Genome-wide expression analysis suggests a crucial role of dysregulation of matrix metalloproteinases pathway in undifferentiated thyroid carcinoma

Abstract

Background: Thyroid cancer (TC) is the most common malignant cancer of the Endocrine System. Histologically, there are three main subtypes of TC: follicular, papillary and anaplastic. Diagnosing a thyroid tumor subtype with a high level of accuracy and confidence is still a difficult task because genetic, molecular and cellular mechanisms underlying the transition from differentiated to undifferentiated thyroid tumors are not well understood. A genome-wide analysis of these three subtypes of thyroid carcinoma was carried out in order to identify significant differences in expression levels as well as enriched pathways for non-shared molecular and cellular features between subtypes.

Results: Inhibition of matrix metalloproteinases pathway is a major event involved in thyroid cancer progression and its dysregulation may result crucial for invasiveness, migration and metastasis. This pathway is drastically altered in ATC while in FTC and PTC, the most important pathways are related to DNA-repair activation or cell to cell signaling events.

Conclusion: A progression from FTC to PTC and then to ATC was detected and validated on two independent datasets. Moreover, PTX3, COLEC12 and PDGFRA genes were found as possible candidates for biomarkers of ATC while GPR110 could be tested to distinguish PTC over other tumor subtypes. The genome-wide analysis emphasizes the preponderance of pathway-dysregulation mechanisms over simple gene-malfunction as the main mechanism involved in the development of a cancer phenotype.

Figure 1

Pipeline of the followed methodology to perform this study. Red square represents the differences of the used samples. Blue square points to the preprocessing of the data. Finally, the green square is depicted for the results of the analysis.

Figure 2

Volcano plots and heatmaps of the DEGs for each subtype of carcinoma. A) and B) represents the results for FTC, C) and D) for PTC and finally, E) and F) shows the results of ATC. It is worth to mention that for the case of ATC, the Red and green dots are more that those pink, blue and yellow. That is not the case for FTC or PTC. A volcano plot displays information about (the log-odds). Red dots are statistically significant changes in gene expression for whole genome experiments over-expressed genes while green dots are statistically based in calculations for the size of differential expression significant under-regulated genes (the log-fold change) and its statistical significance.

Figure 3

Venn diagrams for the number of DEGs. Both for overexpressed (A) and underexpressed (B) genes. For both cases, the Red circle contains FTC genes, yellow circles are for PTC and the green ones present ATC genes. The columns of the right show the shared genes for the three cancer subtypes.

Figure 4

Pathway for a network related to cell-death and survival process in the anaplastic thyroid carcinoma. This graph shows the interaction network of the differentialy expressed genes of ATC which have a role in death and survival events. Red molecules are overexpressed and green molecules shows underexpression. Color intensity represents the difference between the ATC samples compared with the normal ones. Notice the high degree of conection of MMP1 and Jnk molecules. It is also worth to mention that most molecules in the plasma membrane are overexpressed meanwhile those in nucleus and cytoplasm have low expression values.

Figure 5

Pathway for a network related to cell to cell signaling process in the anaplastic thyroid carcinoma. Please notice the overexpression of PLAU, PLAUR and SPP1.

Figure 6

Venn diagrams for shared pathways from the WebGestalt for common pathways analysis. It is remarkable that the non-shared pathways for FTC (the less malignant) are related to DNA repairing and Regulation of cell cycle; for PTC the paracrine events and for ATC the mitosis pathways. The shared pathways also reflects the inter-type events. Again, FTC-PTC share Direct p53 effectors, meanwhile PTC-ATC share ce–to-cell signaling pathways as well as grow factor-related events.

Figure 7

Inhibition of matrix metalloproteinases pathway for each case: A) FTC, B) PTC and C) ATC. It is shown the contrast in the differentially expressed genes for each case. FTC does not have DEGs, PTC has only a few but ATC has very high differentially expressed genes, specially, ADAM, TIMP and MMPs, suggesting a very important role of this pathway in the progression of ATC.

Figure 8

Possible biomarkers to differentiate among thyroid carcinomas. A) Venn diagrams which contain the overexpressed genes of ATC together with those which are underexpressed in FTC and PTC. B) follows the same logic but the overexpressed genes belong to PTC meanwhile the underexpressed are for ATC-FTC. C) Boxplot of the expression levels of those genes for each case with respect to control.

Figure 9

ROC curves for the possible biomarkers to differentiate among thyroid carcinomas. For each molecule it is showed the ROC curve as well as the Area Under the Curve (AUC) value. The color code is the same than in Figure 8. A) curve for PTX3; B) COLEC12; C) PDGFRA. Those 3 genes were overexpressed in ATC meanwhile underexpressed in PTC. D) shows GPR110 ROC curve, which resulted overexpressed in PTC and underexpressed for ATC. Results are in full agreement with those in Figure 8.

Figure 10

Relevant crosstalk of altered signaling pathways involved in cell death for PTC and ATC. Molecules enriched in PTC are depicted in turquoise meanwhile those enriched in ATC are depicted in yellow. Notice that both pathways start in both intra and extracellular space and also both culminate with the inhibition of caspases.