Gene Expression Profile of Papillary Thyroid Cancer: Sources of Variability and Diagnostic Implications

The objective was to identify gene expression profile of papillary thyroid microcarcinoma. To help improve diagnosis of papillary thyroid microcarcinoma, we performed gene expression profiling and compared it to pair normal thyroid tissues. We performed microarray analysis with 6 papillary thyroid microcarcinoma and 6 pair normal thyroid tissues. Differentially expressed genes were selected using paired t test, linear models for microarray data, and significance analysis of microarrays. Real-time quantitative reverse transcription–polymerase chain reaction was used to validate the representative 10 genes (MET, TIMP1, QPCT, PROS1, LRP4, SDC4, CITED1, DPP4, LRRK2, RUNX2). We identified 91 differentially expressed genes (84 upregulated and 7 downregulated) in the gene expression profile and validated 10 genes of the profile. We identified a significant genetic difference between papillary thyroid microcarcinoma and normal tissue by 10 upregulated genes greater than 2-fold (P < 0.05).

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BCL2 and hsa-miR-181a-5p are potential biomarkers associated with papillary thyroid cancer based on bioinformatics analysis

World Journal of Surgical Oncology ◽

10.1186/s12957-019-1755-9 ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 2

Author(s):

Cong Zhang ◽

Chunrui Bo ◽

Lunhua Guo ◽

Pingyang Yu ◽

Susheng Miao ◽

...

Keyword(s):

Gene Expression ◽

Thyroid Cancer ◽

Gene Regulatory Network ◽

Papillary Thyroid Cancer ◽

Regulatory Network ◽

Mirna Gene ◽

Cancer Type ◽

Papillary Thyroid ◽

Ppi Network ◽

Gene Regulatory

Abstract Background The morbidity of thyroid carcinoma has been rising worldwide and increasing faster than any other cancer type. The most common subtype with the best prognosis is papillary thyroid cancer (PTC); however, the exact molecular pathogenesis of PTC is still not completely understood. Methods In the current study, 3 gene expression datasets (GSE3678, GSE3467, and GSE33630) and 2 miRNA expression datasets (GSE113629 and GSE73182) of PTC were selected from the Gene Expression Omnibus (GEO) database and were further used to identify differentially expressed genes (DEGs) and deregulated miRNAs between normal thyroid tissue samples and PTC samples. Then, Gene Ontology (GO) and pathway enrichment analyses were conducted, and a protein-protein interaction (PPI) network was constructed to explore the potential mechanism of PTC carcinogenesis. The hub gene detection was performed using the CentiScaPe v2.0 plugin, and significant modules were discovered using the MCODE plugin for Cytoscape. In addition, a miRNA-gene regulatory network in PTC was constructed using common deregulated miRNAs and DEGs. Results A total of 263 common DEGs and 12 common deregulated miRNAs were identified. Then, 6 significant KEGG pathways (P < 0.05) and 82 significant GO terms were found to be enriched, indicating that PTC was closely related to amino acid metabolism, development, immune system, and endocrine system. In addition, by constructing a PPI network and miRNA-gene regulatory network, we found that hsa-miR-181a-5p regulated the most DEGs, while BCL2 was targeted by the most miRNAs. Conclusions The results of this study suggested that hsa-miR-181a-5p and BCL2 and their regulatory networks may play important roles in the pathogenesis of PTC.

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Characteristics of lipid metabolism-related gene expression-based molecular subtype in papillary thyroid cancer

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmaa092 ◽

2020 ◽

Vol 52 (10) ◽

pp. 1166-1170

Author(s):

Midie Xu ◽

Tuanqi Sun ◽

Shishuai Wen ◽

Tingting Zhang ◽

Xin Wang ◽

...

Keyword(s):

Gene Expression ◽

Thyroid Cancer ◽

Lipid Metabolism ◽

Papillary Thyroid Cancer ◽

Molecular Subtype ◽

Papillary Thyroid ◽

Related Gene

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TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma

Cancers ◽

10.3390/cancers12061597 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1597 ◽

Cited By ~ 2

Author(s):

Dagmara Rusinek ◽

Aleksandra Pfeifer ◽

Marta Cieslicka ◽

Malgorzata Kowalska ◽

Agnieszka Pawlaczek ◽

...

Keyword(s):

Gene Expression ◽

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Gene Expression Profile ◽

Expression Profile ◽

Distant Metastases ◽

Gene Set Enrichment Analysis ◽

Braf V600e ◽

Papillary Thyroid ◽

Mutational Status

Background: Telomerase reverse transcriptase promoter (TERTp) mutations are related to a worse prognosis in various malignancies, including papillary thyroid carcinoma (PTC). Since mechanisms responsible for the poorer outcome of TERTp(+) patients are still unknown, searching for molecular consequences of TERTp mutations in PTC was the aim of our study. Methods: The studied cohort consisted of 54 PTCs, among them 24 cases with distant metastases. BRAF V600E, RAS, and TERTp mutational status was evaluated in all cases. Differences in gene expression profile between TERTp(+) and TERTp(−) PTCs were examined using microarrays. The evaluation of signaling pathways and gene ontology was based on the Gene Set Enrichment Analysis. Results: Fifty-nine percent (32/54) of analyzed PTCs were positive for at least one mutation: 27 were BRAF(+), among them eight were TERTp(+), and 1 NRAS(+), whereas five other samples harbored RAS mutations. Expression of four genes significantly differed in BRAF(+)TERTp(+) and BRAF(+)TERTp(−) PTCs. Deregulation of pathways involved in key cell processes was observed. Conclusions: TERTp mutations are related to higher PTC aggressiveness. CRABP2 gene was validated as associated with TERTp mutations. However, its potential use in diagnostics or risk stratification in PTC patients needs further studies.

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