Hepatocellular Carcinoma Transcriptome Analysis

Data analysis and RNA isolation details were summarized in Additional file 4: Supplementary Materials and Methods online. The diagnosis of all the HCC patients had been tissue-verified by pathological examination of the surgically removed HCC and neighboring liver tissue. All 44 young HCCs (≤40 years old at the diagnosis; 23 cases in the training set while another 21 in the validation cohort) were positive for serum hepatitis B surface antigen (HBsAg), but negative for antibodies to hepatitis C virus (anti-HCV). All 48 elderly (>40 years old; 38 in the training set while another 10 in the validation cohort) HCC patients enrolled were also serum HBsAg positive and anti-HCV negative. The HCC samples used in this study were the original tumors obtained from the first operations of patients. The current study complies with the Helsinki Declaration. Informed consents for taking small part of the resected HCC and the surrounding non-tumor liver specimens for study were obtained from patients. The tissue sample analysis was approved by the Institutional Review Board of Taipei Veterans General Hospital (VGHIRB No.: 97-09-17A), Taiwan.
Fresh HCC tissues and non-tumor counter parts that had been removed during surgery were snap frozen and kept in liquid nitrogen for RNA extraction. All array data were deposited into the NCBI Gene expression omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database [37 (link)] with the accession number GSE45436 (see Additional file 1: Figure S1; training set 1 GSE45267, training set 2 GSE45434, and validation set GSE45435).
The embryonic stem cell (ESC) array data had been published previously [38 (link)]. HCV (+) HCC array data were downloaded from the GEO database (accession number GSE6764) [20 (link)]. Array data of the induced pluripotent stem cells (iPS cells) and ESCs, as well as their hepatic differentiated progenies, were from GEO dataset GSE14897 [19 (link)]. The second batch of elderly HCCs of the training data set were downloaded from the Expression Project for Oncology (expO) of the International Genomics Consortium (http://www.intgen.org/, accession number GSE2109 in the GEO database).