The Role of DNMT3B in the DNA Methylation of Cancer Cells

Summary

Principal Investigator: LUCY ANN GODLEY
Affiliation: University of Chicago
Country: USA
Abstract: Epigenetic changes, such as DNA methylation and histone modifications, alter chromatin structure and regulate gene transcription. Cancer cells are characterized by abnormal DNA methylation: Repetitive DNA sequences and some gene promoters are hypomethylated and transcriptionally active, whereas many tumor suppressor gene promoters are hypermethylated and transcriptionally inactive without the presence of mutations. My laboratory discovered that cancer cells exhibit aberrant splicing of the DNMT3B gene, which encodes one of the three DNA methyltransferases. The aberrant splicing produces DNMT3B transcripts containing premature stop codons and encoding truncated proteins lacking the catalytic domain. Tissue culture cells expressing DNMT3B7, the most frequently observed aberrant DNMT3B transcript in cancer cells, show DNA methylation changes that correlate with altered gene expression. Furthermore, transgenic mice that express DNMT3B7 display disrupted embryonic development and changes in DNA methylation that are dependent on DNMT3B7 transgene levels. We hypothesize that truncated DNMT3B proteins influence DNA methylation in cancer cells, and we propose to test this idea using three Specific Aims: (1) To examine the effect of DNMT3B7 on mouse development by: (A) determining the pattern of DNMT3B7 transgene expression within embryos by in situ hybridization;and (B) examining the effects of DNMT3B7 transgene expression on DNA methylation, histone modifications, and gene expression;(2) To study the effect of DNMT3B7 expression on the DNA methylation patterns and phenotypes of cancer cells by: (A) inhibiting DNMT3B7 expression in breast cancer cells via shRNA and examining the effects on DNA methylation;(B) correlating DNMT3B7 expression with particular phenotypes in two distinctive types of neuroblastoma cell lines;and (C) quantifying DNMT3B7 levels in primary leukemia samples and correlating those with DNA methylation levels;and (3) To determine how DNMT3B7 could alter DNA methylation by: (A) testing the predictions of our models, and (B) further characterizing the interactions between DNMT3B/DNMT3B7 and three exciting interacting proteins, ZNF445, CHTF18, and NPM. Our proposed studies address the mechanism by which epigenetic alterations originate within cancer cells. The knowledge gained from the proposed work is likely to provide a basis for novel diagnostic and therapeutic strategies applicable to virtually all forms of cancer. Moreover, the pathways found to mediate the effects of DNMT3B7 are likely to reveal paradigms common to other processes that use DNA methylation to control gene expression. PUBLIC HEALTH RELEVANCE: The DNA within a cell can be modified by methylation to alter its structure and affect gene expression. DNA methylation is involved in many normal cellular processes and is abnormally distributed in cancer cells, leading to some of the phenotypes of cancer cells. The mechanism by which cancer cells acquire and maintain abnormal DNA methylation is not understood. We have discovered that cancer cells express shortened forms of DNMT3B, one of the enzymes that carries out the DNA methylation reaction, and we hypothesize that truncated DNMT3B proteins contribute to abnormal DNA methylation patterns in cancer cells. The knowledge gained from the proposed experiments is likely to provide a basis for novel diagnostic and therapeutic strategies that will be applicable to virtually all forms of cancer. Furthermore, the cellular pathways found to mediate the effects of truncated DNMT3B proteins are likely to reveal paradigms common to other processes that involve DNA methylation, such as mammalian embryonic development, X-chromosome inactivation, genomic imprinting, and aging.
Funding Period: ----------------2008 - ---------------2013-
more information: NIH RePORT

Top Publications

  1. pmc Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins
    K R Ostler
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Oncogene 26:5553-63. 2007
  2. pmc Mechanism-based epigenetic chemosensitization therapy of diffuse large B-cell lymphoma
    Thomas Clozel
    1Division of Hematology and Oncology, Department of Medicine, 2Division of Biostatistics and Epidemiology, Department of Public Health, 3Weill Cornell Cancer Center, and Departments of 4Pathology and 5Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York 6Section of Hematology Oncology, Department of Medicine, The University of Chicago Department of Pathology, Northwestern University, Chicago, Illinois 8Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec 9Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada 10IBM Research, Rio de Janeiro, Brazil and 11Department of Oncological Sciences, University of Turin, Turin, Italy
    Cancer Discov 3:1002-19. 2013
  3. pmc Dnmt3b is a haploinsufficient tumor suppressor gene in Myc-induced lymphomagenesis
    Aparna Vasanthakumar
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Blood 121:2059-63. 2013
  4. pmc Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis
    Lambert Busque
    Research Centre, Maisonneuve Rosemont Hospital, Montreal, Quebec, Canada
    Nat Genet 44:1179-81. 2012
  5. pmc Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma
    Kelly R Ostler
    Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
    Cancer Res 72:4714-23. 2012
  6. pmc Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis
    Jozef Madzo
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Cell Rep 6:231-44. 2014
  7. pmc DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation
    Rita Shaknovich
    Division of Hematology Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
    Blood 118:3559-69. 2011
  8. pmc Inhibition of TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine disturbs erythroid and granulomonocytic differentiation of human hematopoietic progenitors
    Elodie Pronier
    INSERM, U1009, Institut Gustave Roussy, Villejuif, France
    Blood 118:2551-5. 2011
  9. pmc Dnmt3a is essential for hematopoietic stem cell differentiation
    Grant A Challen
    Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 44:23-31. 2012
  10. pmc Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia
    Jumpei Yamazaki
    Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Epigenetics 7:201-7. 2012

Detail Information

Publications15

  1. pmc Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins
    K R Ostler
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Oncogene 26:5553-63. 2007
    ..These results suggest that truncated DNMT3B proteins could play a role in the abnormal distribution of DNA methylation found in cancer cells...
  2. pmc Mechanism-based epigenetic chemosensitization therapy of diffuse large B-cell lymphoma
    Thomas Clozel
    1Division of Hematology and Oncology, Department of Medicine, 2Division of Biostatistics and Epidemiology, Department of Public Health, 3Weill Cornell Cancer Center, and Departments of 4Pathology and 5Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York 6Section of Hematology Oncology, Department of Medicine, The University of Chicago Department of Pathology, Northwestern University, Chicago, Illinois 8Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec 9Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada 10IBM Research, Rio de Janeiro, Brazil and 11Department of Oncological Sciences, University of Turin, Turin, Italy
    Cancer Discov 3:1002-19. 2013
    ..Pre- and post-azacitidine treatment biopsies confirmed SMAD1 demethylation and chemosensitization, delineating a personalized strategy for the clinical use of DNMTIs...
  3. pmc Dnmt3b is a haploinsufficient tumor suppressor gene in Myc-induced lymphomagenesis
    Aparna Vasanthakumar
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Blood 121:2059-63. 2013
    ..This study offers insight into how de novo DNA methyltransferases function as tumor suppressors and the sensitivity of Myc-induced lymphomas to DNA methylation...
  4. pmc Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis
    Lambert Busque
    Research Centre, Maisonneuve Rosemont Hospital, Montreal, Quebec, Canada
    Nat Genet 44:1179-81. 2012
    ..TET2 mutations were specific to individuals with clonal hematopoiesis without hematological malignancies and were associated with alterations in DNA methylation...
  5. pmc Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma
    Kelly R Ostler
    Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
    Cancer Res 72:4714-23. 2012
    ..Our results indicate that DNMT3B7 modifies the epigenome in neuroblastoma cells to induce changes in gene expression, inhibit tumor growth, and increase sensitivity to ATRA...
  6. pmc Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis
    Jozef Madzo
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Cell Rep 6:231-44. 2014
    ....
  7. pmc DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation
    Rita Shaknovich
    Division of Hematology Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
    Blood 118:3559-69. 2011
    ..Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair...
  8. pmc Inhibition of TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine disturbs erythroid and granulomonocytic differentiation of human hematopoietic progenitors
    Elodie Pronier
    INSERM, U1009, Institut Gustave Roussy, Villejuif, France
    Blood 118:2551-5. 2011
    ..Our results indicate that TET2 disruption affects 5-hmC levels in human myeloid cells and participates in the pathogenesis of myeloid malignancies through the disturbance of myeloid differentiation...
  9. pmc Dnmt3a is essential for hematopoietic stem cell differentiation
    Grant A Challen
    Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 44:23-31. 2012
    ..These data establish Dnmt3a as a critical participant in the epigenetic silencing of HSC regulatory genes, thereby enabling efficient differentiation...
  10. pmc Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia
    Jumpei Yamazaki
    Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Epigenetics 7:201-7. 2012
    ..0% and 9.8%, respectively) (p = 0.016). Thus, TET2 mutations affect global methylation in CMML but most of the changes are likely to be outside gene promoters...
  11. doi TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis
    Cyril Quivoron
    INSERM, U, Villejuif, France
    Cancer Cell 20:25-38. 2011
    ....
  12. pmc Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation
    Kelly Moran-Crusio
    Department of Pathology, NYU Cancer Institute, New York University School of Medicine, NY 10016, USA
    Cancer Cell 20:11-24. 2011
    ..In addition, Tet2(+/-) mice also displayed increased stem cell self-renewal and extramedullary hematopoiesis, suggesting that Tet2 haploinsufficiency contributes to hematopoietic transformation in vivo...
  13. pmc DNMT3B7, a truncated DNMT3B isoform expressed in human tumors, disrupts embryonic development and accelerates lymphomagenesis
    Mrinal Y Shah
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois 60637 1470, USA
    Cancer Res 70:5840-50. 2010
    ..These data represent the first in vivo modeling of cancer-associated DNA methylation changes and suggest that truncated DNMT3B isoforms contribute to the redistribution of DNA methylation characterizing virtually every human tumor...
  14. pmc 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging
    Keith E Szulwach
    Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
    Nat Neurosci 14:1607-16. 2011
    ..These data suggest that 5-hmC-mediated epigenetic modification is critical in neurodevelopment and diseases...