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Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

ABSTRACT: Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

PROVIDER: PRJNA638395 | ENA |

REPOSITORIES: ENA

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Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

Project description:Pancreatic cancers are typically diagnosed at late stage where disease prognosis is poor as exemplified by a 5-year survival rate of 10%. Earlier diagnosis would be beneficial by enabling surgical resection or earlier application of therapeutic regimens. We investigated non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by interrogating changes in 5-hydroxymethylation cytosines (5hmC) of circulating cell free DNA in the plasma of a PDAC cohort (n=64) in comparison with a non-cancer cohort (n=243). 5hmC density is reduced in promoters and enhancers, whereas it is increased over 3’UTR, intron and TTS regions in PDAC compared to non-cancer cfDNA. Differential hydromethylation is rampant and found in thousands of genes. Stringent filtering by significance reveals genes related to pancreas function or development (GATA4, GATA6, PROX1, ONECUT1, MEIS2), and/or cancer pathogenesis (YAP1, TEAD1, PROX1, ONECUT1, ONECUT2 and IGF1). Furthermore, we observe enrichment for genes that are de-regulated upon activation of KRAS and inactivation of TP53, both of which are commonly observed in PDAC tumors. Regularized regression models, built using 5hmC densities in genes with the most variable 5hmC counts, performed with AUC of 0.92 on discovery dataset and 0.92-0.94 on two independent test sets. Furthermore, investigation of 5hmC occupancy in PDAC tumor tissue revealed that tissue-derived features can be used to accurately classify PDAC cfDNA (AUC=0.88). These findings suggest that 5hmC changes, at least partially derived from tumor tissue, enable classification of PDAC patients with high fidelity and are worth further investigation on larger cohorts of patient samples.

2020-08-26 | GSE152137 | GEO

Cell-free DNA 5-hydroxymethylcytosine as a marker for common cancer detection

Project description:We used a highly sensitive nano-5hmC-Seal method and profiled the genome-wide distribution of 5-hydroxymethylcytosine (5hmC) in plasma cell-free DNA (cfDNA) from 384 patients with bladder, breast, colorectal, kidney, lung, or prostate cancer and 221 controls. We used machine learning and developed plasma cfDNA 5hmC signatures that are highly sensitive for cancer detection and cancer origin determination. We also identified genes and signaling pathways with aberrant DNA hydroxymethylation in six cancers.

2022-09-23 | GSE202988 | GEO

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA.

Project description:Pancreatic cancer is often detected late, when curative therapies are no longer possible. Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5-hydroxymethylcytosine (5hmC) changes in circulating cell free DNA from a PDAC cohort (n = 64) in comparison with a non-cancer cohort (n = 243). Differential hydroxymethylation is found in thousands of genes, most significantly in genes related to pancreas development or function (GATA4, GATA6, PROX1, ONECUT1, MEIS2), and cancer pathogenesis (YAP1, TEAD1, PROX1, IGF1). cfDNA hydroxymethylome in PDAC cohort is differentially enriched for genes that are commonly de-regulated in PDAC tumors upon activation of KRAS and inactivation of TP53. Regularized regression models built using 5hmC densities in genes perform with AUC of 0.92 (discovery dataset, n = 79) and 0.92-0.94 (two independent test sets, n = 228). Furthermore, tissue-derived 5hmC features can be used to classify PDAC cfDNA (AUC = 0.88). These findings suggest that 5hmC changes enable classification of PDAC even during early stage disease.

| S-EPMC7572413 | biostudies-literature

Cell-free DNA 5-hydroxymethylcytosine as a marker for common cancer detection

Project description:Cell-free DNA 5-hydroxymethylcytosine as a marker for common cancer detection

| PRJNA837976 | ENA

Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution

Project description:High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.

2018-10-09 | GSE112048 | GEO

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

Project description:Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

| PRJNA448064 | ENA

Cell-free DNA 5-hydroxymethylcytosine is highly sensitive for MRD assessment in acute myeloid leukemia

Project description:Measurable residual disease (MRD) is an important biomarker in acute myeloid leukemia (AML). However, MRD cannot be detected in many patients using current methods. We developed a highly sensitive 5-hydroxymethylcytosine (5hmC) signature in cell-free DNA by analyzing 115 AML patients and 86 controls. The 5hmC method detected MRD in 20 of 29 patients with negative MRD by multiparameter flow cytometry and 11 of 14 patients with negative MRD by molecular methods. MRD detection by the 5hmC method was significantly associated with relapse-free survival. This novel method can be used in most AML patients and may significantly impact AML patient management.

2023-12-31 | GSE237057 | GEO

A Model for the Early Diagnosis of Colorectal Cancer by the Detection of 5-hydroxymethylcytosine (5-hmC) in Plasma Cell-free DNA

Project description:In this study, the investigators establish a model for the early diagnosis of colorectal cancer based on detection of 5-hydroxymethylcytosine (5-hmC) in training group and validate the effectiveness of the model using a validation group.

| 2278673 | ecrin-mdr-crc

Circulating Tumor Cell(CTC) Isolation and Genonic varation Detection from Liquid Samples of Lung Cancer

Project description:We developed an enrichment-free, metabolic-based assay for rapid detection of tumor cells in the pleural effusion and peripheral blood samples. All nucleated cells are plated on microwell chips that contain 200,000 addressable microwells and then screened the chips. After candidate tumor cells were identified, retrieved single tumor cells with micromanipultor. To detection and analysis molecular characterization of these circulating tumor cells, we performed single cell whole genome amplification with multiple displacement amplification (MDA) technology and whole exome sequencing.

2017-02-17 | E-MTAB-4948 | biostudies-arrayexpress

Prognostic Value of Circulating Tumoral Free DNA Versus Circulating Tumoral Cells in Patients With Colorectal Cancer Stage II-III

Project description:After curative surgical resection, detection of metastatic lymph node remains the main prognostic validated criteria on which is based the decision of adjuvant therapy. To date, none of the molecular alterations, identified as potentially predictive factor, are used in routine for therapeutic decision. The circulating markers, either in the form of free circulating DNA or in the form of circulating tumoral cells seems important potential candidates. To investigators knowledge, only one study estimated with several interesting results the prognostic interest of a coupled detection of the free circulating mutant DNA (gene KRAS) and by the hypermethylation of the p16 gene. Definitive conclusions remain however difficult to achieve because of the small number of patient included (n=58) and the fact that this study included different stages. For colorectal cancer a Chinese team presented a series of results suggesting that the presence of CTC during the postoperative course is a factor significantly related to the risk of recurrence. In multivariate analysis integrating the lymph node status and the vascular invasion, the presence of CTC appeared as an independent factor for recurrence with a hazard ratio of 29.5. The aim of the present study is to compare the prognostic value of two circulating tumoral markers KRAS point mutations and RASSF2A methylation (free tumoral DNA) and Circulating tumoral cells (CTC). The primary objective is to compare sensibility and specificity of two circulating markers (free tumoral DNA and tumoral cells) on 2 years disease free survival rate. Secondary objective is to confirm the prognostic value of circulating free tumoral DNA and circulating tumoral cells in localised colorectal cancer.

| 2198606 | ecrin-mdr-crc

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