Molecular characterization of papillary thyroid carcinoma: a potential three-lncRNA prognostic signature

Abstract

PurposePapillary thyroid carcinoma (PTC), the most frequent type of malignant thyroid tumor, lacks novel and reliable biomarkers of patients’ prognosis. In the current study, we mined The Cancer Genome Atlas (TCGA) to develop lncRNA signature of PTC.Patients and methodsThe intersection of PTC lncRNAs was obtained from the TCGA database using integrative computational method. By the univariate and multivariate Cox analysis, key lncRNAs were identified to construct the prognostic model. Then, all patients were divided into the high-risk group and low-risk group to perform the Kaplan–Meier (K–M) survival curves and time-dependent receiver operating characteristic (ROC) curve, estimating the prognostic power of the prognostic model. Functional enrichment analysis was also performed. Finally, we verified the results of the TCGA analysis by the Gene Expression Omnibus (GEO) databases and quantitative real-time PCR (qRT-PCR).ResultsAfter the comprehensive analysis, a three-lncRNA signature (PRSS3P2, KRTAP5-AS1 and PWAR5) was obtained. Interestingly, patients with low-risk scores tended to gain obviously longer survival time, and the area under the time-dependent ROC curve was 0.739. Furthermore, gene ontology (GO) and pathway analysis revealed the tumorigenic and prognostic function of the three lncRNAs. We also found three potential transcription factors to help understand the mechanisms of the PTC-specific lncRNAs. Finally, the GEO databases and qRT-PCR validation were consistent with our TCGA bioinformatics results.ConclusionWe built a three-lncRNA signature by mining the TCGA database, which could effectively predict the prognosis of PTC.

Development of a prognostic index based on an immunogenomic landscape analysis of papillary thyroid cancer

“…Cheng et al combined genomic alterations and clinical parameters to develop a risk index model that could monitor the progression of PTC [46]. Beyond that, several researchers also have proposed prognostic signatures for PTC patients’ survival prediction [47–49]. Comparing with previous publications, the present study proposed a signature that chose the PFI as the endpoint, which was the most suitable for PTC patients’ survival monitoring.…”

Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma—Do They Exist?

“…In addition, next-generation RNA sequencing (RNA-Seq) might introduce newer transcripts. Noteworthily, TCGA-based analyses paid our attention to lncRNA, playing an essential role in PTC [45][46][47][48][49] and other malignancies [50]. Numerous papers raised the role of lncRNA in the aggressiveness/invasiveness of thyroid carcinoma [45,[51][52][53][54][55].…”

Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells

“…Not much is known about the roles of many of these novel target genes (LRRC31, FAM3D, FRMD1, TPRXL, and ZNF321P) in cancer. Others have been implicated in tumor progression (HNF4G, ST6GALNAC1, DGUOK-AS1, LINC00365, HNF1A-AS1, HOTAIR, and PRSS3P2) (48)(49)(50)(51)(52)(53), tumor suppression (CAPN9, ERN2, and LINC00589) (54-56), or both, in varied cancer types (FABP1, SMPD3, and RPLP0P2) (57)(58)(59)(60).…”