Among the 664 miRNA species included in the array, 374 miRNAs had expression
detected in more than 50% of the specimens, including 212 miRNAs that were consistently detected in all specimens, and were therefore selected for further investigations. On the other hand, 290 miRNAs with a detection rate less than 50%, including 151 miRNAs that were not detected in any samples tested, were excluded from the study (Supporting Fig. 1A,B). The miRNA expression profiles in the paired nontumorous livers, primary HCCs, and venous metastases were analyzed by unsupervised clustering approach. As shown in Fig. 2, the nontumorous liver samples exhibited a distinct miRNA expression profile and was clearly separated from their corresponding primary HCCs and venous metastases in the clustering analysis. However, the clustering analysis was not able to segregate venous metastases from the primary HCC samples. Primary HCCs and venous metastases from the IWR1 same patients often clustered together, indicating that the miRNA Ibrutinib supplier expression profiles of primary HCCs and corresponding venous metastases were similar. To further investigate the miRNA deregulation in hepatocarcinogenesis and metastasis, the expression changes of individual miRNA (i.e., ΔΔCt) were plotted against their statistical significance (P value, paired t test) across different sample groups in volcano diagrams. To maintain the statistical stringency in multiple comparisons,
tests were considered significant when P < 1.34 × 10−4 (based on Bonferroni correction). When comparing 20 pairs of primary HCCs with their corresponding nontumorous liver samples, learn more significant deregulation was observed in 30 miRNAs, 23 of which were significantly down-regulated in primary HCC
samples, and 7 of which were up-regulated (Fig. 3A and Table 1). miR-139-5p and miR-18a were the most significantly down- and up-regulated miRNAs, respectively. These 30 miRNAs, representing the most deregulated miRNAs in primary HCC, could be used as a specific miRNA signature for primary HCC. To determine whether miRNA deregulation contributes to HCC metastatic growth, we compared the miRNA expression levels between paired primary HCCs and venous metastases by volcano plot as described above. However, we found that no miRNA reached the Bonferroni adjusted significance level, indicating that there was no significant deregulation of individual miRNAs between primary HCCs and venous metastasis. However, a global trend of miRNA down-regulation was evidently observed in venous metastases (Fig. 3B). Using a one-sample t test to interrogate the global miRNA expression changes between the nontumorous livers, primary HCC, and venous metastases, we found that venous metastases exhibited a significant global miRNA down-regulation of approximately 0.5ΔΔCt (equivalent to 30% of miRNA expression) when compared with either the nontumorous livers and primary HCCs (P < 0.0001 for each).