Integrated DNA methylation analysis identifies topographical and tumoral biomarkers in pilocytic astrocytomas

Abstract

// Manila Antonelli 1, * , Antonio Fadda 2, * , Eleonora Loi 2 , Loredana Moi 2, 3 , Cesare Zavattari 4 , Pia Sulas 5 , Davide Gentilini 6, 7 , Cinzia Cameli 8 , Elena Bacchelli 8 , Manuela Badiali 3 , Antonella Arcella 9 , Isabella Morra 10 , Felice Giangaspero 1, 9 and Patrizia Zavattari 2 1 Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy 2 Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy 3 Bone Marrow Transplantation Unit, Microcitemico Children's Hospital, Cagliari, Italy 4 Independent Researcher, Machine Learning, Lucca, Italy 5 Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy 6 Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy 7 Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy 8 Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy 9 IRCCS Neuromed, Pozzilli, Italy 10 Department of Pathology OIRM-S, Anna Hospital, A.O.U. City of Health and Science, Turin, Italy * These authors contributed equally to this work Correspondence to: Patrizia Zavattari, email: pzavattari@unica.it Keywords: pilocytic astrocytomas; methylome alteration; topographic and tumor biomarkers; gene expression alteration; human methylation beadchips Received: October 19, 2017      Accepted: January 31, 2018      Published: February 12, 2018 ABSTRACT Pilocytic astrocytoma (PA) is the most common glioma in pediatric patients and occurs in different locations. Chromosomal alterations are mostly located at chromosome 7q34 comprising the BRAF oncogene with consequent activation of the mitogen-activated protein kinase pathway. Although genetic and epigenetic alterations characterizing PA from different localizations have been reported, the role of epigenetic alterations in PA development is still not clear. The aim of this study was to investigate whether distinctive methylation patterns may define biologically relevant groups of PAs. Integrated DNA methylation analysis was performed on 20 PAs and 4 normal brain samples by Illumina Infinium HumanMethylation27 BeadChips. We identified distinct methylation profiles characterizing PAs from different locations (infratentorial vs supratentorial) and tumors with onset before and after 3 years of age. These results suggest that PA may be related to the specific brain site where the tumor arises from region-specific cells of origin. We identified and validated in silico the methylation alterations of some CpG islands. Furthermore, we evaluated the expression levels of selected differentially methylated genes and identified two biomarkers, one, IRX2 , related to the tumor localization and the other, TOX2 , as tumoral biomarker.