Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Although the incidence of thyroid carcinoma is reported to be the highest among malignancies of endocrine system, its diagnosis is still unsatisfactory. This study sought to explore the key DNA methylation-driven genes in the development of papillary thyroid carcinoma (PTC) via a bioinformatic analysis based on the Cancer Genome Atlas (TCGA) database and was validated using the Gene Expression Omnibus (GEO) database. The level 3 DNA methylation, mRNA expression, and clinical data of 499 patients with PTC were obtained from the TCGA database. The R package LIMMA, edgeR, and MethylMix were applied to explore the DNA methylation-driven genes in PTC. The ConsensusPathDB software, DAVID, and STRING databases were used for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses, as well as protein/protein interaction network construction individually. To verify the result, the explored genes were validated using GSE97466 data set retrieved from the GEO database. Fifty-seven (57) methylation-driven genes were detected via MethylMix based on a beta mixture model that compared the DNA methylation state of tumor tissues with that of the normal tissues. Eventually, three genes (TNFRSF1A, CLDN1, and CASP1) were identified to be the most potential biomarkers for the diagnosis or treatment of PTC. These results suggest the crucial roles of TNFRSF1A, CLDN1, and CASP1 in the tumorigenesis of PTC and provide a vital bioinformatic basis for further experimental validations and clinical applications.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1089/cmb.2019.0471 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Clinicopathological significance of histological diversity in gastric adenocarcinoma with primitive enterocyte phenotype: A methylation-driven aggressive entity.
World J Gastroenterol
July 2025
Department of Pathology, Fuzhou University Affiliated Provincial Hospital, Fuzhou 350001, Fujian Province, China.
Background: Gastric adenocarcinoma with primitive phenotypes has recently attracted increasing attention due to its aggressive nature and challenging diagnosis. Gastric adenocarcinoma with enteroblastic differentiation (GAED) and hepatoid adenocarcinoma (HAC) were previously regarded as gastric adenocarcinoma with primitive enterocyte phenotype (GAPEP). GAPEP is known for its poor prognosis, and the accurate diagnosis of GAPEP directly affects therapeutic decision-making.
View Article and Find Full Text PDFAZU1 as a DNA Methylation-Driven Gene: Promoting Oxidative Stress in High-Altitude Pulmonary Edema.
Antioxidants (Basel)
July 2025
School of Elderly Care Services and Management, Nanjing University of Chinese Medicine, Nanjing 210023, China.
High-altitude pulmonary edema (HAPE) is a severe condition associated with high-altitude environments, and its molecular mechanism has not been fully elucidated. This study systematically analyzed the DNA methylation status of HAPE patients and healthy controls using reduced-representation bisulfite sequencing (RRBS) and 850K DNA methylation chips, identifying key differentially methylated regions (DMRs). Targeted bisulfite sequencing (TBS) revealed significant abnormalities in DMRs of five genes, azurocidin 1 (AZU1), growth factor receptor bound protein 7 (GRB7), mannose receptor C-type 2 (MRC2), RUNX family transcription factor 3 (RUNX3), and septin 9 (SEPT9).
View Article and Find Full Text PDFIdentification and validation of DNA methylation-driven gene OSR1 as a novel tumor suppressor for the diagnosis and prognosis of breast cancer.
Front Genet
July 2025
Department of Oncology, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
Introduction: Aberrant DNA methylation plays a critical role in the initiation and progression of cancer, yet its association with breast cancer remains inadequately defined. This study aims to clarify the link between methylation-driven genes and breast cancer pathogenesis.
Methods: RNA sequencing and DNA methylation data for breast cancer were retrieved from The Cancer Genome Atlas (TCGA).
Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer.
Nat Commun
July 2025
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Castration-resistant prostate cancer is a heterogeneous disease with variable phenotypes commonly observed in later stages of the disease. These include cases that retain expression of luminal markers and those that lose hormone dependence and acquire neuroendocrine features. While there are distinct transcriptomic and epigenomic differences between castration-resistant adenocarcinoma and neuroendocrine prostate cancer, the extent of overlap and degree of diversity across tumor metastases in individual patients has not been fully characterized.
View Article and Find Full Text PDFExploring the Clinical Implication of S100A9 in Ulcerative Colitis and Its Progression to Cancer: A Journey from Inflammation to Cancer.
Int J Mol Sci
June 2025
Department of Otorhinolaryngology-Head & Neck Surgery, Korea University College of Medicine, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea.
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by mucosal inflammation and debilitating symptoms that considerably impair life quality. UC is particularly prevalent in younger populations, where early diagnosis remains challenging owing to nonspecific symptoms and the potential progression to colitis-associated cancer (CAC). The GSE177044 dataset, consisting of whole blood samples, was analyzed to identify differentially expressed genes, perform gene annotation, analyze key signaling pathways, and detect key hub genes in UC using protein-protein interaction networks.
View Article and Find Full Text PDF