A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples
dc.contributor.author | Gallardo-Gómez, María | |
dc.contributor.author | Moran, Sebastian | |
dc.contributor.author | Páez de la Cadena, María | |
dc.contributor.author | Martínez-Zorzano, Vicenta Soledad | |
dc.contributor.author | Rodríguez-Berrocal, Francisco Javier | |
dc.contributor.author | Rodríguez-Girondo, Mar | |
dc.contributor.author | Esteller, Manel | |
dc.contributor.author | Cubiella, Joaquín | |
dc.contributor.author | Bujanda Fernández de Pierola, Luis | |
dc.contributor.author | Castells, Antoni | |
dc.contributor.author | Balaguer, Francesc | |
dc.contributor.author | Jover, Rodrigo | |
dc.contributor.author | De Chiara, Loretta | |
dc.date.accessioned | 2019-04-05T07:27:50Z | |
dc.date.available | 2019-04-05T07:27:50Z | |
dc.date.issued | 2018-04-16 | |
dc.identifier.citation | Clinical Epigenetics 10 : (2018) // Article ID 53 | es_ES |
dc.identifier.issn | 1868-7083 | |
dc.identifier.uri | http://hdl.handle.net/10810/32344 | |
dc.description.abstract | Background: Colorectal cancer is the fourth cause of cancer-related deaths worldwide, though detection at early stages associates with good prognosis. Thus, there is a clear demand for novel non-invasive tests for the early detection of colorectal cancer and premalignant advanced adenomas, to be used in population-wide screening programs. Aberrant DNA methylation detected in liquid biopsies, such as serum circulating cell-free DNA (cfDNA), is a promising source of non-invasive biomarkers. This study aimed to assess the feasibility of using cfDNA pooled samples to identify potential serum methylation biomarkers for the detection of advanced colorectal neoplasia (colorectal cancer or advanced adenomas) using microarray-based technology. Results: cfDNA was extracted from serum samples from 20 individuals with no colorectal findings, 20 patients with advanced adenomas, and 20 patients with colorectal cancer (stages I and II). Two pooled samples were prepared for each pathological group using equal amounts of cfDNA from 10 individuals, sex-, age-, and recruitment hospital-matched. We measured the methylation levels of 866,836 CpG positions across the genome using the MethylationEPIC array. Pooled serum cfDNA methylation data meets the quality requirements. The proportion of detected CpG in all pools (> 99% with detection p value < 0.01) exceeded Illumina Infinium methylation data quality metrics of the number of sites detected. The differential methylation analysis revealed 1384 CpG sites (5% false discovery rate) with at least 10% difference in the methylation level between no colorectal findings controls and advanced neoplasia, the majority of which were hypomethylated. Unsupervised clustering showed that cfDNA methylation patterns can distinguish advanced neoplasia from healthy controls, as well as separate tumor tissue from healthy mucosa in an independent dataset We also observed that advanced adenomas and stage I/II colorectal cancer methylation profiles, grouped as advanced neoplasia, are largely homogenous and clustered close together. Conclusions: This preliminary study shows the viability of microarray-based methylation biomarker discovery using pooled serum cfDNA samples as an alternative approach to tissue specimens. Our strategy sets an open door for deciphering new non-invasive biomarkers not only for colorectal cancer detection, but also for other types of cancers. | es_ES |
dc.description.sponsorship | This work received funding from Plan Nacional I + D + I 2015-2018 (Accion Estrategica en Salud) Instituto de Salud Carlos III (Spain)-FEDER (PI15/02007), "Fundacion Cientifica de la Asociacion Espanola contra el Cancer" (GCB13131592CAST), and support from Centro Singular de Investigacion de Galicia (Conselleria de Cultura, Educacion e Ordenacion Universitaria) (ED431G/02, Xunta de Galicia and FEDER- European Union). Maria Gallardo-Gomez is supported by a predoctoral fellowship from Ministerio de Educacion, Cultura y Deporte (Spanish Government) (FPU15/02350). | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Biomed Central | es_ES |
dc.rights | info:eu-repo/semantics/openAccess | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/es/ | * |
dc.subject | advanced adenomas | es_ES |
dc.subject | circulating cell-free dna | es_ES |
dc.subject | colorectal cancer | es_ES |
dc.subject | dna methylation | es_ES |
dc.subject | methylationepic | es_ES |
dc.subject | non-invasive diagnostic biomarkers | es_ES |
dc.subject | pooled samples | es_ES |
dc.subject | serum large-scale association | es_ES |
dc.subject | human genome | es_ES |
dc.subject | hypomethylation | es_ES |
dc.subject | neoplasms | es_ES |
dc.subject | benign | es_ES |
dc.subject | tool | es_ES |
dc.title | A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.rights.holder | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | es_ES |
dc.rights.holder | Atribución 3.0 España | * |
dc.relation.publisherversion | https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-018-0487-y | es_ES |
dc.identifier.doi | 10.1186/s13148-018-0487-y | |
dc.departamentoes | Medicina | es_ES |
dc.departamentoeu | Medikuntza | es_ES |
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