Abstract
BackgroundPapillary thyroid carcinoma (PTC), which is the most common endocrine malignancy, has been steadily increasing worldwide in incidence over the years, while mechanisms underlying the pathogenesis and diagnostic for PTC are incomplete. The purpose of this study is to identify potential biomarkers for diagnosis of PTC, and provide new insights into pathogenesis of PTC.MethodsBased on weighted gene co-expression network analysis, Robust Rank Aggregation, functional annotation, GSEA and DNA methylation, were employed for investigating potential biomarkers for diagnosis of PTC.ResultsBlack and turquoise modules were identified in the gene co-expression network constructed by 1807 DEGs that from 6 eligible gene expression profiles of Gene Expression Omnibus database based on Robust Rank Aggregation and weighted gene co-expression network analysis. Hub genes were significantly down-regulated and the expression levels of the hub genes were different in different stages in hub gene verification. ROC curves indicated all hub genes had good diagnostic value for PTC (except for ABCA6 AUC = 89.5%, the 15 genes with AUC > 90%). Methylation analysis showed that hub gene verification ABCA6, ACACB, RMDN1 and TFPI were identified as differentially methylated genes, and the decreased expression level of these genes may relate to abnormal DNA methylation. Moreover, the expression levels of 8 top hub genes were correlated with tumor purity and tumor-infiltrating immune cells. These findings, including functional annotations and GSEA provide new insights into pathogenesis of PTC.ConclusionsThe hub genes and methylation of hub genes may as potential biomarkers provide new insights for diagnosis of PTC, and all these findings may be the direction to study the mechanisms underlying of PTC in the future.
Highlights
Papillary thyroid carcinoma (PTC), which is the most common endocrine malignancy, has been steadily increasing worldwide in incidence over the years, while mechanisms underlying the pathogenesis and diagnostic for PTC are incomplete
Gene lists of six datasets were integrated by Rank Aggregation (RRA) method and 1807 differentially expressed genes (DEGs) including 796 up-regulated genes and 1011 down-regulated genes were identified to the threshold of P-value < 0.05
In summary, we identified 1807 DEGs from 6 datasets of PTC data based on RRA methods
Summary
Papillary thyroid carcinoma (PTC), which is the most common endocrine malignancy, has been steadily increasing worldwide in incidence over the years, while mechanisms underlying the pathogenesis and diagnostic for PTC are incomplete. TSH inhibition therapy and radioactive iodine therapy are the conventional treatment methods for PTC [4]. With these therapeutic approaches, most patients with PTC have a good prognosis, but there were some challenges for both patients and clinicians. The study of DNA methylation is very important for the pathogenesis, early diagnosis and prognosis prediction of tumors and methylation drugs are the darlings of recent targeted therapies for cancer for DNA methylation itself is reversible. More accurate diagnosis leads to more personalized treatment, which is valuable in further improving patient survival
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