Prediction of novel target genes and pathways involved in tall cell variant papillary thyroid carcinoma

Abstract

Background: Tall cell variant papillary thyroid carcinoma (TCPTC) is reportedly associated with aggressive clinicopathological parameters and poor outcomes; however, the molecular mechanisms underlying TCPTC remain poorly understood.

Methods: The gene mutation types and mRNA expression profiles of patients with TCPTC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) were identified. Pathways in the interaction network and the diagnostic approaches of candidate markers for TCPTC were investigated.

Results: BRAF mutation was particularly prevalent in TCPTC with a mutation frequency of 78%. TCPTC was associated with a patient age >45 years, tumor multifocality, extrathyroidal extension, a higher T stage, advanced AJCC TNM stages, BRAF V600E mutation, and poor disease-free survival. We identified 4138 TCPTC-related DEGs and 301 TCPTC-specific DEGs. Intriguingly, the gene expression pattern revealed that the dysregulated levels of both putative oncogenes and tumor suppressors in TCPTC were higher than those in classical/conventional variant PTC (cPTC). Functional enrichment analyses revealed that these DEGs were involved in several cancer-related pathways. A protein-protein interaction (PPI) network was constructed from the 301 TCPTC-specific DEGs, and 3 subnetworks, and 8 hub genes were verified. Receiver operating characteristic (ROC) analyses revealed that 6 hub genes, including COL5A1, COL1A1, COL10A1, COL11A1, CCL20, and CXCL5, could be used not only for the differential diagnosis of PTC from normal samples, but also for the differential diagnosis of TCPTC from cPTC samples.

Conclusions: Our study might provide further insights into the investigations of the tumorigenesis mechanism of TCPTC and assists in the discovery of novel candidate diagnostic markers for TCPTC.

Figure 1

OncoPrint of mutated genes in TCPTC. Ten altered genes (mutation in more than 2 cases) in patients with TCPTC are presented. BRAF mutation is the predominant mutation type, whereas other gene mutation types occurred at a much lower rate. cPTC = classical/conventional variant Papillary Thyroid Carcinoma, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 2

Kaplan–Meier survival analyses of patients with TCPTC and cPTC. A. No difference in the overall survival rate was evident between the patients with TCPTC and those with cPTC. B. Disease-free survival analysis revealed that patients with TCPTC had a poorer disease-free survival rate. HR = hazards ratios. cPTC = classical/conventional variant Papillary Thyroid Carcinoma, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 3

Venn diagram of 301 TCPTC-specific DEGs. A total of 301 TCPTC-specific DEGs were identified from the 3 comparison groups (TCPTC versus NT, cPTC versus NT, and TCPTC versus cPTC). DEGs = differentially expressed genes, NT = normal tissues, cPTC = classical/conventional variant Papillary Thyroid Carcinoma, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 4

Heatmap of the 301 TCPTC-specific DEGs. Hierarchical analysis of the 301 TCPTC-specific DEGs based on their expression values in the TCPTC and cPTC tissues. All values are presented as log10 (RSEM), DEGs = differentially expressed genes, cPTC = classical/conventional variant Papillary Thyroid Carcinoma, RSEM = RNAseq by expectation-maximization, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 5

GO and KEGG pathway enrichment analyses of TCPTC DEGs. A. GO annotation for TCPTC-related upregulated DEGs. GO biological process, cellular component and molecular function terms, the number of enriched genes and –log10 (P value) is presented. B. KEGG pathway enrichment analysis of TCPTC-related upregulated DEGs. The pathway terms, enriched genes numbers, –log10 (P value) and fold enrichment scores are presented. C. GO annotation for TCPTC-related downregulated DEGs. D. KEGG Pathway enrichment analysis of TCPTC-related downregulated DEGs. E. GO annotation for TCPTC-specific DEGs. F. KEGG pathway enrichment analysis of TCPTC-specific DEGs. DEGs = differentially expressed genes, GO = gene ontology, KEGG = kyoto encyclopedia of genes and genomes, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 6

The PPI network of the TCPTC-specific DEGs. A. The network of 301 TCPTC-specific DEGs includes 166 nodules and 321 edges. The red nodules represent the upregulated genes, and the blue nodules represent the downregulated genes. Green edges indicate a combined score of interactive genes >0.9. B. The 3 subnetworks identified by the MCODE application in Cytoscape (networks were constructed through the STRING database). DEGs = Differentially expressed genes, MCODE = plugin molecular complex detection, PPI = protein-protein interaction, TCPTC = tall cell variant papillary thyroid carcinoma.

Figure 7

ROC curves for the diagnostic performances of the hub genes. A. Diagnostic performance of the hub genes for differentiating TCPTC from normal tissues. All 8 hub genes showed high diagnostic accuracy. B. Diagnostic performance of the hub genes for differentiating cPTC from normal tissues. Seven hub genes could be used to distinguish cPTC from normal tissues. C. Diagnostic performance of the hub genes for differentiating TCPTC from cPTC tissues. All 7 upregulated hub genes showed high diagnostic accuracy. cPTC = classical/conventional variant Papillary Thyroid Carcinoma, ROC = receiver operating characteristic, TCPTC = tall cell variant papillary thyroid carcinoma.