Colon Cancer Progression Is Reflected to Monotonic Differentiation in Gene Expression and Pathway Deregulation Facilitating Stage-specific Drug Repurposing

Abstract

Background/aim: Colon cancer is one of the most common cancer types and the second leading cause of death due to cancer. Many efforts have been performed towards the investigation of molecular alterations during colon cancer progression. However, the identification of stage-specific molecular markers remains a challenge. The aim of this study was to develop a novel computational methodology for the analysis of alterations in differential gene expression and pathway deregulation across colon cancer stages in order to reveal stage-specific biomarkers and reinforce drug repurposing investigation.

Materials and methods: Transcriptomic datasets of colon cancer were used to identify (a) differentially expressed genes with monotonicity in their fold changes (MEGs) and (b) perturbed pathways with ascending monotonic enrichment (MEPs) related to the number of the participating differentially expressed genes (DEGs), across the four colon cancer stages. Through an in silico drug repurposing pipeline we identified drugs that regulate the expression of MEGs and also target the resulting MEPs.

Results: Our methodology highlighted 15 MEGs and 32 candidate repurposed drugs that affect their expression. We also found 51 MEPs divided into two groups according to their rate of DEG content alteration across colon cancer stages. Focusing on the target MEPs of the highlighted repurposed drugs, we found that one of them, the neuroactive ligand-receptor interaction, was targeted by the majority of the candidate drugs. Moreover, we observed that two of the drugs (PIK-75 and troglitazone) target the majority of the resulting MEPs.

Conclusion: These findings highlight significant genes and pathways that can be used as stage-specific biomarkers and facilitate the discovery of new potential repurposed drugs for colon cancer. We expect that the computational methodology presented can be applied in a similar way to the analysis of any progressive disease.

Keywords: Monotonically expressed genes; colon cancer progression; colon cancer staging; drug repurposing; monotonically enriched pathways.

Figure 1. (A) Boxplot with monotonic over-expressed genes for the five Gene Expression Omnibus (GEO) datasets. (B) Boxplot with monotonic under-expressed genes for the five GEO datasets. (C) Polar plot with the monotonic over- and under-expressed genes of each GEO dataset. Degrees represent the corresponding slopes of monotonically expressed genes (MEGs) and color the R-squared values.

Figure 2. Bipartite network with the resulting monotonically expressed genes (MEGs) and the corresponding candidate repurposed drugs that are predicted to influence their expression. Monotonically over- and under-expressed genes are presented as circular nodes with red and green color respectively and drugs with grey rhombus-shaped nodes.

Figure 3. Heatmap visualization of monotonically enriched pathways (MEPs). Color scale indicates the normalized number of differentially expressed genes (DEGs) in each stage.

Figure 4. Pathway network from monotonically enriched pathways (MEPs) biochemical connectivity. Low perturbation rate monotonically enriched pathways (LPR MEPs) from the first group are presented with cyan color and high perturbation rate monotonically enriched pathways (HPR MEPs) from the second group with orange color. Edge width corresponds to the common genes that the two pathways are shared.

Figure 5. Circos plot that summarizes the associations between repurposed drugs and monotonically enriched pathways (MEPs).