Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hierarchal gene master regulators of papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

ABSTRACT: The incidence of thyroid cancer (TC) has doubled in recent years but the molecular mechanisms responsible for various TC forms are largely unknown. We hypothesize that, in a thyroid tumor, cancer nodules and surrounding benign tissue are governed by different gene master regulators (GMRs). GMRs are defined as coding/non-coding RNAs whose strongly protected (by the homeostatic mechanisms) abundance modulates most functional pathways by coordinating the expression of their composing genes. GMRs are the most legitimate targets for TC gene therapy. However, because of strong expression control, GMRs are not selectable among TC biomarkers whose frequent regulation in large cancer patient populations indicates low protection as for minor players. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97002 | GEO | 2017/03/25

SECONDARY ACCESSION(S): PRJNA380372

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Validation of the Personalized Gene Therapy by stably transfection of PANK2 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of PANK2 gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. PANK2 was selected because it has significantly different GCHs in the two cell lines: 44.64 in BCPAP and 3.61 in 8505C. The significantly more up- and down-regulated genes in the transfected BCPAP than in the transfected 8505C cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

2017-03-25 | GSE97030 | GEO

Validation of the Personalized Gene Therapy by stably transfection of DDX19B in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of DDX19B gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. DDX19B was selected because it has significantly different GCHs in the two cell lines: 1.64 in BCPAP and 6.03 in 8505C. The significantly more up- and down-regulated genes in the transfected 8505C than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

2017-03-25 | GSE97028 | GEO

Validation of the Personalized Gene Therapy by stably transfection of UBALD1 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of UBALD1 gene in the BCPAP and 8505C thyroid cancer cell lines. UBALD1 was selected because it has significantly different GCHs in the two cell lines: 10.31 in 8505C and 1.12 in BCPAP. The significantly more up- and down-regulated genes in the transfected 8505C cells than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

2017-04-06 | GSE97427 | GEO

Hierarchal gene master regulators of one case of papillary thyroid cancer

Project description:The incidence of thyroid cancer (TC) has doubled in recent years but the molecular mechanisms responsible for various TC forms are largely unknown. We hypothesize that, in a thyroid tumor, cancer nodules and surrounding benign tissue are governed by different gene master regulators (GMRs). GMRs are defined as coding/non-coding RNAs whose strongly protected (by the homeostatic mechanisms) abundance modulates most functional pathways by coordinating the expression of their composing genes. GMRs are the most legitimate targets for TC gene therapy. However, because of strong expression control, GMRs are not selectable among TC biomarkers whose frequent regulation in large cancer patient populations indicates low protection as for minor players. We tested the hypothesis by profiling the transcriptomes of the papillary cancer and benign tissue from a surgically removed TC. The hierarchy of the known biomarkers was established for both cancer and benign regions of the tumor based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that 1/3 of the 544 known biomarkers had higher GCH in the malignant region, 1/3 in the benign region, while the rest did not discriminate between the two, raising the question of the biomarkers’ utility.

2017-03-25 | GSE97001 | GEO

Validation of the Personalized Gene Therapy by stably transfection of NEMP1 (TMEM194A) in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of NEMP1 (TMEM194A) gene encoding a nuclear envelope protein in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. NEMP1 was selected because it has significantly different GCHs in the two cell lines: 5.95 in BCPAP and 0.40 in 8505C. The significantly more up- and down-regulated genes in the transfected BCPAP than in the transfected 8505C cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

2017-03-25 | GSE97031 | GEO

Expression data of BCPAP cells with EPB41L4A knockdown

Project description:A recent genome-wide association study in thyroid cancer discovered 5q22 as one of five loci implicated in thyroid cancer predisposition. The tag single-nucleotide polymorphism, rs73227498, is located downstream of coding isoforms of EPB41L4A and has a significant association with the expression of EPB41L4A in thyroid tissue, according to the GTEx Portal. In order to reveal the regulatory gene network of EPB41L4A in thyroid cells, microarray analysis was performed in the BCPAP cell line treated with siRNA against EPB41L4A.

2020-11-24 | GSE148485 | GEO

Expression data of BCPAP cells with LRRC34 knockdown

Project description:A recent genome-wide association study (GWAS) in thyroid cancer discovered 3q26 as one of five loci implicated in thyroid cancer predisposition. The tag SNP, rs6793295, is located in exon 7 of LRRC34. However, there are genetically distinct, but population-specific signals upstream of LRRC34 that demonstrate allele-specific expression. In order to reveal the regulatory gene network of LRRC34 in thyroid cells, microarray analysis was performed in the BCPAP cell line treated with siRNA against LRRC34.

2019-12-31 | GSE134694 | GEO

Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity

Project description:Background: thyroid transcription factor-1 (TTF-1) is known to play key roles in thyroid organogenesis, in thyroid cell proliferation and in the expression of genes involved in thyroid differentiated function. Objective: to understand why many human thyroid cancer cell lines keep producing TTF-1 despite the loss of differentiation. Methods: a chimeric protein acting as a functional antagonist of TTF-1 transcriptional activity was expressed conditionally in 8505C cells originating from an undifferentiated thyroid carcinoma. The consequences of the inhibition of TTF-1 activity in the cells expressing the antagonist on cell proliferation, mRNA and miRNA expression were analyzed. Results: we observed a growth arrest of 8505C thyroid cancer cells when the endogenous TTF-1 transcriptional activity was inhibited. It correlated with decreased levels of several mRNAs encoding positive effectors of cell proliferation like CDK1 and cyclinB1, and increased levels of various mRNAs encoding negative regulators of cell division like CDKN2B and DUSP6. By contrast, no significant change was observed in the miRNA population. Conclusion: the persistence of TTF-1 expression observed in most dedifferentiated human thyroid cancer cell lines is likely to be explained by the fact that TTF-1 activity is still required for proliferation of these tumor cells as demonstrated here in the 8505C cell line.

2016-06-01 | GSE58243 | GEO

Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity

2015-06-15 | GSE58587 | GEO

Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity

2015-06-15 | E-GEOD-58587 | biostudies-arrayexpress