tumorigenesis and/or from a different cell of origin. Here we address whether the transcriptional characteristics of HCC can provide insight into the cellular origin of the tumor. We integrated gene expression data from rat fetal hepatoblasts and adult hepatocytes with HCC from human and mouse models. Individuals with HCC who shared a gene expression pattern with fetal hepatoblasts had a poor prognosis. The gene expression program that distinguished this subtype from other types of HCC included markers of hepatic oval cells, suggesting that HCC of this subtype may arise from hepatic progenitor cells. Analyses of gene networks showed that activation of AP-1 transcription factors in this newly identified HCC subtype might have key roles in tumor development.

We analyzed global gene expression patterns of 91 human hepatocellular carcinomas (HCCs) to define the molecular characteristics of the tumors and to test the prognostic value of the expression profiles. Unsupervised classification methods revealed two distinctive subclasses of HCC that are highly associated with patient survival. This association was validated via 5 independent supervised learning methods. We also identified the genes most strongly associated with survival by using the Cox proportional hazards survival analysis. This approach identified a limited number of genes that accurately predicted the length of survival and provides new molecular insight into the pathogenesis of HCC. Tumors from the low survival subclass have strong cell proliferation and antiapoptosis gene expression signatures. In addition, the low survival subclass displayed higher expression of genes involved in ubiquitination and histone modification, suggesting an etiological involvement of these processes in accelerating the progression of HCC. In conclusion, the biological differences identified in the HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. H epatocellular carcinoma (HCC) is the fifth most common cancer in the world, accounting for an estimated 500,000 deaths annually. 1 Although HCC is prevalent in Southeast Asia and sub-Sahara Africa, the incidence of HCC has doubled in the United States over the past 25 years, and incidence and mortality rates are likely to double over the next 10 -20 years. 2 Although much is known about both the cellular changes that lead to HCC and the etiological agents responsible for the majority of HCC cases (hepatitis B virus, hepatitis C virus, alcohol), the molecular pathogenesis of HCC is not well understood. 3 Considerable efforts have been devoted to establishing a prognostic model for HCC by using clinical information and pathological classification to provide information at diagnosis on both survival and treatment options. 4 -10 Although much progress has been made (reviewed by Llovet et al. 11 ), many issues still remain unresolved. For example, a staging system that reliably separates patients with early HCC as well as intermediate to advanced HCC into homogeneous groups with respect to prognosis does not exist. This is particularly important because the natural course of early HCC is unknown and the natural progression of intermediate and advanced HCC are known to be quite heterogeneous. 12 It therefore appears axiomatic that improving the classification of HCC patients into groups with homogeneous prognosis would at least improve the application of currently available treatment modalities and at best provide new treatment strategies.Recently, microarray technologies have been successfully used to predict clinical outcome and survival as well as classify different types of cancer. [13][14][15]