title: DNA methylation profiling of esophageal adenocarcinoma using Methylation Ligation-dependent Macroarray (MLM).
abstract: Most types of cancer cells are characterized by aberrant methylation of promoter genes. In this study, we described a rapid, reproducible, and relatively inexpensive approach allowing the detection of multiple human methylated promoter genes from many tissue samples, without the need of bisulfite conversion. The Methylation Ligation-dependent Macroarray (MLM), an array-based analysis, was designed in order to measure methylation levels of 58 genes previously described as putative biomarkers of cancer. The performance of the design was proven by screening the methylation profile of DNA from esophageal cell lines, as well as microdissected formalin-fixed and paraffin-embedded (FFPE) tissues from esophageal adenocarcinoma (EAC). Using the MLM approach, we identified 32 (55%) hypermethylated promoters in EAC, and not or rarely methylated in normal tissues. Among them, 21promoters were found aberrantly methylated in more than half of tumors. Moreover, seven of them (ADAMTS18, APC, DKK2, FOXL2, GPX3, TIMP3 and WIF1) were found aberrantly methylated in all or almost all the tumor samples, suggesting an important role for these genes in EAC. In addition, dysregulation of the Wnt pathway with hypermethylation of several Wnt antagonist genes was frequently observed. MLM revealed a homogeneous pattern of methylation for a majority of tumors which were associated with an advanced stage at presentation and a poor prognosis. Interestingly, the few tumors presenting less methylation changes had a lower pathological stage. In conclusion, this study demonstrated the feasibility and accuracy of MLM for DNA methylation profiling of FFPE tissue samples.
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Guilleret
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy. Electronic address: lorena.losi@unimore.it.
authors.forename: Lorena
authors.initials: L
authors.lastname: Losi
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
authors.forename: Sonia T
authors.initials: ST
authors.lastname: Chelbi
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Fonda
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland; Aurigen, Centre de Génétique et Pathologie, 1004 Lausanne, Switzerland.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Bougel
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Saponaro
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy.
authors.forename: Gaia
authors.initials: G
authors.lastname: Gozzi
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
authors.forename: Loredana
authors.initials: L
authors.lastname: Alberti
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
authors.forename: Richard
authors.initials: R
authors.lastname: Braunschweig
authors.affiliation: Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland; Aurigen, Centre de Génétique et Pathologie, 1004 Lausanne, Switzerland. Electronic address: jean.benhattar@gmail.com.
authors.forename: Jean
authors.initials: J
authors.lastname: Benhattar
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D014408:Biomarkers, Tumor / Q000235:genetics; D045744:Cell Line, Tumor; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology; D005240:Feasibility Studies; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D046228:Microarray Analysis / Q000379:methods; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000379:methods; D011401:Promoter Regions, Genetic / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D016707:Tissue Fixation; D060449:Wnt Signaling Pathway / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; D005404:Fixatives; D005557:Formaldehyde
keywords: DNA methylation; Esophageal adenocarcinoma; FFPE; Profiling