Project description:Familial thyroid cancer originating from follicular cells accounts for 5-15% of all the thyroid carcinoma cases in humans. Previously, we described thyroid follicular cell carcinomas in a large number of the Dutch German longhaired pointers (GLPs) with likely an autosomal recessive inheritance pattern. Here, we investigated the genetic causes of the disease using a combined approach of genome-wide association study, selective sweep analysis, and ROH analysis based on 170k SNP array genotype data. A region 0-5 Mb on chromosome 17 harboring the TPO gene was identified to be associated with the disease.
Project description:Familial nonmedullary thyroid cancer (FNMTC) is a disease with the inheritance pattern is autosomal dominant with incomplete penetrance, but the causative gene is not clear. To identify the disease related locus in the FNMTC family, whole-genome SNPs of nine family members (five affected and four unaffected) were genotyped. We analyzed the SNP data with a novel method and mapped the disease-causing gene to several regions on the whole genome.
Project description:The aim of the experiment was to explore the RUNX2 genomic functions in the papillary thyroid carcinoma. To this end, we performed Chromatin Immunoprecipitation followed by deep-sequencing using an antibody against RUNX2 in TPC1 thyroid cancer cell line, in order to define the genomic regions bound by this transcription factor.
Project description:We performed single-cell RNA sequencing (scRNA-seq) on 3 normal thyroid, 7 papillary thyroid cancer (PTC), and 5 anaplstic thyroid cancer (ATC) cases. We used scRNA-seq to analyze serirne/glycine metabolism in thyroid tumors.
Project description:There is a challenge of thyroid cancer versus benign follicular denoma differential diagnostics using fine-needle biopsy. RNA expression profiles can be used to identify biomarkers suitable for molecular diagnostics. Here we present raw RNA sequencing data obtained during Oncobox platform observational study for 96 human pathological thyroid biosamples. Data are compatible with Oncobox Atlas of Normal Tissue Expression (ANTE) database including profiles for healthy thyroid tissues. . The data provided are helpful to those implicated in thyroid cancer research and diagnostics, and in comparative analyses of human cancers.
Project description:Paillary thyroid cancer (PTC) is the most common type of thyroid malignancy. Extrathyroidal invasion (ETİ), lymph node metastasis, and distance organ metastasis is poor prognostic factor in PTC. The metastasis is still a leading cause of papillary thyroid cancer death. The early detection of metastatic signature is crucial for identification of thyroid cancer prognosis and personalized therapeutic strategies. In the present study, we present thyroid cancer metastasis and invasivenes related miRNAs identified by comprehensive miRNA expression profiling of formalin-fixed paraffin embedded (FFPE) thyroid tissues obtained from patients belonging to intrathyroidal, invasive and metastatic thyroid carcinoma groups
Project description:We performed Chromatin Immunoprecipitation followed by deep-sequencing in TPC1 thyroid cancer cell line model, in order to identify the genomic elements enriched in RNA-Polymerase II, the enzymatic complex required for gene transcription. These data were integrated with RUNX2 genomic occupancy to map the RUNX2 responsive elements that are actively transcribed.
Project description:<p><strong>BACKGROUND:</strong> Novel biomarkers are urgently needed to distinguish between benign and malignant thyroid nodules and detect thyroid cancer in the early stage. The associations between serum IgG N-glycosylation and thyroid cancer risk have been revealed. We aimed to explore the potential of IgG N-glycan traits as biomarkers in the differential diagnosis of thyroid cancer.</p><p><strong>METHODS:</strong> Plasma IgG N-glycome analysis was applied to a discovery cohort followed by independent validation. IgG N-glycan profiles were obtained using a robust quantitative strategy based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. IgG N-glycans were relatively quantified, and classification performance was evaluated based on directly detected and derived glycan traits.</p><p><strong>RESULTS: </strong>Four directly detected glycans were significantly changed in thyroid cancer patients compared to that in non-cancer controls. Derived glycan traits and a classification glycol-panel were generated based on the directly detected glycan traits. In the discovery cohort, derived trait BN (bisecting type neutral N-glycans) and the glyco-panel showed potential in distinguishing between thyroid cancer and non-cancer controls with AUCs of 0.920 and 0.917, respectively. The diagnostic potential was further validated. Derived trait BN and the glycol-panel displayed “accurate” performance (AUC>0.8) in discriminating thyroid cancer from benign thyroid nodules and healthy controls in the validation cohort. Meanwhile, derived trait BN and the glycol-panel also showed diagnostic potential in detecting early-stage thyroid cancer.</p><p><strong>CONCLUSIONS:</strong> IgG N-glycome analysis revealed N-glycomic differences that allow classification of thyroid cancer from non-cancer controls. Our results suggested that derived trait BN and the classification glyco-panel rather than single N-glycans may serve as candidate biomarkers for further validation.</p>