Tennessee Colorectal Polyp Study
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ABSTRACT:
PROVIDER: PRJNA788585 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tennessee Colorectal Polyp Study
| PRJNA788615 | ENA
Project description:Colorectal polyp is known a precursor of colorectal cancer (CRC) that holds an increased risk for progression to CRC. Circulating cell-free DNA(cfDNA) methylation has shown favorable performance in the detection and monitoring the malignant progression in a variety of cancers. Here, we conducted a study to discovery cfDNA methylation markers for the diagnosis of CRC. We first performed a genome-wide analysis using the Infinium HumanMethylationEPIC BeadChip array to identify differentially methylated CpGs (DMCs) between 8 CRC and 8 polyp tissues. Then, we validated DMCs in a larger tissue cohort and four methylation markers (cg04486886, cg06712559, cg13539460 and cg27541454) were selected as the methylation markers in tissue by LASSO and random forest models. A diagnosis prediction model was bulit based on the four markers and the methylaion diagnosis score (md-score) can effectively discriminate patients with CRC from polyp tissues. Finally, a single cfDNA methylation marker, cg27541454, was confirmed hypermethylated in CRC in the plasma validation cohort. Together, our findings suggested that the md-score derived from tissue could robustly detect CRC from polpy patients, and cg27541454 may be a promising candidate non-invasive biomarker for CRC early diagnosis.
2024-01-01 | GSE220160 | GEO
Project description:Genome-wide DNA methylation analysis of colorectal cancer and polyp
| PRJNA908893 | ENA
Project description:Here we investigate the transcriptional landscapes of nasal polyp IgD+ (naïve-like) B cells, nasal polyp ASC, and blood naïve B cells using RNA-seq. These data found that nasal polypP IgD+ naïve-like B cells are activated and similar to nasal polyp ASC and distinct from circulating B cells in the blood.
2021-05-20 | GSE174681 | GEO
Project description:Hispanic Colorectal Cancer Study
| PRJNA339338 | ENA
Project description:We report the RNA-seq data of 40 advanced colorectal adenoma patients form Dongguk University Ilsan International Hospital. The polyps with a diameter of 1cm or greater were regarded as advenced colorectal adenoma and obtained through colonoscopy. The data consist of 22 tublar adenoma, 6 tublovillous adenoma, 5 sessile serrated adenoma/polyp, 1 traditional serrated adenoma, intramucosal adenocarcinoma, neuroendocrine tumor, hyperplastic polyp, inflammatory polyp, high grade dysplasia, and atypical glands with adjacent hyperplastic mucosa.
2023-08-07 | GSE154548 | GEO
Project description:Colon polyps represent precursor lesions of colon cancers and their malignant potential varies according to histological subtype. A rare subtype of colon polyps is the Peutz-Jeghers (PJ) polyp. PJ polyps mostly occur in the context of Peutz-Jeghers Syndrome which is characterized by the development of multiple polyps in the intestinal tract and hyperpigmentation of oral mucosa and lips. Peutz-Jeghers Syndrome is an autosomal dominant disorder caused by germline mutations of the Serine Threonin Kinase STK11 (LKB1). PJ polyps very rarely occur outside of Peutz-Jeghers Syndrome and are then referred to as solitary PJ polyps. Contrary to Peutz-Jeghers Syndrome, the genetic basis and the malignant potential of solitary PJ polyps is currently unknown. To date, only one study described a sporadic PJ polyp finding no mutations of STK11, indicating that the molecular profile of solitary PJ polyps differs from Peutz-Jeghers syndrome. Methylome analysis revealed global hypomethylation and CpG island hypermethylation, two features that have been described as hallmarks of the colorectal cancer epigenome. These results provide a paradigm for a premalignant lesion that is defined by epigenetic changes.
2017-01-23 | E-MTAB-5255 | biostudies-arrayexpress
Project description:Background: The change of cellular energy metabolism in colorectal carcinogenesis is poorly understood. It is widely accepted tht most, if not all, colorectal cancers (CRCs) arise from adenomatous polyps (APs). Our aim was to characterize the mitochondrial and bioenergetic alternations in the adenoma-carcinoma sequence. Results: Two glycolysis-related genes, aldolase B (ALDOB) and solute carrier family 16 member 4 (SLC16A4), were upregulated in polyps. This result was further confirmed by the real-time PCR analysis showing that the both ALDOB and SLC16A4 mRNA expressions were higher in the polyps with villous component compared with their adjacent normal mucosa.
2017-05-23 | GSE81804 | GEO
Project description:The well-known colorectal adenoma-carcinoma sequence suggests that a normal epithelial cell, through accumulations of genetic lesion and epigenetic disregulation can transform into a benign adenoma then further develop into a cancer. Using microarray-based comparative genomic hybridization (CGH), we reveal genome-wide copy number variations in colorectal cancer and polyp and use them to determine the tissueM-^Rs clonal relationship.
2011-06-30 | E-MEXP-3149 | biostudies-arrayexpress
Project description:Colorectal tumors have an impaired gene expression. As microRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression we performed high-troughput miRNA profiling of 20 Adenomatous Polyp, 20 CRC and 32 healthy control formalin-fixed and paraffin-embedded samples using small RNA sequencing approach.
2022-03-03 | GSE160432 | GEO