A Seven-microRNA Expression Signature Predicts Survival in Hepatocellular Carcinoma

<div><p>Hepatocellular carcinoma (HCC) is the fifth common cancer. The differential expression of microRNAs (miRNAs) has been associated with the prognosis of various cancers. However, limited information is available regarding genome-wide miRNA expression profiles in HCC to generate a tumor-specific miRNA signature of prognostic values. In this study, the miRNA profiles in 327 HCC patients, including 327 tumor and 43 adjacent non-tumor tissues, from The Cancer Genome Atlas (TCGA) Liver hepatocellular carcinoma (LIHC) were analyzed. The associations of the differentially expressed miRNAs with patient survival and other clinical characteristics were examined with t-test and Cox proportional regression model. Finally, a tumor-specific miRNA signature was generated and examined with Kaplan–Meier survival, univariate\multivariate Cox regression analyses and KEGG pathway analysis. Results showed that a total of 207 miRNAs were found differentially expressed between tumor and adjacent non-tumor HCC tissues. 78 of them were also discriminatively expressed with gender, race, tumor grade and AJCC tumor stage. Seven miRNAs were significantly associated with survival (P value <0.001). Among the seven significant miRNAs, six (hsa-mir-326, hsa-mir-3677, hsa-mir-511-1, hsa-mir-511-2, hsa-mir-9-1, and hsa-mir-9-2) were negatively associated with overall survival (OS), while the remaining one (hsa-mir-30d) was positively correlated. A tumor-specific 7-miRNAs signature was generated and validated as an independent prognostic predictor. Collectively, we have identified and validated an independent prognostic model based on the expression of seven miRNAs, which can be used to assess patients’ survival. Additional work is needed to translate our model into clinical practice.</p></div

Heatmap of KEGG pathways enriched in seven miRNA target genes.

<p>The isoforms of 7-miRNA signature were involved in multiple pathways, especially cancer-specific pathways. (DIANA-mirpath computes log₁₀ P-values).</p

Kaplan-Meier survival curves for 7-miRNA signature.

<p>Six miRNA (hsa-mir-326, hsa-mir-3677, hsa-mir-511-1, hsa-mir-511-2, hsa-mir-9-1, and hsa-mir-9-2) were negatively associated with OS and one (hsa-mir-30d) was positively correlated. (Red line: overexpressed, Blue line: under-expressed, Horizontal axis: overall survival time, Vertical axis: survival function).</p

Fifty differentially expressed miRNAs (Absolute fold changes >3).

<p>The expression levels of the significant miRNAs in hepatocellular cell carcinoma (HCC) are compared to those of adjacent non-tumor liver tissue, as fold change (tumor vs. non-tumor).</p

Heatmap of 207 differentially expressed miRNAs in tumor/non-tumor.

<p>The miRNA expression levels are mean-centered across samples, and an unsupervised hierarchical clustering with complete linkage is carried out by Cluster 3.0.</p

Clinical characteristics of patients with hepatocellular cell carcinoma.

<p>AJCC: American Joint Committee on Cancer; NA: Not Available; Risk factors: Alcohol consumption, Hepatitis B/C, Hemochromatosis, Nonalcoholic Fatty Liver Disease, Alpha-1 Antitrypsin Deficiency</p><p>^a Statistical significant results (in bold)</p><p>Clinical characteristics of patients with hepatocellular cell carcinoma.</p

Differentially expressed miRNAs from Tumor/Non-tumor according to clinical parameters.

<p>AJCC American Joint Committee on Cancer; Tumor grade: neoplasm histologic grade; vs. versus.</p><p>Differentially expressed miRNAs from Tumor/Non-tumor according to clinical parameters.</p

Kaplan–Meier survival curves for hepatocellular cell carcinoma patients.

<p>The 327 hepatocellular cell carcinoma patients are compared in two groups according to: a 7-miRNA signature (1 high risk vs. 2 low risk); b Tumor status (1 Tumor free vs. 2 With tumor); c AJCC pathological (1 I + II vs. 2 stage III + IV); and d AJCC T stage (1 T1+T2 vs. 2 T3+T4). Log Rank (Mantel-Cox) P value are 0.000, 0.001, 0.042 and 0.002, respectively. (Blue line: group 1, Green line: group 2, Horizontal axis: overall survival time, Vertical axis: survival function).</p