title: Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma.
abstract: BACKGROUND
  Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5-8.7 % of CRCs. It has been shown that SAC has a worse prognosis and different histological and molecular features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile.
  
  
  RESULTS
  The methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array was investigated in 103 colorectal specimens, including 39 SACs and 34 matched CCs, from Spanish and Finnish patients. Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA and protein level using pyrosequencing, methylation-specific PCR, quantitative polymerase chain reaction (qPCR) and immunohistochemistry. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing SAC with CRC showing molecular and histological features of high-level microsatellite instability.
  
  
  CONCLUSIONS
  This methylome study demonstrates distinct epigenetic regulation patterns in SAC which are consistent to previous expression profile studies and that DIO3 and FOXD2 might be molecular targets for a specific histology-oriented treatment of CRC.
authors.affiliation: Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain ; Facultad de Ciencias de la Salud, Catholic University of Murcia (UCAM), Murcia, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Conesa-Zamora
authors.affiliation: Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain ; Facultad de Ciencias de la Salud, Catholic University of Murcia (UCAM), Murcia, Spain.
authors.forename: José
authors.initials: J
authors.lastname: García-Solano
authors.affiliation: Francisco de Vitoria University, Madrid, Spain.
authors.forename: María Del Carmen
authors.initials: Mdel C
authors.lastname: Turpin
authors.affiliation: Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Yúfera, 3, 46012 Valencia, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sebastián-León
authors.affiliation: Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Torres-Moreno
authors.affiliation: Department of Social Psychology and Methodology, Autónoma University, Madrid, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Estrada
authors.affiliation: Department of Pathology, University of Oulu, Oulu, Finland.
authors.forename: Anne
authors.initials: A
authors.lastname: Tuomisto
authors.affiliation: Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
authors.forename: Jamie
authors.initials: J
authors.lastname: Wilce
authors.affiliation: Department of Pathology, University of Oulu, Oulu, Finland.
authors.forename: Markus J
authors.initials: MJ
authors.lastname: Mäkinen
authors.affiliation: Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pérez-Guillermo
authors.affiliation: Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Yúfera, 3, 46012 Valencia, Spain ; Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
keywords: Colorectal cancer; CpG island; DIO3; FOXD2; Methylome; Microarray analysis; Pyrosequencing; Serrated carcinoma