The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

Johanna Klughammer, Barbara Kiesel, Thomas Roetzer, Nikolaus Fortelny, Amelie Nemc, Karl-Heinz Nenning, Julia Furtner, Nathan C. Sheffield, Paul Datlinger, Nadine Peter, Martha Nowosielski, Marco Augustin, Mario Mischkulnig, Thomas Ströbel, Donat Alpar, Bekir Ergüner, Martin Senekowitsch, Patrizia Moser, Christian F. Freyschlag, Johannes Kerschbaumer, Claudius Thomé, Astrid E. Grams, Günther Stockhammer, Melitta Kitzwoegerer, Stefan Oberndorfer, Franz Marhold, Serge Weis, Johannes Trenkler, Johanna Buchroithner, Josef Pichler, Johannes Haybaeck, Stefanie Krassnig, Kariem Mahdy Ali, Gord von Campe, Franz Payer, Camillo Sherif, Julius Preiser, Thomas Hauser, Peter A. Winkler, Waltraud Kleindienst, Franz Würtz, Tanisa Brandner-Kokalj, Martin Stultschnig, Stefan Schweiger, Karin Dieckmann, Matthias Preusser, Georg Langs, Bernhard Baumann, Engelbert Knosp, Georg Widhalm, Christine Marosi, Johannes A. Hainfellner, Adelheid Woehrer, Christoph Bock

Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we present genome-scale maps of DNA methylation in matched primary and recurring glioblastoma tumors, using data from a highly annotated clinical cohort that was selected through a national patient registry. We demonstrate the feasibility of DNA methylation mapping in a large set of routinely collected FFPE samples, and we validate bisulfite sequencing as a multipurpose assay that allowed us to infer a range of different genetic, epigenetic, and transcriptional characteristics of the profiled tumor samples. On the basis of these data, we identified subtle differences between primary and recurring tumors, links between DNA methylation and the tumor microenvironment, and an association of epigenetic tumor heterogeneity with patient survival. In summary, this study establishes an open resource for dissecting DNA methylation heterogeneity in a genetically diverse and heterogeneous cancer, and it demonstrates the feasibility of integrating epigenomics, radiology, and digital pathology for a national cohort, thereby leveraging existing samples and data collected as part of routine clinical practice.