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ABSTRACT: Study on related genes of Hashimoto's thyroiditis and thyroid papillary carcinoma

PROVIDER: PRJNA786202 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17163800_1.fastq.gz	Fastqsanger.gz
	SRR17163800_2.fastq.gz	Fastqsanger.gz
	SRR17163900_1.fastq.gz	Fastqsanger.gz
	SRR17163900_2.fastq.gz	Fastqsanger.gz
	SRR17163801_1.fastq.gz	Fastqsanger.gz

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Human papillary thyroid carcinoma landscape and its immunological link with Hashimoto's thyroiditis at single cell resolution

Project description:Tumor microenvironment heterogeneity sheltered our understanding of papillary thyroid cancer. However, molecular characteristics of papillary thyroid cancer has not been reported at single cell resolution. The immunological link between papillary thyroid cancer and Hashimoto's thyroiditis is also in doubt.We identified 24 cell clusters in human papillary thyroid cancer based on their heterogeneous gene expression pattern. Follicular epithelial cell subsets in papillary thyroid cancer with Hashimoto's thyroiditis and papillary thyroid cancer without Hashimoto's thyroiditis showed different malignant level. Machine learning model identified potential biomarker to evaluate tumor epithelial cell development. Together with immunostaining, lymphocytes heterogeneity indicated an obvious B cell infiltration pattern in papillary thyroid cancer with Hashimoto's thyroiditis. Additionally, trajectory analysis of B cell and plasma cell suggest the migration potential from normal adjacent tissue of Hashimoto's thyroiditis to papillary thyroid cancer tissue. Our results provide the first single cell landscape of Papillary thyroid cancer. Single cell data resource of Papillary thyroid cancer with Hashimoto's thyroiditis promote our understanding of molecular heterogeneity and immunological link between papillary thyroid cancer and Hashimoto's thyroiditis.

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Spatial transcriptome gene expression profile in 2 patients with Hashimoto's thyroiditis and 2 patients with papillary thyroid cancer combined with Hashimoto's thyroiditis.

Project description:Hashimoto's thyroiditis and papillary thyroid cancer are the most common thyroid disorders. We used spatial transcriptome sequencing (ST-seq) to investigate their potential relationship.

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Project description:Papillary thyroid carcinoma, as a malignant tumor with high incidence, is often accompanied by Hashimoto's thyroiditis. The pathogenesis of papillary thyroid carcinoma has not been fully clarified, and new molecular diagnostic methods are urgently needed to help the early and accurate diagnosis. In this study, the proteomic characteristics of papillary thyroid carcinoma in the context of Hashimoto's thyroiditis were analyzed by mass spectrometry, and the corresponding differential proteins and key pathways were screened to further study the pathogenesis and development mechanism.

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Project description:Identification of long noncoding RNAs involved in clinicopathological features of papillary thyroid carcinoma complicated with Hashimoto's thyroiditis

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Spatial transcriptome gene expression profile in 2 patients with Hashimoto's thyroiditis and 2 patients with papillary thyroid cancer combined with Hashimoto's thyroiditis.

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Deep Sequencing Identifies Multiple Fusion Transcripts, Differentially Expressed Genes, and Generalized Immune Suppression in BRAF (V600E) mutant vs. BRAF wild-type Papillary Thyroid Carcinoma

Project description:CONTEXT: BRAF V600E mutation (BRAF-mut.) confers aggressiveness in papillary thyroid carcinoma, but unidentified genomic abnormalities may be required for full phenotypic expression. OBJECTIVE: To perform deep sequencing to identify genes differentially expressed between BRAF-mut. and BRAF-wild-type (BRAF-WT) tumors, and to compare to patient clinical status. DESIGN: BRAF-mut. and BRAF-WT tumors were identified in patients with T1N0 and with T23N1 tumors. Expression levels of genes were determined from RNA sequencing (RNA-Seq) data and fusion transcripts were detected. NanoString was used to validate the RNA-Seq data for immune genes. SETTING: Patients were seen at two sites of a major referral medical center. PATIENTS: Twenty patients were studied. BRAF-mut. patients included 9 women, 3 men; 9 were TNM stage I and 3 were stage III; 3 (25%) had lymphocytic thyroiditis. BRAF-WT included 5 women; 3 men; all were stage I; 5 (62.5%) had lymphocytic thyroiditis. RESULTS: 560 of 13,085 genes were differentially expressed by RNA-Seq, and MetaCore analysis identified 55 immune function genes that were differentially expressed as a function of BRAF mutational status. Immune function genes were broadly underexpressed in BRAF-mut. tumors, with only 4 genes (HLA-G, CXCL14, TIMP1, IL1RAP) more highly expressed. NanoString validated the RNA Seq data for immune genes. Eleven high confidence fusion transcripts were detected, four being inter-chromosomal and seven intra-chromosomal. CONCLUSION: BRAF-mut. papillary thyroid cancers have less expression of immune and inflammatory response genes than BRAF-WT tumors. Thirteen of 20 (65%) tumors had between one and three fusion transcripts. Functional studies will be required to determine the potential role of the newly identified genomic abnormalities in contributing to the aggressiveness of BRAF-mut. and wild-type tumors. RNA-seq was performed on 20 thyroid carcinoma tumors

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2024-06-06 | GSE248205 | GEO

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Project description:To understand Hashimoto's Thyroiditis and translate this knowledge to clinical applications, we took mass spectrometric analysis on thyroid tissue fine-needle puncture from HT patients and healthy people in an attempt to make a further understanding of the pathogenesis of Hashimoto's Thyroiditis.

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Project description:We tried to analyze the effect of FTO on papillary thyroid carcinoma. We constructed a FTO overexpression stable cell line of papillary thyroid carcinoma cells. We performed meRIP-seq sequencing analysis of the FTO overexpression stable transfer cell line to try to assess which genes were changed at the m6A level in papillary thyroid cancer cells by overexpressing FTO.

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