Systems Biology Approaches to Investigate Genetic and Epigenetic Molecular Progression Mechanisms for Identifying Gene Expression Signatures in Papillary Thyroid Cancer

Abstract

Thyroid cancer is the most common endocrine cancer. Particularly, papillary thyroid cancer (PTC) accounts for the highest proportion of thyroid cancer. Up to now, there are few researches discussing the pathogenesis and progression mechanisms of PTC from the viewpoint of systems biology approaches. In this study, first we constructed the candidate genetic and epigenetic network (GEN) consisting of candidate protein-protein interaction network (PPIN) and candidate gene regulatory network (GRN) by big database mining. Secondly, system identification and system order detection methods were applied to prune candidate GEN via next-generation sequencing (NGS) and DNA methylation profiles to obtain the real GEN. After that, we extracted core GENs from real GENs by the principal network projection (PNP) method. To investigate the pathogenic and progression mechanisms in each stage of PTC, core GEN was denoted in respect of KEGG pathways. Finally, by comparing two successive core signaling pathways of PTC, we not only shed light on the causes of PTC progression, but also identified essential biomarkers with specific gene expression signature. Moreover, based on the identified gene expression signature, we suggested potential candidate drugs to prevent the progression of PTC with querying Connectivity Map (CMap).

Keywords: carcinogenic biomarkers; drug data mining; genetic and epigenetic drug targets; genetic and epigenetic network; next-generation sequencing (NGS) data; papillary thyroid cancer.

Figure 1

The core signaling pathways are obtained by projecting core GENs to KEGG pathways to investigate the carcinogenic progression mechanism from normal thyroid cells to early-stage papillary thyroid cancer cells. The blue dotted lines represent the signaling pathways in normal stage of thyroid cells; the blue dashed lines indicate the signaling pathways in early-stage of PTC; the blue solid lines denote the signal pathways in both stages; the gray solid lines represent translocation; the blue arrow head of lines represents upregulation; the blue circle head of lines represents downregulation; the black arrow head of solid lines represents activating cellular function; the black circle head of solid lines represents inhibiting cellular function; the red gene nodes indicate a higher gene expression in early-stage PTC cells compared with normal thyroid cells; the blue gene nodes indicate a lower gene expression in early-stage PTC cells compared with normal thyroid cells; the orange background covers the cellular molecules in normal stage of thyroid cells; the green background covers the cellular molecules in early-stage of thyroid cancer cells.

Figure 2

The core signaling pathways are obtained by projecting core GENs to KEGG pathways to investigate the carcinogenic progression mechanism from early-stage thyroid cancer cells to late-stage papillary thyroid cancer cells. The blue dotted lines represent the signaling pathways in early-stage of thyroid cells; the blue dashed lines indicate the signaling pathways in late-stage of PTC; the blue solid lines denote the signal pathways in both stage; the gray solid lines represent translocation; the blue arrow head of lines represents upregulation; the blue circle head of lines represents downregulation; the black arrow head of solid lines represents activating cellular function; the black circle head of solid lines represents inhibiting cellular function; the red gene nodes indicate a higher gene expression in late-stage PTC cells compared with early-stage cells; the blue gene nodes indicate a lower gene expression in late-stage PTC cells compared with early-stage PTC cells; the orange background covers the cellular molecules in early-stage of thyroid cancer cells; the green background covers the cellular molecules in late-stage of thyroid cancer cells.

Figure 3

The overview of the proposed carcinogenic progression mechanism from normal to late-stage papillary thyroid cancer cells. This figure summarizes the genetic and epigenetic progression mechanisms of papillary thyroid cancer cells in Figure 1 and Figure 2. The upper horizontal part is the genetic and epigenetic progression mechanism from normal thyroid cells to early-stage papillary thyroid cancer cells; the top-right to bottom-left part denotes the genetic and epigenetic progression mechanisms from early-stage papillary thyroid cancer cells to late-stage papillary thyroid cancer cells; the red rectangle with yellow background represents cellular functions; the purple rounded rectangle indicates the biomarker to induce genetic and epigenetic progression mechanism of successive stages; the yellow dashed ellipse circles represent the microenvironment; the red dash lines denote biomarkers that appear in two consecutive stages of papillary thyroid cancer cells; the black arrow lines represent the protein–protein interaction or transcriptional regulation; the black circle head of lines indicates miRNA downregulation by miRNA; the red arrow lines represent the genes to induce cellular function; the red circle head of lines indicates the genes to repress cellular function.

Figure 4

Flowchart of using systems biology methods to construct candidate genetic and epigenetic network (GEN), real GENs, core GENs, and core signaling pathways of carcinogenic progression mechanism in each stage of papillary thyroid cancer (PTC) for exploring drug combinations by querying CMap based on identified abnormal gene expression signatures. The pink trapezoid blocks represent the candidate protein–protein interaction network (PPIN), which was mined by databases DIP, IntAct, BioGRID, BIND, and MINT, and candidate gene, miRNA, and lncRNA regulatory networks (GRN), which were mined by databases HTRIdb, ITFP, StarBase2.0, TRANSFAC, CircuitDB, and TargetScanHuman; The orange round blocks denote NGS data of DNA methylation profile, mRNA, miRNA, and lncRNA. The white rectangular blocks indicate the methods applied to construct real GENs and extract core GENs. The blue rounded rectangular blocks are the real GENs and core GENs in normal thyroid cells, early-stage PTC cells, and late-stage PTC cells. The pink cuboid blocks represent core signaling pathways of two consecutive stages from normal thyroid cells to early-stage PTC cells and from early-stage to late-stage PTC cells. The green rounded rectangular blocks denote the identified gene expression signatures consisting of essential biomarkers lead to the progression of PTC. The following white rectangular block represents the querying CMap approach. The yellow rounded rectangular blocks show potential compounds after querying CMap based on our identified gene signatures.