Computational analysis of mRNA expression profiles identifies microRNA-29a/c as predictor of colorectal cancer early recurrence

Abstract

Colorectal cancer (CRC) is one of the leading malignant cancers with a rapid increase in incidence and mortality. The recurrences of CRC after curative resection are sometimes unavoidable and often take place within the first year after surgery. MicroRNAs may serve as biomarkers to predict early recurrence of CRC, but identifying them from over 1,400 known human microRNAs is challenging and costly. An alternative approach is to analyze existing expression data of messenger RNAs (mRNAs) because generally speaking the expression levels of microRNAs and their target mRNAs are inversely correlated. In this study, we extracted six mRNA expression data of CRC in four studies (GSE12032, GSE17538, GSE4526 and GSE17181) from the gene expression omnibus (GEO). We inferred microRNA expression profiles and performed computational analysis to identify microRNAs associated with CRC recurrence using the IMRE method based on the MicroCosm database that includes 568,071 microRNA-target connections between 711 microRNAs and 20,884 gene targets. Two microRNAs, miR-29a and miR-29c, were disclosed and further meta-analysis of the six mRNA expression datasets showed that these two microRNAs were highly significant based on the Fisher p-value combination (p = 9.14 × 10(-9) for miR-29a and p = 1.14 × 10(-6) for miR-29c). Furthermore, these two microRNAs were experimentally tested in 78 human CRC samples to validate their effect on early recurrence. Our empirical results showed that the two microRNAs were significantly down-regulated (p = 0.007 for miR-29a and p = 0.007 for miR-29c) in the early-recurrence patients. This study shows the feasibility of using mRNA profiles to indicate microRNAs. We also shows miR-29a/c could be potential biomarkers for CRC early recurrence.

Figure 1. Up-regulation of genes targeted by miR-29a in the recurrence group in the six datasets.

The y axis is a score representing the expression levels of miR-29a and the x axis is the groups with and without recurrence of CRC. The group “1” refers to the recurrence group and “0” refers to the non-recurrence group. The score was calculated from a set of miR-29a targeted genes' expression values, a higher score means that these targeted genes were up-regulated in the recurrence group “1”.The similar pattern was found for miR-29c.

Figure 2. The results of meta-analysis for miR-29a and miR-29c in the six datasets.

In the meta-analysis, effect size (the difference in predicted scores between the recurrent and non-recurrent CRC patients) and standard error were calculated for each study. An overall effect size and 95% confidence intervals (95% CIs) were reported with p values estimated based on the Fisher's combination of p-values .