8 in the process of carcinogenesis [55]. Thus, chromosomal aberrations are common in this type of cancer. However, there is an enormous variety of alterations that can occur, and they have been found throughout the genome. Many of these chromosomal alterations are undoubtedly “passenger” changes, rather than the “drivers” of tumor progression. In the past decade, advances in genomics technologies such as the development of array-based comparative genomic hybridization (array CGH) have allowed investigators to map HCC-associated chromosomal alterations at a much higher resolution than was previously possible. A number of chromosomal regions have now been identiﬁed in which gains or losses occur frequently in HCCs (reviewed in [56]), and progress is being made in determining which genes are the targets of these recurrent changes. For example, by comparing array CGH data with global gene expression patterns (determined using DNA microarrays) in 49 HCC samples, Patil et al. were able to correlate the recurrent gain in chromosome 8q with Jab1 overexpression [57]. Interestingly, this is the same gene (also known as CSN5) whose overex- pression was recently implicated in the activation of MYC that appears to drive the progression of DN to early HCC [37]. Thus, 8q gain may be a common mechanism promoting early hepatocarcinogenesis. Although high-resolution mapping of chromosomal alterations in cancer is valuable mostly as a research tool, a group in Japan has demonstrated that HCCs can be subclassiﬁed into distinct, clinically meaningful groups based solely on their patterns of chromosomal alterations [58]. In this study, hierarchical cluster analysis was performed on the genomic gain/loss proﬁles of 87 HCCs, and the tumors were found to partition into two classes, termed A and B. Chromosomal alterations were more numerous in cluster A and typically included gains of 1q, 6p, and 8q as well as 8p losses; this group of tumors was associated with poor patient survival. Cluster A was further subdivided into three subgroups, each characterized by speciﬁc high- level ampliﬁcations (1q and 6p, 8q, and 17q). Cluster B contained two important subgroups, one without frequent chromosomal alterations and another with ampliﬁcation of 17q. The authors reasoned that by analogy with known gene ampliﬁcations in other cancer types, the recurrent ampliﬁcations they discovered in HCC subgroups might indicate the presence of important oncogenes and that these oncogenes might be suitable therapeutic targets. Accordingly, the vascular endothelial growth factor A gene (VEGFA) was found to be contained within the ampliﬁed region of chromosome 6p in a subgroup of cluster A tumors, and a gene encoding an eﬀector molecule of the mTOR signaling pathway was found to reside within the ampliﬁed region of 17q. The frequent high-level copy number gain of the 6p region encompassing VEGFA has been conﬁrmed in a larger set of HCC tumors and correlated with VEGFA overexpression [59]. Both VEGF and the mTOR pathway are promising therapeutic targets in liver cancer. Therefore, the predictive value of ampliﬁcations at 6p and 17q in HCCs as molecular markers of response to VEGF- and mTOR- targeted therapies should be further explored in clinical studies. Pathology Research International The quantitative assessment of genomic alterations as an indicator of tumor aggressiveness has proven useful in pre- dicting the risk of HCC recurrence after liver transplantation. In an eﬀort to identify molecular markers of recurrence risk in HCC patients who had undergone transplantation, Marsh et al. analyzed explanted tumors for loss of heterozygosity (LOH) of microsatellite markers at nine tumor suppressor gene loci [60]. They found that the amount of allelic loss demonstrated within a particular tumor, when combined with other parameters such as tumor size and patient gender, correlated signiﬁcantly with risk of tumor recurrence. In a subsequent study, the panel of microsatellite markers used in this analysis was reﬁned, and a simple measure of the amount of LOH detected in each tumor was developed, called the fractional allelic imbalance (FAI) [61]. The measurement of FAI and determination of the presence or absence of macrovascular tumor invasion form the basis of the Pittsburgh staging system [62], which is reported to more accurately predict the risk of HCC recurrence after transplantation than staging systems based on radiologic and clinical parameters [63]. HCCs have been extensively analyzed for the detection of somatic mutations aﬀecting known oncogenes and tumor suppressors (reviewed in [64]). The gene encoding β-catenin (CTNNB1), which is mutated in approximately 30% of HCC, is the oncogene most frequently activated in this cancer. HCC bearing β-catenin mutations are more likely than their nonmutant counterparts to show chromosome stability, an absence of HBV infection [65], a well-diﬀerentiated histology, and cholestasis [66]. However, there are conﬂicting data in the literature on the question of whether β-catenin mutation in HCC is associated with favorable or unfavorable prognosis [67, 68]. In general, tumor suppressor genes are more often mutated in HCC than oncogenes. The tumor suppressor most commonly mutated in HCC, overall, is TP53 (encoding the well-known cell cycle regulator, p53), but its frequency of mutation varies with geographical location. TP53 mutation in HCC occurs most commonly in Asia and Africa, where the combination of widespread dietary aﬂatoxin exposure and endemic hepatitis B fosters a high rate of mutagenesis in the liver [69]. In the West, TP53 mutations are considerably less frequent, aﬀecting about 20% of HCCs. TP53 mutation in these tumors is associated with poor prognosis, chromosomal instability, and HBV infection [64]. 4.5. Gene Expression Proﬁling and Molecular Subtypes of HCCs. A large number of studies have examined global gene expression patterns in HCCs using DNA microarray technol- ogy (reviewed in [70, 71]). The advantage of this approach is that it provides information about which signaling pathways and cellular processes are activated or suppressed in these tumors, regardless of the mechanisms (e.g., mutational or epigenetic) underlying the aberrant regulation. Indeed, transcriptomic analysis has led to the identiﬁcation of repro- ducible HCC subtypes with diﬀering cellular diﬀerentiation and biological behavior that correlate well with prognosis