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

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.

Alterations in the Ca2+ toolkit in oesophageal adenocarcinoma

“…Wang et al [107] identified CACNA1D as part of an 18-ion-channel, prognostic-gene signature in glioma (the direction of the association with survival outcomes was not reported); this finding was observed even though CACNA1D-expression was downregulated in these cells. Xing et al [108] noted that CACNA1D was one of 8 out of 3,747 differentiallyexpressed genes associated with survival outcomes in colon adenocarcinoma: consistent with our findings, those with higher CACNA1D-expression lived longer than those with lower expression [108]. Similar to our metastasis-related findings, CACNA1D was among the 6 genes associated with tumor node metastasis staging in colon adenocarcinoma [108].…”

“…Xing et al [108] noted that CACNA1D was one of 8 out of 3,747 differentiallyexpressed genes associated with survival outcomes in colon adenocarcinoma: consistent with our findings, those with higher CACNA1D-expression lived longer than those with lower expression [108]. Similar to our metastasis-related findings, CACNA1D was among the 6 genes associated with tumor node metastasis staging in colon adenocarcinoma [108]. Additionally, Fourbon et al [105] showed that colon cancer cell migration was affected by CACNA1D-expression: the migration was decreased when CACNA1D was silenced.…”

“…Furthermore, the use of Ca 2+ -channel blockers (dihydropyridines, phenylalkylamines, and benzothiazepines) was associated with a reduced risk for a higher Gleason score and ERG-positive prostate cancer [ 106 ]. Two studies focused on the association of CACNA1D with survival outcomes [ 107 , 108 ]. Wang et al [ 107 ] identified CACNA1D as part of an 18-ion-channel, prognostic-gene signature in glioma (the direction of the association with survival outcomes was not reported); this finding was observed even though CACNA1D -expression was downregulated in these cells.…”

RNA-Sequencing Based microRNA Expression Signature of Colorectal Cancer: The Impact of Oncogenic Targets Regulated by miR-490-3p

“…A total of 70 miR-NAs are identified by our RNA sequence based signature. In order to ensure the validity of our signature created in this study, we compared to previous miRNA signatures of CRC [23][24][25]. Two miRNAs, miR-592 (upregulated miRNA) and miR-139-5p (downregulated miRNA) were common miRNAs to all four independent signatures (Table S4).…”

Diverse expression patterns of mucin 2 in colorectal cancer indicates its mechanism related to the intestinal mucosal barrier

“…Due to large changes in lifestyle and dietary habits, the incidence and mortality of CRC will continue to rise. In China, there are 300000 new CRC cases each year, with an annual average increase of 4.2%[ 2 ]. There are obvious gender and regional differences in the incidence and mortality rate of CRC cases, with the overall distribution being more in males than in females, and more in urban areas than in rural areas[ 3 ].…”