| Literature DB >> 30560088 |
Jia Ji1,2, Yuan Rong1, Chang-Liang Luo1, Shuo Li1, Xiang Jiang3, Hong Weng4, Hao Chen5, Wu-Wen Zhang1, Wen Xie1, Fu-Bing Wang1.
Abstract
Objective: To investigate the potential biomarkers for venous metastasis of hepatocellular carcinoma (HCC), and briefly discuss their target genes and the signaling pathways they are involved in. Materials and Method: The dataset GSE6857 was downloaded from GEO. Significantly differentially expressed miRNAs were identified using the R package "limma," After that, the survival analysis was conducted to discover the significance of these up-regulated miRNAs for the prognosis of HCC patients. Additionally, miRNAs which were up-regulated in venous metastasis positive HCC tissues and were significant for the prognosis of HCC patients were further verified in clinical samples using RT-qPCR. The miRNAs were then analyzed for their correlations with clinical characteristics including survival time, AFP level, pathological grade, TNM stage, tumor stage, lymph-node metastasis, distant metastasis, child-pugh score, vascular invasion, liver fibrosis and race using 375 HCC samples downloaded from the TCGA database. The target genes of these miRNAs were obtained using a miRNA target gene prediction database, and their functions were analyzed using the online tool DAVID.Entities:
Keywords: RT-qPCR; bioinformatics analysis; hepatocellular carcinoma; hsa-miR-210; prognosis; public gene database; venous metastasis
Year: 2018 PMID: 30560088 PMCID: PMC6287006 DOI: 10.3389/fonc.2018.00569
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
Figure 1The Overview of the strategy.
Significantly differentially expressed miRNAs in venous metastasis positive HCC tissues.
| hsa-miR-301 | 0.842786 | 0.000267078 | Up |
| hsa-let-7e | 0.847988 | 9.04E-11 | Up |
| hsa-let-7b | 0.850236 | 2.94E-12 | Up |
| hsa-miR-31 | 0.853136 | 5.34E-07 | Up |
| hsa-miR-210 | 0.868472 | 1.68E-06 | Up |
| hsa-miR-371 | 0.991324 | 1.92E-10 | Up |
| hsa-miR-183 | 1.027867 | 1.14E-05 | Up |
| hsa-miR-367 | −1.08021 | 1.81E-06 | Down |
| hsa-miR-22 | −0.9947 | 0.00055601 | Down |
| hsa-miR-182 | −0.94816 | 0.00023209 | Down |
| hsa-miR-100 | −0.94307 | 9.38E-07 | Down |
| hsa-miR-1b-1 | −0.87813 | 0.00015521 | Down |
| hsa-miR-101 | −0.84328 | 0.000209509 | Down |
| hsa-miR-124a-1 | −0.81885 | 2.27E-08 | Down |
| hsa-miR-101 | −0.80452 | 9.15E-10 | Down |
Figure 2The correlation of 6 up-regulated miRNAs with overall survival of HCC patients. Survival analysis of hsa-miR-210 (A); hsa-let-7e (B); hsa-let-7b (C); hsa-miR-31 (D); hsa-miR-183 (E); hsa-miR-371 (F).
Univariate analysis of factors affecting overall survival of HCC patients.
| Age | < 50 | 71 | 0.173 |
| ≥50 | 301 | ||
| Gender | Male | 253 | 0.309 |
| Female | 119 | ||
| AFP | < 20 | 150 | |
| ≥20 | 130 | ||
| Grade | 1 | 55 | 0.858 |
| 2 | 176 | ||
| 3 | 123 | ||
| 4 | 13 | ||
| TNM stage | I | 173 | |
| II | 85 | ||
| III | 85 | ||
| IV | 5 | ||
| Tumor stage | T1 | 183 | |
| T2 | 93 | ||
| T3 | 80 | ||
| T4 | 13 | ||
| Lymph-node metastasis | N0 | 254 | 0.317 |
| N1 | 4 | ||
| Distant metastasis | M0 | 269 | |
| M1 | 4 | ||
| Child-pugh | A | 219 | 0.357 |
| B | 21 | ||
| C | 1 | ||
| Liver fibrosis | No | 75 | 0.316 |
| Yes | 139 | ||
| Vascular invasion | No | 206 | 0.162 |
| Yes | 110 | ||
| Race | Asian | 160 | 0.129 |
| Others | 202 |
Note: The statistically significant values are in bold.
Cox proportional hazards regression analysis of factors affecting overall survival of HCC patients.
| hsa-miR-210 | 0.966 | 0.280 | 0.001 | 2.627 | 1.516–4.551 |
| Distant metastasis | 1.638 | 0.602 | 0.007 | 5.146 | 1.580–16.760 |
Figure 3The expression of hsa-miR-210 in HCC samples with positive and negative portal vein metastasis. The relative expression was determined using RT-qPCR. hsa-miR-210 levels in the portal vein metastasis positive tissues were higher than those in portal vein metastasis negative tissues.
The relationship between hsa-mir-210 and the clinicopathological variables of HCC.
| Age | < 50 | 71 | 0.072 | 0.164 |
| ≥50 | 300 | |||
| Gender | Male | 253 | 0.093 | 0.074 |
| Female | 119 | |||
| AFP | < 20 | 150 | 0.095 | 0.112 |
| ≥20 | 131 | |||
| Grade | 1 | 55 | ||
| 2–4 | 313 | |||
| TNM stage | I–II | 258 | ||
| III–IV | 90 | |||
| Tumor stage | T0–T1 | 182 | ||
| T2–T4 | 187 | |||
| Lymph-node metastasis | N0 | 254 | 0.061 | 0.332 |
| N1 | 4 | |||
| Distant metastasis | M0 | 269 | −0.005 | 0.934 |
| M1 | 4 | |||
| Child-pugh | A | 220 | 0.028 | 0.67 |
| B–C | 22 | |||
| Liver fibrosis | No | 75 | −0.087 | 0.206 |
| Yes | 140 | |||
| Vascular invasion | No | 206 | ||
| Yes | 111 | |||
| Race | Asian | 160 | −0.024 | 0.647 |
| Others | 202 | |||
Note: The statistically significant values are in bold.
Figure 4GO analysis of hsa-miR-210 target genes. GO enrichment of target genes in biological process ontology (A), cellular component ontology (B) and molecular function ontology (C).
Figure 5KEGG analysis of hsa-miR-210 target genes. The circle represents target genes; the diamonds represent signaling pathways. Circles with the same color with diamonds indicate the target genes participating in the corresponding signaling pathways. The relationship between each signaling pathway and each gene is represented by a gray line. The network was generated by Cytoscape_3.5.1.
Figure 6The aberrantly expressed mRNAs in HCC tissues. Aberrantly expressed miRNAs calculated by edgeR R. 3847 up-regulated and 1048 down-regulated miRNAs were found (A); Aberrantly expressed miRNAs calculated by DESeq R. 1290 up-regulated and 883 down-regulated miRNAs were found (B). Red dots indicate up-regulated miRNAs and green dots indicate down-regulated miRNAs. Black dots show the miRNAs expression with |log2FC| < 1. The X-axis represents an adjusted FDR value and the Y-axis represents the log2FC value. The volcano plot was generated by the ggplot2 package of R language. The intersection of up-regulated mRNAs obtained using edgeR R and DESeq R (C). The intersection of down-regulated mRNAs obtained using edgeR R and DESeq R (D).