title: Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma.
abstract: 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.
  
  
  
  Dose escalation of the alkylating agent mafosfamide was used to create a series of increasingly drug-resistant 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.
  
  
  
  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 (Immgen.org), we showed that these transcriptional changes track the B-cell maturation axis.
  
  
  
  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.
authors.affiliation: Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.|Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
authors.forename: Colin
authors.initials: C
authors.lastname: Flinders
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Larry
authors.initials: L
authors.lastname: Lam
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Liudmilla
authors.initials: L
authors.lastname: Rubbi
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Roberto
authors.initials: R
authors.lastname: Ferrari
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Sorel
authors.initials: S
authors.lastname: Fitz-Gibbon
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Heather
authors.initials: H
authors.lastname: Christofk
authors.affiliation: Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.|Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
authors.forename: David
authors.initials: D
authors.lastname: B Agus
authors.affiliation: Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.|Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ruderman
authors.affiliation: Canary Center, Stanford University, Palo Alto, CA, 94305, USA. paragm@stanford.edu.|Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA. paragm@stanford.edu.
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA. matteop@mcdb.ucla.edu.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
mesh_terms: D000818:Animals; D000970:Antineoplastic Agents / Q000378:metabolism*; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism*; D002051:Burkitt Lymphoma / Q000188:drug therapy* / Q000235:genetics*; D045744:Cell Line, Tumor; D003520:Cyclophosphamide / Q000031:analogs & derivatives / Q000494:pharmacology; D019175:DNA Methylation; D019008:Drug Resistance, Neoplasm; D044127:Epigenesis, Genetic / Q000187:drug effects; D006657:Histones / Q000378:metabolism; D006801:Humans; D051379:Mice; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism*; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic
chemical_list: D000970:Antineoplastic Agents; D051792:Basic Helix-Loop-Helix Proteins; D003520:Cyclophosphamide; D006657:Histones; D063151:Polycomb Repressive Complex 2; C075668:Tcf3 protein, mouse; C048341:mafosfamide
keywords: Burkitt’s lymphoma; Epigenetics; Histone; Mafosfamide; Methylation; Resistance