Abstract
Extrathyroidal extension (ETE) affects papillary thyroid cancer (PTC) prognosis. The objective of this study was to identify biomarkers for ETE and explore the mechanisms controlling its development in PTC. We performed a comprehensive bioinformatics analysis using several datasets. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) on 58 paired PTC samples from The Cancer Genome Atlas (TCGA) were used to detect ETE-related mRNA and long noncoding (lnc) RNA modules and construct an lncRNA/mRNA network. An independent TCGA dataset containing 438 samples was utilized to validate and characterize the WGCNA results. Functional annotation was used to identify the biological functions and related pathways of ETE modules. Two independent RNA sequencing datasets were combined to crossvalidate relationships between lncRNAs and mRNAs by Pearson correlation analysis. Transcription factors (TFs) for affected genes were predicted using the binding motif data from Ensembl Biomart to construct a TF/lncRNA/mRNA network. Other two independent datasets were used to crossvalidate TF-mRNA associations. Finally, receiver operating characteristic, survival analyses, and Cox proportional hazard regression model were performed to explore the significance of hub genes in ETE diagnosis and PTC prognosis. Three mRNA modules and two lncRNA modules were significantly associated with ETE. Enrichment analysis showed extracellular matrix changes was closely related to the development of ETE. A TF/lncRNA/mRNA regulatory network was constructed containing 33 validated hub genes, 64 lncRNAs, and 64 TFs, all differentially expressed between ETE and non-ETE samples. Unc-5 family C-terminal like [area under the curve (AUC): 0.711], sushi repeat containing protein X-linked 2 (AUC: 0.706), lysyl oxidase (AUC: 0.704), collagen type I alpha 1 chain (AUC: 0.704), and collagen type X alpha 1 chain (AUC: 0.704) were the most highly significant hub genes for ETE diagnosis. The Cox proportional hazard regression model constructed with hub genes showed significant survival differences between low- and high-risk groups (p = 0.00025) and performed good prediction for PTC prognosis(AUC = 0.794; C-index = 0.895). The identification of 33 biomarkers and TF/lncRNA/mRNA regulatory network would provide new insights into the molecular mechanisms of ETE besides the prognosis model may have important clinical implications in the improvement of PTC risk stratification, therapeutic decision-making, and prognosis prediction.
Highlights
Papillary thyroid cancer (PTC) is the most common type of thyroid cancer (TC), accounting for approximately 90% of all cases (Kitahara et al, 2017; Xia et al, 2019)
5http://gepia.cancer-pku.cn/detail.php samples was obtained from the The Cancer Genome Atlas (TCGA) database
After removing one follicular TC sample, eight metastatic samples, and five samples without complete ETE clinical information, 496 primary tumor samples, and 58 healthy samples from patients with PTC remained. These 554 samples were divided into two subsets: one, called TCGA58, contained tumor samples and matched healthy samples from 58 patients with PTC; the other, called TCGA438, contained tumor samples from the remaining 438 patients
Summary
Papillary thyroid cancer (PTC) is the most common type of thyroid cancer (TC), accounting for approximately 90% of all cases (Kitahara et al, 2017; Xia et al, 2019). Based on the scope of ETE, PTC is considered stage II if only the strap muscles are grossly invaded (T3b) and stage III with gross invasion of the subcutaneous tissue, larynx, trachea, esophagus, or recurrent laryngeal nerve (T4a; Perrier et al, 2018). This means that ETE plays an important role in PTC risk stratification, treatment strategy decisions, and survival prognosis. Despite its significance, few reports exist on the molecular mechanisms controlling ETE
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