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Background The development of hepatocellular carcinoma (HCC) may be associated with dedifferentiation. To understand the relation between the development and dedifferentiation of HCC, we used oligonucleotide microarray (huU95A DNA Chips®, Affymetrix). Methods We analyzed expression levels of 12600 genes in 50 HCC samples with positive hepatitis C virus (HCV) serology (7 well (G1), 35 moderately (G2), and 8 poorly (G3) differentiated tumors) and 11 nontumorous livers (L1 and L0) with and without HCV infection. To test our hypothesis that this disease develops sequentially from L0 to L1 to G1 to G2 to G3, we searched for discriminatory genes of transition (L0 vs. L1, L1 vs. G1, G1 vs. G2, G2 vs. G3) with a supervised learning method. We then arranged the samples by self-organizing map (SOM) with the discriminatory gene sets. Findings We identified discriminatory genes at each transition. In all of the discriminatory gene sets, the false discovery rate was less than 0.3%. The 40 most discriminatory genes for each transition clearly divided samples into pre-transition and post-transition stages. The minimum distance classifier determined with these 40 genes reproduced this finding mathematically, suggesting that these genes represent molecular signatures for each transition. The SOM arranged the five clusters on a unique sigmoidal curve in the order L0, L1, G1, G2, and G3. Strikingly, G2 tumors without venous invasion were located closer to the G1 cluster, and most G2 tumors with venous invasion were located closer to the G3 cluster (P=0.001). Additionally, the sample arrangement reproduced development-related features of HCC such as venous invasion and p53 abnormality. Such an arrangement was not observed in 26 HCV-negative HCCs. Interpretation Our molecular profiling verified our hypothesis, supporting the multi-step carcinogenesis theory of this disease. Genes identified in this study likely play important roles at each aspect of the development of HCC with positive HCV serology.

[Proc Amer Assoc Cancer Res, Volume 46, 2005]