Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA564401 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in cell-free DNA (cfDNA), the circulating DNA found in human plasma which represents a noninvasive window into the health status of the body. We showed that the genome-wide 5hmC distribution in cfDNA can be reliably sequenced by chemical labeling-based 5hmC enrichment. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that can be used for monitoring disease status and progression. Specifically, we discovered that lung cancer leads to a stage-dependent hypohydroxymethlation in cfDNA, whereas hepatocellular carcinoma (HCC) and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our results demonstrate that cell-free 5hmC can be used not only to track the stage of cancer but also to identify tissue of origin in some solid tumors.
2017-07-13 | GSE81314 | GEO
Project description:Background & Aims. Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is growing in incidence but treatment options remain limited, particularly for late stage disease. As liver cirrhosis is the principal risk state for HCC development, markers to detect early HCC within this patient population are urgently needed. Perturbation of epigenetic marks, such as DNA methylation (5mC), is a hallmark of human cancers, including HCC. Identification of regions with consistently altered 5mC levels in circulating cell free DNA (cfDNA) during progression from cirrhosis to HCC could therefore serve as markers for development of minimally-invasive screens of early HCC diagnosis and surveillance. Methods. To discover DNA methylation derived biomarkers of HCC in the background of liver cirrhosis, we profiled genome-wide 5mC landscapes in patient cfDNA using the Infinium HumanMethylation450k BeadChip Array. We further linked these findings to primary tissue data available from TCGA and other public sources. Using biological and statistical frameworks, we selected CpGs that robustly differentiated cirrhosis from HCC in primary tissue and cfDNA followed by validation in an additional independent cohort. Results. We identified CpGs that segregate patients with cirrhosis, from patients with HCC within a cirrhotic liver background, through genome-wide analysis of cfDNA 5mC landscapes. Lasso regression analysis pinpointed a panel of probes in our discovery cohort that were validated in two independent datasets. A panel of five CpGs (cg04645914, cg06215569, cg23663760, cg13781744, and cg07610777) yielded AUROCs of 0.9525, 0.9714, and 0.9528 in cfDNA discovery and tissue validation cohorts 1 and 2, respectively. Conclusions. 5mC markers derived from cfDNA robustly identify HCC within a cirrhotic liver background indicating that further validation is warranted. Our finding that 5mC markers derived from primary tissue did not perform well in cfDNA, compared to those identified directly from cfDNA, reveals potential advantages of starting with cfDNA to discover high performing markers for liquid biopsy development.
2019-08-16 | GSE129374 | GEO
Project description:Transcriptome sequencing of human hepatocellular carcinoma
2025-01-24 | E-GEOD-33294 | ExpressionAtlas
Project description:This is a single blind, case control, multicenter study jointly developed by Zhongshan Hospital of Fudan University, Shanghai Public Health Clinical Center, Shanghai Xuhui Central Hospital, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, and Shanghai Singlera Genomics Company. The enrolled population will include positive group, precancerous lesions and healthy control group, which is expected to enroll 2,430 participants. The primary objective is to establish molecular testing methods for non-invasive screening and early diagnosis of digestive system cancers through ctDNA methylation and mutation, cfDNA and ctDNA fragment size, and end motif based model (for esophageal, gastric, colorectal cancer), and through ctDNA methylation detection, ctDNA low-pass WGS, miRNA7 and CTC detection and analysis technology based model (for hepatocellular carcinoma). The sensitivity and specificity of the models in cancer early detection will be evaluated.
| 2736788 | ecrin-mdr-crc
Project description:Transcriptomic characterization of Hepatocellular Carcinoma with CTNNB1 mutation
2025-01-24 | E-GEOD-55048 | ExpressionAtlas
Project description:Proteomic characterization of human hepatocellular carcinoma (HCC) tumor biopsies
2024-06-05 | E-PROT-142 | ExpressionAtlas
Project description:Gene expression profiles from the hepatocellular carcinoma (HCC) tissues
2025-01-24 | E-GEOD-33006 | ExpressionAtlas
Project description:Expression profiling of PBMC from patients with hepatocellular carcinoma
2025-01-24 | E-GEOD-49515 | ExpressionAtlas