Author:
Godfrey Laura K.,Forster Jan,Liffers Sven-Thorsten,Schröder Christopher,Köster Johannes,Henschel Leonie,Ludwig Kerstin U.,Lähnemann David,Trajkovic-Arsic Marija,Behrens Diana,Scarpa Aldo,Lawlor Rita T.,Witzke Kathrin E.,Sitek Barbara,Johnsen Steven A.,Rahmann Sven,Horsthemke Bernhard,Zeschnigk Michael,Siveke Jens T.
Abstract
Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. It is marked by extraordinary resistance to conventional therapies including chemotherapy and radiation, as well as to essentially all targeted therapies evaluated so far. More than 90% of PDAC cases harbor an activating KRAS mutation. As the most common KRAS variants in PDAC remain undruggable so far, it seemed promising to inhibit a downstream target in the MAPK pathway such as MEK1/2, but up to now preclinical and clinical evaluation of MEK inhibitors (MEKi) failed due to inherent and acquired resistance mechanisms. To gain insights into molecular changes during the formation of resistance to oncogenic MAPK pathway inhibition, we utilized short-term passaged primary tumor cells from ten PDACs of genetically engineered mice. We followed gain and loss of resistance upon MEKi exposure and withdrawal by longitudinal integrative analysis of whole genome sequencing, whole genome bisulfite sequencing, RNA-sequencing and mass spectrometry data.
Results
We found that resistant cell populations under increasing MEKi treatment evolved by the expansion of a single clone but were not a direct consequence of known resistance-conferring mutations. Rather, resistant cells showed adaptive DNA hypermethylation of 209 and hypomethylation of 8 genomic sites, most of which overlap with regulatory elements known to be active in murine PDAC cells. Both DNA methylation changes and MEKi resistance were transient and reversible upon drug withdrawal. Furthermore, MEKi resistance could be reversed by DNA methyltransferase inhibition with remarkable sensitivity exclusively in the resistant cells.
Conclusion
Overall, the concept of acquired therapy resistance as a result of the expansion of a single cell clone with epigenetic plasticity sheds light on genetic, epigenetic and phenotypic patterns during evolvement of treatment resistance in a tumor with high adaptive capabilities and provides potential for reversion through epigenetic targeting.
Funder
Deutsche Forschungsgemeinschaft
Associazione Italiana per la Ricerca sul Cancro
Fondazione Cassa di Risparmio di Verona Vicenza Belluno e Ancona
Ministry of Science, North Rhine-Westphalia, Germany.
German Federal Ministry of Education and Research
Ministry of Culture and Science of the State of North Rhine-Westphalia
Universitätsklinikum Essen
Publisher
Springer Science and Business Media LLC
Subject
Genetics (clinical),Developmental Biology,Genetics,Molecular Biology