scholarly journals Mining Prognostic Significance Genes in Human Thyroid Cancer Using Bioinformatics Analysis

2021 ◽  
Author(s):  
Hui Zhao ◽  
Pengjie Li ◽  
Junjian Li ◽  
Lian Duan ◽  
Yanzhu Jiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Thyroid Cancer ◽  
Function Analysis ◽  
Akt Signaling ◽  
Differentially Expressed ◽  
Human Thyroid ◽  
Marker Genes ◽  
Clinical Prognosis ◽  
Mesenchymal Transition

Abstract Background Thyroid carcinoma (THC) is very common, yet its pathogenesis and the key tumor marker genes remain unclear.Methods Gene expression datasets from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas Project (TCGA) were used for gene differential expression analysis. Functional annotation analysis, Clinical prognosis analysis and Differential DNA methylation analysis were conducted on the differentially expressed genes (DEGs). Results Compared with induced pluripotent stem cells (iPSCs), 237 differentially expressed THC intersection genes derived from GEO and TCGA were obtained, of which 153 genes were closely related to clinicopathological features and prognostic effects. Biological function analysis indicated that most of these DEGs were involved in the proteinaceous extracellular matrix, epithelial-to-mesenchymal transition (EMT), and PI3K-Akt signaling pathway, resulting in effects on tumor invasion and metastasis. Finally, the results of differential methylation levels demonstrated that the high expression of 4 genes (CHI3L1, NFE2L3, S100A2, and LAMB3) was strongly correlated with the development of thyroid cancer.Conclusions Proteinaceous extracellular matrix, EMT, and PI3K-Akt signaling pathways were of great significance in the metastasis and invasion of THC. Genes such as CHI3L1, NFE2L3, S100A2, and LAMB3 were susceptible to THC.

scholarly journals Notch Signaling Is Involved in Expression of Thyrocyte Differentiation Markers and Is Down-Regulated in Thyroid Tumors

2008 ◽  
Vol 93 (10) ◽  
pp. 4080-4087 ◽  
Author(s):  
E. Ferretti ◽  
E. Tosi ◽  
A. Po ◽  
A. Scipioni ◽  
R. Morisi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Notch Signaling ◽  
Notch Pathway ◽  
Human Thyroid ◽  
Thyroid Tumors ◽  
Follicular Cells ◽  
Differentiation Markers ◽  
Thyroid Follicular Cells ◽  
Thyroid Cancer Cells

Context: Notch genes encode receptors for a signaling pathway that regulates cell growth and differentiation in various contexts, but the role of Notch signaling in thyroid follicular cells has never been fully published. Objective: The objective of the study was to characterize the expression of Notch pathway components in thyroid follicular cells and Notch signaling activities in normal and transformed thyrocytes. Design/Setting and Patients: Expression of Notch pathway components and key markers of thyrocyte differentiation was analyzed in murine and human thyroid tissues (normal and tumoral) by quantitative RT-PCR and immunohistochemistry. The effects of Notch overexpression in human thyroid cancer cells and FTRL-5 cells were explored with analysis of gene expression, proliferation assays, and experiments involving transfection of a luciferase reporter construct containing human NIS promoter regions. Results: Notch receptors are expressed during the development of murine thyrocytes, and their expression levels parallel those of thyroid differentiation markers. Notch signaling characterized also normal adult thyrocytes and is regulated by TSH. Notch pathway components are variably expressed in human normal thyroid tissue and thyroid tumors, but expression levels are clearly reduced in undifferentiated tumors. Overexpression of Notch-1 in thyroid cancer cells restores differentiation, reduces cell growth rates, and stimulates NIS expression via a direct action on the NIS promoter. Conclusion: Notch signaling is involved in the determination of thyroid cell fate and is a direct regulator of thyroid-specific gene expression. Its deregulation may contribute to the loss of differentiation associated with thyroid tumorigenesis.

scholarly journals DDR1 regulates thyroid cancer cell differentiation via IGF-2/IR-A autocrine signaling loop

2019 ◽  
Vol 26 (1) ◽  
pp. 197-214 ◽  
Author(s):  
Veronica Vella ◽  
Maria Luisa Nicolosi ◽  
Patrizia Cantafio ◽  
Michele Massimino ◽  
Rosamaria Lappano ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Cell Differentiation ◽  
Epithelial To Mesenchymal Transition ◽  
Human Thyroid ◽  
Autocrine Signaling ◽  
Differentiation Markers ◽  
Autocrine Loop ◽  
Mesenchymal Transition ◽  
Poorly Differentiated ◽  
Induced Changes

Patients with thyroid cancers refractory to radioiodine (RAI) treatment show a limited response to various therapeutic options and a low survival rate. The recent use of multikinase inhibitors has also met limited success. An alternative approach relies on drugs that induce cell differentiation, as the ensuing increased expression of the cotransporter for sodium and iodine (NIS) may partially restore sensitivity to radioiodine. The inhibition of the ERK1/2 pathway has shown some efficacy in this context. Aggressive thyroid tumors overexpress the isoform-A of the insulin receptor (IR-A) and its ligand IGF-2; this IGF-2/IR-A loop is associated with de-differentiation and stem-like phenotype, resembling RAI-refractory tumors. Importantly, IR-A has been shown to be positively modulated by the non-integrin collagen receptor DDR1 in human breast cancer. Using undifferentiated human thyroid cancer cells, we now evaluated the effects of DDR1 on IGF-2/IR-A loop and on markers of cell differentiation and stemness. DDR1 silencing or downregulation caused significant reduction of IR-A and IGF-2 expression, and concomitant increased levels of differentiation markers (NIS, Tg, TSH, TPO). Conversely, markers of epithelial-to-mesenchymal transition (Vimentin, Snail-2, Zeb1, Zeb2 and N-Cadherin) and stemness (OCT-4, SOX-2, ABCG2 and Nanog) decreased. These effects were collagen independent. In contrast, overexpression of either DDR1 or its kinase-inactive variant K618A DDR1-induced changes suggestive of less differentiated and stem-like phenotype. Collagen stimulation was uneffective. In conclusion, in poorly differentiated thyroid cancer, DDR1 silencing or downregulation blocks the IGF-2/IR-A autocrine loop and induces cellular differentiation. These results may open novel therapeutic approaches for thyroid cancer.

scholarly journals A Combinatory Approach for Selecting Prognostic Genes in Microarray Studies of Tumour Survivals

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Qihua Tan ◽  
Mads Thomassen ◽  
Kirsten M. Jochumsen ◽  
Ole Mogensen ◽  
Kaare Christensen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Expression Analysis ◽  
Survival Data ◽  
Gene Expression Analysis ◽  
Cancer Survival ◽  
Feature Space ◽  
Differentially Expressed ◽  
Selection Strategy ◽  
Marker Genes

Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations shows that the feature space can be largely reduced while achieving improved testing performances.

scholarly journals Sterculic Acid Alters Adhesion Molecules Expression and Extracellular Matrix Compounds to Regulate Migration of Lung Cancer Cells

Cancers ◽  
2021 ◽  
Vol 13 (17) ◽  
pp. 4370
Author(s):  
Rafael Pelaez ◽  
Rodrigo Ochoa ◽  
Ana Pariente ◽  
Angela Villanueva-Martínez ◽  
Álvaro Pérez-Sala ◽  
...  
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Cancer Cells ◽  
Adhesion Molecules ◽  
Epithelial To Mesenchymal Transition ◽  
Sterculic Acid ◽  
Main Function ◽  
Cyclopropenoid Fatty Acid ◽  
Mesenchymal Transition ◽  
Migration Capacity

Sterculic acid (SA) is a cyclopropenoid fatty acid isolated from Sterculia foetida seeds. This molecule is a well-known inhibitor of SCD1 enzyme, also known as ∆9-desaturase, which main function is related to lipid metabolism. However, recent studies have demonstrated that it also modifies many other pathways and the underlying gene expression. SCD overexpression, or up-regulated activity, has been associated with tumor aggressiveness and poor prognosis in many cancer types. Scd1 down-regulation, with different inhibitors or molecular strategies, reduces tumor cell survival and cell proliferation, as well as the chemoresistance associated with cancer stem cell presence. However, SA effects over cancer cell migration and extracellular matrix or adhesion molecules have not been described in cancer cells up to now. We used different migration assays and qPCR gene expression analysis to evaluate the effects of SA treatment in cancer cells. The results reveal that SA induces tumoral cell death at high doses, but we also observed that lower SA-treatments induce cell adhesion-migration capacity reduction as a result of modifications in the expression of genes related to integrins and extracellular matrix compounds. Overall, the functional and transcriptomic findings suggest that SA could represent a new inhibitor activity of epithelial to mesenchymal transition.

scholarly journals Identification of Methylated Differentially Expressed Hub Genes and Immune Infiltration in Diabetic Retinopathy

2021 ◽  
Author(s):  
Qi Zhou ◽  
Xin Xiong ◽  
Min Tang ◽  
Yingqing Lei ◽  
Hongbin Lv
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Immune Cell ◽  
Interaction Network ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Hub Genes ◽  
Critical Pathways

Abstract BackgroundDiabetic retinopathy (DR), a severe complication of diabetes mellitus (DM), is a global social and economic burden. However, the pathological mechanisms mediating DR are not well-understood. This study aimed to identify differentially methylated and differentially expressed hub genes (DMGs and DEGs, respectively) and associated signaling pathways, and to evaluate immune cell infiltration involved in DR. MethodsTwo publicly available datasets were downloaded from the Gene Expression Omnibus database. Transcriptome and epigenome microarray data and multi-component weighted gene coexpression network analysis (WGCNA) were utilized to determine hub genes within DR. One dataset was utilized to screen DEGs and to further explore their potential biological functions using functional annotation analysis. A protein-protein interaction network was constructed. Gene set enrichment and variation analyses (GSVA and GSEA, respectively) were utilized to identify the potential mechanisms mediating the function of hub genes in DR. Infiltrating immune cells were evaluated in one dataset using CIBERSORT. The Connectivity Map (CMap) database was used to predict potential therapeutic agents. ResultsIn total, 673 DEGs (151 upregulated and 522 downregulated genes) were detected. Gene expression was significantly enriched in the extracellular matrix and sensory organ development, extracellular matrix organization, and glial cell differentiation pathways. Through WGCNA, one module was found to be significantly related with DR (r=0.34, P =0.002), and 979 hub genes were identified. By comparing DMGs, DEGs, and genes in WGCNA, we identified eight hub genes in DR ( AKAP13, BOC, ACSS1, ARNT2, TGFB2, LHFPL2, GFPT2, TNFRSF1A ), which were significantly enriched in critical pathways involving coagulation, angiogenesis, TGF-β, and TNF-α-NF-κB signaling via GSVA and GSEA. Immune cell infiltration analysis revealed that activated natural killer cells, M0 macrophages, resting mast cells, and CD8 + T cells may be involved in DR. ARNT2, TGFB2, LHFPL2 , and AKAP13 expression were correlated with immune cell processes, and ZG-10, JNK-9L, chromomycin-a3, and calyculin were identified as potential drugs against DR. Finally, TNFRSF1A , GFPT2 , and LHFPL2 expression levels were consistent with the bioinformatic analysis. ConclusionsOur results are informative with respect to correlations between differentially methylated and expressed hub genes and immune cell infiltration in DR, providing new insight towards DR drug development and treatment.

scholarly journals FOXE1 regulates migration and invasion in thyroid cancer cells and targets ZEB1

2020 ◽  
Vol 27 (3) ◽  
pp. 137-151 ◽  
Author(s):  
Jesús Morillo-Bernal ◽  
Lara P Fernández ◽  
Pilar Santisteban
Keyword(s):  
Cell Migration ◽  
Thyroid Cancer ◽  
Cancer Cells ◽  
Cell Lines ◽  
Cancer Susceptibility ◽  
Human Thyroid ◽  
Migration And Invasion ◽  
Migration Ability ◽  
Mesenchymal Transition ◽  
Thyroid Cancer Cells

FOXE1 is a thyroid-specific transcription factor essential for thyroid gland development and maintenance of the differentiated state. Interestingly, a strong association has been recently described between FOXE1 expression and susceptibility to thyroid cancer, but little is known about the mechanisms underlying FOXE1-induced thyroid tumorigenesis. Here, we used a panel of human thyroid cancer-derived cell lines covering the spectrum of thyroid cancer phenotypes to examine FOXE1 expression and to test for correlations between FOXE1 expression, the allele frequency of two SNPs and a length polymorphism in or near the FOXE1 locus associated with cancer susceptibility, and the migration ability of thyroid cancer cell lines. Results showed that FOXE1 expression correlated with differentiation status according to histological sub-type, but not with SNP genotype or cell migration ability. However, loss-and-gain-of-function experiments revealed that FOXE1 modulates cell migration, suggesting a role in epithelial-to-mesenchymal transition (EMT). Our previous genome-wide expression analysis identified Zeb1, a major EMT inducer, as a putative Foxe1 target gene. Indeed, gene silencing of FOXE1 decreased ZEB1 expression, whereas its overexpression increased ZEB1 transcriptional activity. FOXE1 was found to directly interact with the ZEB1 promoter. Lastly, ZEB1 silencing decreased the ability of thyroid tumoral cells to migrate and invade, pointing to its importance in thyroid tumor mestastases. In conclusion, we have identified ZEB1 as a bona fide target of FOXE1 in thyroid cancer cells, which provides new insights into the role of FOXE1 in regulating cell migration and invasion in thyroid cancer.

scholarly journals Gene expression profile of human thyroid cancer in relation to its mutational status

2011 ◽  
Vol 47 (3) ◽  
pp. R91-R103 ◽  
Author(s):  
Dagmara Rusinek ◽  
Sylwia Szpak-Ulczok ◽  
Barbara Jarzab
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Cancer Biology ◽  
Mapk Pathway ◽  
Human Thyroid ◽  
Thyroid Cell ◽  
Thyroid Cancers ◽  
The Difference

This review describes the gene expression profile changes associated with the presence of different mutations that contribute to thyroid cell carcinogenesis. The results are discussed in the context of thyroid cancer biology and of the implications for disease prognosis, while the diagnostic aspect has been omitted. For papillary thyroid cancer (PTC), the most characteristic gene expression profile is associated with the presence ofBRAFmutation. BRAF-associated PTC differ profoundly from RET/PTC or RAS-associated cancers. Simultaneously, they retain many characteristic gene expression features common for all PTCs, induced by the alternative mutations activating MAPK pathway. Although the difference between papillary and follicular thyroid cancer (FTC) is significant at the gene expression profile level, surprisingly, the RAS-related signature of FTC is not well specified.PAX8/peroxisome proliferator-activated receptor γ (PPARγ) rearrangements, which occur in FTC as an alternative to theRASmutation, are associated with specific changes in gene expression. Furthermore, the difference between well-differentiated thyroid cancers and poorly differentiated and anaplastic thyroid cancers is mainly a reflection of tumor degree of differentiation and may not be attributed to the presence of characteristic mutations.

scholarly journals Characterization of a thyroid hormone-mediated short-loop feedback control of TSH receptor gene in an anaplastic human thyroid cancer cell line

2002 ◽  
Vol 175 (2) ◽  
pp. 459-465 ◽  
Author(s):  
ST Chen ◽  
JD Lin ◽  
KH Lin
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Thyroid Hormone ◽  
Cell Line ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Human Thyroid ◽  
Thyroid Cancer Cell ◽  
Thyroid Cancer Cell Line ◽  
Tshr Gene

The expression of TSH receptor (TSHR) gene is frequently lost in thyroid cancers during the process of dedifferentiation that involves perturbation of several nuclear transcription factors. We have established that thyroid hormone receptor beta1 (TRbeta1) is associated with the loss of TSHR gene expression in an anaplastic human thyroid cancer cell line, ARO. To demonstrate that TRbeta1 regulates TSHR gene expression, we performed electrophoresis mobility shift and 3,5,3'-triiodothyronine (T3) transactivation assays. As expected, TRbeta1 bound the synthesized oligomer containing TSHR promoter sequence by heterodimerizing with retinoid X receptor. When a chimeric reporter pTRCAT5'-146 enclosing the minimal TSHR promoter was applied for T3 transactivation assay, two TRbeta1-overexpressing transfectants of ARO cells (ARO1 and ARO2) demonstrated higher basal activity than their parental cells. Consequentially, T3 suppressed the reporter gene activity only in ARO1 and ARO2, but not in ARO cells. A point mutation creating a cAMP response element (CRE) in the reporter pTRCAT5'-146 CRE led to T3-induced suppression of the reporter gene in ARO cells without changing the basal or T3-induced activities in ARO1 and ARO2 cells. We conclude that the regulatory effect of T3 on TSHR gene expression is TR- and promoter DNA sequence-determined.

scholarly journals Sexually Dimorphic Transcriptomic Changes of Developing Fetal Brain Reveal Signaling Pathways and Marker Genes of Brain Cells in Domestic Pigs

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2439
Author(s):  
Monica Strawn ◽  
Joao G. N. Moraes ◽  
Timothy J. Safranski ◽  
Susanta K. Behura
Keyword(s):  
Gene Expression ◽  
Brain Development ◽  
Signaling Pathways ◽  
Expression Patterns ◽  
Fetal Brain ◽  
Differentially Expressed ◽  
Marker Genes ◽  
Pathway Enrichment Analysis ◽  
Female Brain ◽  
Transcriptomic Changes

In this study, transcriptomic changes of the developing brain of pig fetuses of both sexes were investigated on gestation days (GD) 45, 60 and 90. Pig fetal brain grows rapidly around GD60. Consequently, gene expression of the fetal brain was distinctly different on GD90 compared to that of GD45 and GD60. In addition, varying numbers of differentially expressed genes (DEGs) were identified in the male brain compared to the female brain during development. The sex of adjacent fetuses also influenced gene expression of the fetal brain. Extensive changes in gene expression at the exon-level were observed during brain development. Pathway enrichment analysis showed that the ionotropic glutamate receptor pathway and p53 pathway were enriched in the female brain, whereas specific receptor-mediated signaling pathways were enriched in the male brain. Marker genes of neurons and astrocytes were significantly differentially expressed between male and female brains during development. Furthermore, comparative analysis of gene expression patterns between fetal brain and placenta suggested that genes related to ion transportation may play a key role in the regulation of the brain-placental axis in pig. Collectively, the study suggests potential application of pig models to better understand influence of fetal sex on brain development.

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