Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma

Thyroid nodules occur in about 60% of the population. Current diagnostic strategies, however, often fail at distinguishing malignant nodules before surgery, thus leading to unnecessary, invasive treatments. As proteins are involved in all physio/pathological processes, a proteome investigation of biopsied nodules may help correctly classify and identify malignant nodules and discover therapeutic targets. Quantitative mass spectrometry data-independent acquisition (DIA) enables highly reproducible and rapid throughput investigation of proteomes. An exhaustive spectral library of thyroid nodules is essential for DIA yet still unavailable. This study presents a comprehensive thyroid spectral library covering five types of thyroid tissue: multinodular goiter, follicular adenoma, follicular and papillary thyroid carcinoma, and normal thyroid tissue. Our library includes 925,330 transition groups, 157,548 peptide precursors, 121,960 peptides, 9941 protein groups, and 9826 proteins from proteotypic peptides. This library resource was evaluated using three papillary thyroid carcinoma samples and their corresponding adjacent normal thyroid tissue, leading to effective quantification of up to 7863 proteins from biopsy-level thyroid tissues.

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Faculty Opinions recommendation of Differential gene expression of medullary thyroid carcinoma reveals specific markers associated with genetic conditions.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717967672.793471861 ◽

2013 ◽

Author(s):

Gilbert Cote

Keyword(s):

Gene Expression ◽

Thyroid Carcinoma ◽

Medullary Thyroid Carcinoma ◽

Differential Gene Expression ◽

Medullary Thyroid ◽

Differential Gene

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Biomarkers, Master Regulators and Genomic Fabric Remodeling in a Case of Papillary Thyroid Carcinoma

10.20944/preprints202008.0048.v1 ◽

2020 ◽

Author(s):

Dumitru A Iacobas

Keyword(s):

Thyroid Cancer ◽

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Mathematical Object ◽

Human Thyroid ◽

Expression Data ◽

Papillary Thyroid ◽

Hormone Synthesis ◽

Apoptosis Pathways ◽

Thyroid Cancer Cell Lines

Publically available (own) transcriptomic data were re-analyzed to quantify the alteration of functional pathways in the thyroid cancer, establish the gene hierarchy, identify potential gene targets and predict the effects of their manipulation. The expression data were generated from one case of papillary thyroid carcinoma (PTC) and from genetically manipulated BCPAP (papillary) and 8505C (anaplastic) human thyroid cancer cell lines. The study used the genomic fabric perspective that considers the transcriptome as a multi-dimensional mathematical object based on the three independent characteristics that can be derived for each gene from the expression data. We found remarkable remodeling of the thyroid hormone synthesis, cell cycle, oxidative phosphorylation and apoptosis pathways. Serine peptidase inhibitor, Kunitz type, 2 (SPINT2) was identified as the Gene Master Regulator of the investigated PTC. The substantial increase of the expression synergism of SPINT2 with apoptosis genes in the cancer nodule with respect to the surrounding normal tissue (NOR) suggests that its experimental overexpression may force the PTC cells into apoptosis with negligible effect on the NOR cells. The predictive value of the expression coordination for the expression regulation was validated with data from 8505C and BCPAP cells before and after lentiviral transfection with DDX19B.

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Diverse oncogenic fusions and distinct gene expression patterns define the genomic landscape of pediatric papillary thyroid carcinoma

Cancer Research ◽

10.1158/0008-5472.can-21-0761 ◽

2021 ◽

pp. canres.0761.2021

Author(s):

Ana Stosic ◽

Fabio Fuligni ◽

Nathaniel D. Anderson ◽

Scott Davidson ◽

Richard de Borja ◽

...

Keyword(s):

Gene Expression ◽

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Papillary Thyroid ◽

Distinct Gene ◽

Genomic Landscape

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Gene Expression Profiling Identifies Platelet-Derived Growth Factor as a Diagnostic Molecular Marker for Papillary Thyroid Carcinoma

Clinical Cancer Research ◽

10.1158/1078-0432.ccr-0807-03 ◽

2004 ◽

Vol 10 (6) ◽

pp. 2035-2043 ◽

Cited By ~ 43

Author(s):

Yukiko Yano ◽

Naoya Uematsu ◽

Tohru Yashiro ◽

Hisato Hara ◽

Ei Ueno ◽

...

Keyword(s):

Gene Expression ◽

Growth Factor ◽

Papillary Thyroid Carcinoma ◽

Molecular Marker ◽

Thyroid Carcinoma ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Platelet Derived Growth Factor ◽

Papillary Thyroid

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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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Many Thyroid Cancers Detected by Afirma Gene-Expression Classifier Are Noninvasive Encapsulated Follicular Variant of Papillary Thyroid Carcinoma

Clinical Thyroidology ◽

10.1089/ct.2016;28.261-263 ◽

2016 ◽

Vol 28 (9) ◽

pp. 261-263

Author(s):

Masha J. Livhits ◽

Michael W. Yeh

Keyword(s):

Gene Expression ◽

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Papillary Thyroid ◽

Follicular Variant ◽

Thyroid Cancers ◽

Gene Expression Classifier

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

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jcem.86.5.7493 ◽

2001 ◽

Vol 86 (5) ◽

pp. 2170-2177 ◽

Cited By ~ 4

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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