Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma

Background: The genetic origins of chemotherapy resistance are well established; however the role of epigenetics in drug resistance is less well understood To investigate mechanisms of drug resistance we performed systematic genetic epigenetic and transcriptomic analyses of an alkylating agent-sensitive murine lymphoma cell line and a series of resistant lines derived by drug dose escalation   Methods: Dose escalation of the alkylating agent mafosfamide was used to create a series of increasingly drugresistant mouse Burkitt's lymphoma cell lines Whole genome sequencing DNA microarrays reduced representation bisulfite sequencing and chromatin immunoprecipitation sequencing were used to identify alterations in DNA sequence mRNA expression CpG methylation and H3K27me3 occupancy respectively that were associated with increased resistance   Results: Our data suggest that acquired resistance cannot be explained by genetic alterations Based on integration of transcriptional profiles with transcription factor binding data we hypothesize that resistance is driven by epigenetic plasticity We observed that the resistant cells had H3K27me3 and DNA methylation profiles distinct from those of the parental lines Moreover we observed DNA methylation changes in the promoters of genes regulated by E2a and members of the polycomb repressor complex 2 (PRC2) and differentially expressed genes were enriched for targets of E2a The integrative analysis considering H3K27me3 further supported a role for PRC2 in mediating resistance By integrating our results with data from the Immunological Genome Project (Immgenorg) we showed that these transcriptional changes track the B-cell maturation axis   Conclusions: Our data suggest a novel mechanism of drug resistance in which E2a and PRC2 drive changes in the B-cell epigenome; these alterations attenuate alkylating agent treatment-induced apoptosis