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Targeted bisulfite sequencing in PTC [ATAC-Seq]

ABSTRACT: This study illuminates the critical advancement in the personalized management of papillary thyroid cancer (PTC) through the identification and validation of epigenetic biomarkers. We discovered the two distinct PTC subgroups with varying prognoses through TBS and observed the clues that PTC1 may related to immune signatures through multi-omics sequencing analysis. Then, we introduce FNAB, a minimally invasive preoperative test, for prognostication and therapeutic decision-making. Utilizing FNAB coupled with real-time digital PCR, our methodology not only facilitates the sensitive detection of seven pivotal biomarkers, but also integrates seamlessly with the established TNM staging system to significantly refine survival predictions. This approach heralds a new era in the precise, personalized treatment of PTC, promising improved patient outcomes through the strategic application of epigenetic insights in clinical practice.

ORGANISM(S): Homo sapiens

PROVIDER: GSE262493 | GEO | 2025/05/14

REPOSITORIES: GEO

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Project description:PURPOSE: Amino acids (AAs) play important physiological roles in living cells. Some amino acid changes in blood are specific for autoimmune disorders, and some are specific for thyroid cancer. The aims of this study were to profile AA metabolites in the serum of patients with papillary thyroid carcinoma (PTC0) without Hashimoto’s thyroiditis (HT) and patients with PTC with HT (PTC1) and predict whether AA metabolites are associated with thyroid disease, thyroid hormone and thyroid autoantibodies. METHODS: A total of 93 serum samples were collected, including 28 healthy controls (HCs), 28 PTC0 patients and 37 PTC1 patients. Serum samples were analysed by high-performance liquid chromatography-triple stage quadrupole-mass spectrometry (HPLC-TSQ-MS), and 21 amino acids (AAs) were detected.RESULTS: The serum concentration of glutamic acid was significantly elevated in PTC1 patients compared with PTC0 patients. Lysine was the second amino acid that differentiated these two groups of PTC patients. In addition, the serum concentrations of glycine, alanine and tyrosine were significantly reduced in both PTC patient groups compared to the HC group. These AAs were also correlated with thyroid hormones and antibodies. Five amino acid markers, namely, glycine, tyrosine, glutamic acid, glutamine and arginine, separated/distinguished PTC0 patients from healthy subjects, and eight AA markers, the same AAs as above without arginine but with alanine, leucine, valine and histidine, separated/distinguished PTC1 patients from healthy subjects based on ROC analysis.CONCLUSION: Compared with the HCs, changes in AAs in PTC0 and PTC1 patients showed similar patterns, suggesting the possibility of a common pathophysiological basis, which confirms preliminary research that PTC is significantly associated with pathologically confirmed HT. We found two AAs, lysine and alanine, that can perform diagnostic functions in distinguishing PTC1 from PTC0.

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Targeted bisulfite sequencing in PTC [ATAC-Seq]

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