scholarly journals Identification of Potential lncRNAs and miRNAs as Diagnostic Biomarkers for Papillary Thyroid Carcinoma Based on Machine Learning

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Fei Yang ◽  
Jie Zhang ◽  
Baokun Li ◽  
Zhijun Zhao ◽  
Yan Liu ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Epigenetic Modifications ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Endothelial Cell Migration ◽  
Papillary Thyroid ◽  
Diagnostic Biomarkers

Background. Papillary thyroid carcinoma (PTC) accounts for most of the proportion of thyroid cancer (TC). The objective of this study was to identify diagnostic, differentially expressed long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), contributing to understanding the epigenetics mechanism of PTC. Methods. The data of lncRNA, miRNA, and mRNA were downloaded from the Cancer Genome Atlas (TCGA) dataset, followed by functional analysis of differentially expressed mRNAs. Optimal diagnostic lncRNA and miRNA biomarkers were identified via random forest. The regulatory network between optimal diagnostic lncRNA and mRNAs and optimal diagnostic miRNA and mRNAs was identified, followed by the construction of ceRNA network of lncRNA-mRNA-miRNA. Expression validation and diagnostic analysis of lncRNAs, miRNAs, and mRNAs were performed. Overexpression of ADD3-AS1 was performed in PTC-UC3 cell lines, and cell proliferation and invasion assay were used for investigating the role of ADD3-AS1 in PTC. Results. A total of 107 differentially expressed lncRNAs, 81 differentially expressed miRNAs, and 515 differentially expressed mRNAs were identified. 11 lncRNAs and 6 miRNAs were regarded as the optimal diagnostic biomarkers for PTC. The epigenetic modifications via the above diagnostic lncRNAs and miRNAs were identified, including MIR181A2HG-FOXP2-hsa-miR-146b-3p, BLACAT1/ST7-AS1-RPS6KA5-hsa-miR-34a-5p, LBX2-AS1/MIR100HG-CDHR3-hsa-miR-34a-5p, ADD3-AS1-PTPRE-hsa-miR-9-5p, ADD3-AS1-TGFBR1-hsa-miR-214-3p, LINC00506-MMRN1-hsa-miR-4709-3p, and LOC339059-STK32A-hsa-miR-199b-5p. In the functional analysis, MMRN1 and TGFBR1 were involved in cell adhesion and endothelial cell migration, respectively. Overexpression of ADD3-AS1 inhibited cell growth and invasion in PTC cell lines. Conclusion. The identified lncRNAs/miRNAs/mRNA were differentially expressed between normal and cancerous tissues. In addition, identified altered lncRNAs and miRNAs may be potential diagnostic biomarkers for PTC. Additionally, epigenetic modifications via the above lncRNAs and miRNAs may be involved in tumorigenesis of PTC.

scholarly journals Identification of an Autophagy-Related Signature Predicting Overall Survival for Papillary Thyroid Carcinoma

Dose-Response ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 155932581989926 ◽  
Author(s):  
Gang Hu ◽  
Hong-fang Feng ◽  
Hui Zhan
Keyword(s):  
Overall Survival ◽  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Scoring System ◽  
Cox Regression ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Papillary Thyroid ◽  
Cox Regression Analysis

Background: Papillary thyroid carcinoma usually shows an excellent prognosis. However, its recurrence or persistence rate is high. In this study, we used bioinformatics to identify autophagy-related genes (ARGs) and establish a novel scoring system for papillary thyroid carcinoma. Methods: We collected ARGs sequencing data of patients with papillary thyroid carcinoma from The Cancer Genome Atlas database. Differentially expressed ARGs were identified by the “Limma” package in R language. After univariate and multivariate Cox regression analysis, an ARG signature was developed. The established prognostic signature was evaluated by Kaplan-Meier curve and time-dependent receiver operating characteristic. Results: A sum of 26 differentially expressed ARGs were identified. Gene set enrichment analysis revealed that several significantly oncological signatures were enriched, such as autophagy, p53 signaling pathway, apoptosis, human cytomegalovirus infection, and platinum drug resistance. After univariate and multivariate analysis, 3 ARGs ( ITPR1, CCL2, and CDKN2A) were selected to develop autophagy-related signature. Patients with high risk had significantly shorter overall survival than those with low risk. The areas under the curve indicated that the signature showed good accuracy of prediction. Conclusions: We established a novel scoring system based on 3 ARGs, which provides a promising tool for the development of personalized therapy.

scholarly journals Identification of aberrantly methylated differentially expressed genes in papillary thyroid carcinoma using integrated bioinformatic analysis

2021 ◽  
Author(s):  
Qingxian Li ◽  
Weiyi Cai ◽  
Jianhong Chen ◽  
Jie Ning
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Regression Analysis ◽  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Integrative Analysis ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Tumor Biomarker ◽  
Papillary Thyroid

Abstract Background: DNA methylation has been reported as one of the most critical epigenetic aberrations during the tumorigenesis and development of papillary thyroid carcinoma (PTC). Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified.Results: In this study, the comparisons between PTC and NT revealed 4995 methylated probes and 1446 differentially expressed transcripts cross-validated by The Cancer Genome Atlas (TCGA) database. The integrative analysis between DNA methylation and gene expression revealed 123 and 29 genes with hypomethylation/overexpression and hypermethylation/downexpression correlation, respectively. The DNA methylation pattern of seven selected CpGs (A: UNC80-cg04507925; B: TPO-cg09757588; C: LHX8-cg11842415; D: DLG2-cg16986720; E: FOXJ1-cg20373432; F: PALM2-cg21204870; G: IPCEF1-cg24635109, of which the candidate promoter CpG sites were preliminarily identified with the least absolute shrinkage and selection operator (LASSO) regression analysis. Then, the risk prognosis model was constructed by stepwise regression analysis. Furthermore, the receiver operating characteristic (ROC) and nomogram based on the verified independent prognostic factors was established for the prognostic prediction showed that it was able to predict 3-, 5-, and 7-year survival accurately. Kaplan-Meier survival estimate demonstrated that low DLG2 expression and DLG2-cg16986720 hypermethylation were independent biomarkers for OS. From the comprehensive meta-analysis, the combined Standardised Mean Difference (SMD) of DLG2 was 0.94 with 95% CI of (0.46,1.43), indicating that less DLG2 was expressed in the PTC tissue than in the normal tissue (P<0.05). Bisulfite sequencing PCR also showed that DLG2 methylation was higher in tumor group than in normal group. Components of immune microenvironment were analyzed using TIMER, and the correlation between immune cells and DLG2 was found to be distinct across cancer types. Based on Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, DLG2 was implicated in pathways involved in immunity, metabolism, cancer, and infectious diseases. PCT patients with DLG2-cg16986720 hypermethylation showed significantly short survival rates in progression- free survival concomitant with reduced infiltration of myeloid dendritic cells.Conclusions: The current study validated that DLG2 was lowly expressed in PTC. More importantly, DLG2 hypermethylation might function as a latent tumor biomarker in the prognosis prediction for PTC. The results of bioinformatics analyses may present a new method for investigating the pathogenesis of PTC. DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC. In addition to the promoter region, gene body and 3’UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). The integrative analysis revealed genes potentially regulated by DNA methylation pointing out potential drivers and biomarkers related to PTC development.

scholarly journals MiR-195Inhibits Tumor Growth and Metastasis in Papillary Thyroid Carcinoma Cell Lines by TargetingCCND1andFGF2

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Yali Yin ◽  
Shubin Hong ◽  
Shuang Yu ◽  
Yanrui Huang ◽  
Shuwei Chen ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Target Therapy ◽  
The Cancer Genome Atlas ◽  
Migration And Invasion ◽  
Papillary Thyroid ◽  
Data Set

Background. MicroRNA (miRNA) dysregulation was commonly seen in papillary thyroid carcinoma (PTC), andmiR-195was verified to be downregulated in PTC by the large data set analysis from The Cancer Genome Atlas (TCGA). Our study aimed to explore the biological functions and the underlying molecular mechanisms ofmiR-195in PTC.Methods. The relative expression ofmiR-195and its target genes were assessed by quantitative RT-PCR assay in 38 pairs of PTC and the adjacent thyroid tissues. Assays were performed to evaluate the effect ofmiR-195on the proliferation, migration, and invasion in PTC cell lines. Moreover, we searched for targets ofmiR-195and explored the possible molecular pathway ofmiR-195in PTC.Results. We found thatmiR-195was downregulated in PTC cell lines and tissues. Overexpression ofmiR-195significantly inhibited cell proliferation, migration, and invasion in K1 and BCPAP cell lines.CCND1andFGF2, which had inverse correlations withmiR-195in clinical specimens, were found to be the direct targets ofmiR-195. Furthermore,miR-195might be involved in PTC tumorigenesis by suppressing the Wnt/β-catenin signaling pathway.Conclusions. These results highlight an important role ofmiR-195in the initiation and progression of PTC and implicate the potential application ofmiR-195in PTC target therapy.

scholarly journals lncRNA-miRNA-mRNA ceRNA Network in Thyroid Carcinoma from The Cancer Genome Atlas

2020 ◽  
Author(s):  
Guoheng Mo ◽  
Qunguang Jiang ◽  
Zixuan Wang ◽  
Zhaoting Zheng ◽  
XiaoSi Chen
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Molecular Mechanisms ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Papillary Thyroid ◽  
Cerna Network ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Abstract Increasing evidence indicates that the competitive endogenous RNA (ceRNA) hypothesis, that is, long non-coding RNA (LncRNA) can competitively bind microRNA (miRNA) through miRNA response elements to affect the expression of target RNA, and dysregulation of LncRNA expression plays a key role in tumor progression. The papillary thyroid carcinoma that we studied is the most significant pathological type of thyroid cancer, but its ceRNA network has not been extensively evaluated. We analyzed level-3 data from RNA-Seq of 58 para-carcinoma tissues and 501 patients with primary papillary thyroid carcinoma (PTC) using the DEseq software package and downloaded clinical information from The Cancer Genome Atlas (TCGA) to find potential biomarkers or therapeutic targets. As a result, 149 differential miRNAs were selected, including 117 up -regulated, 32 down-regulated, and 3099 differential mRNAs, including 1976 up-regulated, 1123 down-regulated, and 434 differential lncRNAs, including 331 up-regulated and 103 down-regulated (Fold Change > 2, P < 0.05). The interactions between these differentially expressed RNA groups constitute the ceRNA network of PTC. Moreover, we used the microde database to predict the miRNAs that may be acted by the above screened differential lncRNAs and intersected with the selected miRNAs, and further predicted the target genes of the intersecting miRNAs by TargetScan, miRTarBase and miRDB, and intersected with the selected mRNAs. From the constructed ceRNA network we can see that Linc00460 may cause the invasion and metastasis of PTC by competitively inhibiting hsa-mir-150 and upregulating the expression of its downstream target gene EREG. Our study identified a series of lncRNAs associated with PTC progression and prognosis, and this complex ceRNA interaction network provides guidance for better understanding of the molecular mechanisms of PTC and can be used as an effective diagnostic tool for PTC invasion, metastasis and prognosis. Kaplan-Meier analysis of the differentially expressed RNAs associated with PTC pathogenesis confirmed that the lncRNAs AC097717.1, C20orf203, EMX2OS were potentially associated with the prognosis of PTC (P<0.05).

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

scholarly journals SUN-132 KLF5 Is a Poor Prognostic Marker and Therapeutic Target for Middle Eastern Papillary Thyroid Carcinoma

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Khawla S Al-Kuraya ◽  
Abdul K Siraj ◽  
Pratheeshkumar Poyil ◽  
Divya Padmaja ◽  
Sandeep Kumar Parvathareddy ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Therapeutic Target ◽  
Critical Role ◽  
Dependent Manner ◽  
Papillary Thyroid ◽  
Inhibition Of Proliferation ◽  
Over Expression

Abstract Thyroid cancer is the second most common malignancy among females in Saudi Arabia, with Papillary thyroid carcinoma (PTC) accounting for 80-90%. The Kruppel-like factor 5 (Klf5) is a transcription factor that play a critical role in cell transformation, proliferation and oncogenesis. Immunohistochemical analysis of KLF5 was performed in 1219 PTC cases. KLF5 over-expression was noted in 65.1% (793/1219) of PTCs, and was significantly associated with tall-cell variant (p &lt;0.0001), extrathyroidal extension (p = 0.0003), lymph node metastasis (p &lt; 0.0001) and stage IV tumors (p &lt; 0.0001). Significant association was also noted with HIF-1α over-expression (p = 0.0492). Interestingly, KLF5 over-expressing tumors showed poor disease-free survival (p = 0.0066). Functional studies in PTC cell lines showed that KLF5 co-immunoprecipitated with HIF-1α. Knockdown of KLF5 decreased the expression of HIF-1α while KLF5 was not affected by HIF-1α inhibition, suggesting that KLF5 is a functional upstream of HIF-1α. Down-regulation of KLF5 using specific inhibitor, ML264 or siRNA inhibited cell invasion and migration. In addition, treatment of PTC cell lines with ML264 resulted in inhibition of proliferation and induction of apoptosis in a dose-dependent manner. Furthermore, silencing of KLF5 significantly decreased the self-renewal ability of spheroids generated from PTC cells. Our findings confer that KLF5 may be a potential therapeutic target for the treatment of papillary thyroid cancer.

scholarly journals Differential glycolytic profile and Warburg effect in papillary thyroid carcinoma cell lines

2016 ◽  
Vol 36 (6) ◽  
pp. 3673-3681 ◽  
Author(s):  
Raquel Guimarães Coelho ◽  
Juliana De Menezes Cazarin ◽  
João Paulo Albuquerque Cavalcanti De Albuquerque ◽  
Bruno Moulin De Andrade ◽  
Denise P. Carvalho
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Warburg Effect ◽  
Carcinoma Cell ◽  
Papillary Thyroid ◽  
Carcinoma Cell Lines ◽  
Thyroid Carcinoma Cell ◽  
Papillary Thyroid Carcinoma Cell

scholarly journals Metabolomic Alterations in Thyrospheres and Adherent Parental Cells in Papillary Thyroid Carcinoma Cell Lines: A Pilot Study

2018 ◽  
Vol 19 (10) ◽  
pp. 2948 ◽  
Author(s):  
Paola Caria ◽  
Laura Tronci ◽  
Tinuccia Dettori ◽  
Federica Murgia ◽  
Maria Santoru ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Krebs Cycle ◽  
Metabolic Phenotype ◽  
Gas Chromatography Mass Spectrometry ◽  
Papillary Thyroid ◽  
Time Data ◽  
Krebs Cycle Intermediates ◽  
New Biomarkers

Papillary thyroid carcinoma (PTC), is characterized by a heterogeneous group of cells, including cancer stem cells (CSCs), crucially involved in tumor initiation, progression and recurrence. CSCs appear to have a distinct metabolic phenotype, compared to non-stem cancer cells. How they adapt their metabolism to the cancer process is still unclear, and no data are yet available for PTC. We recently isolated thyrospheres, containing cancer stem-like cells, from B-CPAP and TPC-1 cell lines derived from PTC of the BRAF-like expression profile class, and stem-like cells from Nthy-ori3-1 normal thyreocyte-derived cell line. In the present study, gas chromatography/mass spectrometry metabolomic profiles of cancer thyrospheres were compared to cancer parental adherent cells and to non cancer thyrospheres profiles. A statistically significant decrease of glycolytic pathway metabolites and variations in Krebs cycle metabolites was found in thyrospheres versus parental cells. Moreover, cancer stem-like cells showed statistically significant differences in Krebs cycle intermediates, amino acids, cholesterol, and fatty acids content, compared to non-cancer stem-like cells. For the first time, data are reported on the metabolic profile of PTC cancer stem-like cells and confirm that changes in metabolic pathways can be explored as new biomarkers and targets for therapy in this tumor.

scholarly journals Ligands for Peroxisome Proliferator-Activated Receptor γ Inhibit Growth and Induce Apoptosis of Human Papillary Thyroid Carcinoma Cells

2001 ◽  
Vol 86 (5) ◽  
pp. 2170-2177 ◽  
Author(s):  
Kazuyasu Ohta ◽  
Toyoshi Endo ◽  
Kazutaka Haraguchi ◽  
Jerome M. Hershman ◽  
Toshimasa Onaya
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Cell Lines ◽  
Carcinoma Cell ◽  
Carcinoma Cells ◽  
Human Thyroid ◽  
Peroxisome Proliferator ◽  
Papillary Thyroid ◽  
Peroxisome Proliferator Activated Receptor ◽  
Carcinoma Cell Lines

Ligands for peroxisome proliferator-activated receptor γ (PPARγ) induce apoptosis and exert antiproliferative effects on several carcinoma cell lines. The present study investigates the expression of PPARγ and the possibility that agonists for PPARγ also inhibit the growth of human thyroid carcinoma cells. We examined this hypothesis using six cell lines, designated BHP thyroid carcinoma cells, which originated from patients with papillary thyroid carcinoma. RT-PCR analysis revealed that the thyroid carcinoma cell lines BHP2–7, 7–13, 10–3, and 18–21 express PPARγ. More PPARγ was expressed in carcinoma than in adjacent normal thyroid tissue in three of six samples of human papillary carcinoma of the thyroid. PPARγ-positive thyroid carcinoma cells were treated with agonists of PPARγ, troglitazone, BRL 49653, and 15-deoxy-Δ12,14-prostaglandin J2. Troglitazone (10μ mol/L), BRL 49653 (10 μmol/L), and 15-deoxy-Δ12,14-prostaglandin J2 (1 μg/mL) decreased[ 3H]thymidine incorporation and reduced cell number, respectively, in BHP carcinoma cell lines that expressed PPARγ. Under low serum conditions, ligands for PPARγ induced condensation of the nucleus and fragmentation of chromatin into nucleosome ladders. These findings indicate that the death of thyroid carcinoma cells is a form of apoptosis. To investigate the molecular mechanism of the apoptosis, we assessed expression of the apoptosis-regulatory genes bcl-2, bax, and c-myc. Troglitazone significantly increased the expression of c-myc messenger RNA but had no effect on the expression of bcl-2 and bax in thyroid carcinoma cells. These results suggest that, at least in part, the induction of apoptosis in human papillary thyroid carcinoma cells may be due to an increase of c-myc. Troglitazone (500 mg/kg·day) significantly inhibited tumor growth and prevented distant metastasis of BHP18–21 tumors in nude mice in vivo. Taken together, these results suggest that PPARγ agonist inhibit cell growth of some types of human thyroid cancer.

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