Background Identification of stage-specific prognostic/predictive biomarkers could lead to the more efficient clinical management in papillary thyroid carcinoma (PTC). The main objective of this study was to characterize the stage-specific deregulations in gene and miRNA expression in PTC and also to identify potential prognostic biomarkers.
Methods 495 RNASeq and 499 miRNASeq PTC samples (stage I-IV) as well as, respectively, 56 and 57 normal samples were retrieved from The Cancer Genome Atlas (TCGA). DESeq2 was used to identify deregulation of genes and miRNAs between sequential stages of PTC. To identify the minority of patients who progress from stage I to higher stages, we additionally performed a clustering analysis focused on the stage I RNASeq data. Moreover a validation study was done on an independent PTC RNASeq study.
Results Large amount of heterogeneity in gene expression patterns was observed in stage I PTC patients. LTF and PLA2R1 were identified as two promising biomarkers that exhibited down-regulation in a small subgroup of stage I (both in TCGA and in the validation data set) and in the majority of stage IV patients (in TCGA data set). hsa-miR-205, hsa-miR-509-2, hsa-miR-514-1 and hsa-miR-514-2 were also identified as up-regulated miRNAs in both PTC patients with stage I and stage III.
Conclusion Common gene expression alterations in early and advanced stages of PTC, could be used for individualized risk stratification and personalized treatment approach.