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. 2020 Sep 9:2020:7905380.
doi: 10.1155/2020/7905380. eCollection 2020.

MicroRNA-Related Prognosis Biomarkers from High-Throughput Sequencing Data of Colorectal Cancer

Xiao-Liang Xing  1   2 , Zhi-Yong Yao  2 , Ti Zhang  2 , Ning Zhu  2 , Yuan-Wu Liu  3 , Jing Peng  1
Affiliations

MicroRNA-Related Prognosis Biomarkers from High-Throughput Sequencing Data of Colorectal Cancer

Xiao-Liang Xing et al. Biomed Res Int. .

Abstract

Background: Colorectal cancer (CRC) is the third most common cancer in the world, and most of them are adenocarcinomas. CRC could be classified as colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ) according to the original tumorigenesis position. Increasing evidences indicated that microRNAs (miRNAs) play an important role in the occurrence of multiple tumors.

Methods: In this study, we firstly downloaded miRNA (COAD, 8 controls vs. 455 tumors; READ, 3 controls vs. 161 tumors) and mRNA (COAD, 41 controls vs. 478 tumors; READ, 10 controls vs. 166 tumors) data from The Cancer Genome Atlas (TCGA) database and then used DESeq2, RegParallel, miRDB, TargetScanHuman 7.2, DAVID 6.8, STRING, and Cytoscape software to identify the potential prognosis biomarkers.

Results: We identified 175 differential expression miRNAs (DEMs) and 3747 differential expression genes (DEGs) in COAD and 184 DEMs and 3928 DEGs in READ. And then, we obtained 21 (13 in COAD and 8 in READ) DEMs associated with the survival rates, which correlated with 440 (217 in COAD and 223 in READ) overlapping DEGs. Through survival analysis for those overlapping DEGs, we found 11 (8 in COAD and 3 in READ) overlapping DGEs associated with survival rates of patients, which were correlated with 9 (7 in COAD and 2 in READ) DEMs significantly.

Conclusion: In this study, we found several candidate prognostic biomarkers which have been identified in various cancers and also found several new prognosis biomarkers of COAD and READ. In conclusion, this analysis based on theoretical knowledge and clinical outcomes we have done needs further confirmation by more researches.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Volcano plot of differentially expressed miRNAs and mRNAs for COAD and READ. (a, b) Volcano plot of differentially expressed miRNAs for (a) COAD and (b) READ. (c, d) Volcano plot of differentially expressed mRNAs for (c) COAD and (d) READ. The threshold value was set as basemean ≥ 50, padj < 0.05, and ∣logFC | ≥1.0.
Figure 2
Figure 2
Prediction of target genes and functional analysis. (a, b) Overlapping DEGs and DEM target genes for (a) COAD and (b) READ. (c, d) The significantly enriched GO term (p value < 0.01) analyzed by using DAVID 6.8 for (c) COAD and (d) READ. (e, f) The significantly enriched KEGG pathway (p value < 0.05) analyzed by using DAVID 6.8 for (e) COAD and (f) READ. CC: cellular component (orange); BP: biological process (green); MF: molecular functions (purple).
Figure 3
Figure 3
Constructed PPI networks of related genes in COAD. The PPI network was constructed by using the overlapping genes in COAD. Orange represents unregulated genes; green represents downregulated genes.
Figure 4
Figure 4
Constructed PPI networks of related genes in READ. The PPI network was constructed by using the overlapping genes in READ. Orange represents unregulated genes; green represents downregulated genes.
Figure 5
Figure 5
The survival curve of target genes for COAD and READ: (a–h) survival curves of target genes in COAD; (i–k) survival curves of target genes in READ.
Figure 6
Figure 6
Associated analyses of target genes with pathologic TNM. (a, b) Associated analyses of target genes with a pathologic T stage for (a) COAD and (b) READ. (c, d) Associated analyses of target genes with a pathologic N stage for (c) COAD and (d) READ. (e, f) Associated analyses of target genes with a pathologic T stage for (e) COAD and (f) READ. A repeated measures ANOVA followed by unpaired two-tailed Student's t-test was used as indicated. All results are expressed as mean ± SEM.
Figure 7
Figure 7
Network of COAD- and READ-related miRNAs and target genes. Orange represents unregulated genes; green represents downregulated genes.
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