Regulation of Genomic and Epigenomic Stability at CpG Sites

Summary

Principal Investigator: Alfonso Bellacosa
Abstract: DESCRIPTION (provided by applicant): The overall goal of this project is to understand how two related mammalian base excision repair enzymes, MED1 and TDG, maintain genomic and epigenomic stability at CpG sites, by preventing both mutations and altered methylation patterns. DNA methylation is an important epigenetic modification of the mammalian genome consisting in the formation of 5-methylcytosine from cytosine at CpG sites. DNA methylation increases the risk of mutations, because both methylated and unmethylated cytosines have a tendency - higher for the former - to spontaneously deaminate, generating thymine and uracil, respectively. Indeed, deamination at CpG sites is estimated to cause nearly one-third of all mutations in cancer and human genetic diseases. In order to maintain genomic stability at CpG sites, MED1 (also known as MBD4) and TDG, remove the offending thymine or uracil. Organisms also establish and regulate the proper chromatin states/DNA methylation patterns at CpG sites (epigenomic stability). Alterations in epigenomic stability occur in cloned mammals as well as in cancer and thus have implications for both stem cell biology and cancer diagnosis/prognosis/treatment. We made the unexpected discovery of embryonic lethality associated with TDG nullizygosity and found that TDG is required for DNA demethylation at some CpG-rich promoters and modulation of other epigenetic states, such as histone H3 acetylation. These observations suggest a model in which MED1 and TDG promote both the genomic and epigenomic stability of CpG sites, in order to ward off against developmental defects, mutagenesis and tumorigenesis. The Specific Aims are: 1) Characterize the requirement of TDG during development and its role in DNA demethylation and chromatin modification. We will determine whether TDG catalytic activity is required for normal development using a knock-in strain and assess which TDG function is required for ES cell differentiation in vitro and for phenotypes in mouse embryo fibroblasts. We will also study by ChIP-seq the relationship between promoter occupancy by TDG and methylation patterns on a genomic scale;and determine whether TDG is involved in demethylation of the paternal genome after fertilization. 2) Evaluate the in vivo cooperation between MED1 and TDG in avoidance of mutations and altered methylation, by measuring: G:T and G:U mismatch repair in genetically defined cell lines (deficient in TDG, MED1 or both), mutation frequency and altered methylation of single- and MED1-TDG double-mutant mice. 3) Evaluate the role of MED1 and TDG in tumorigenesis. Using the Min mouse model, we will evaluate the role of MED1 and TDG in intestinal tumorigenesis. We will also analyze TDG alterations in human cancer. These studies will shed light on the emerging link between genomic and epigenomic stability at CpG sites and the employment of the DNA repair machinery to effect DNA demethylation. PUBLIC HEALTH RELEVANCE: Some DNA sequences in the genome, known as CpG, are frequently altered in cancer, both in terms of mutation to CpA or TpG, and in terms of change of their physiological modification called methylation. This project focuses on two DNA repair enzymes, MED1/MBD4 and TDG that prevent both CpG mutations and alterations in methylation, thus warding off against cancer and other diseases. These studies may lead to novel strategies for the diagnosis and treatment of cancer.
Funding Period: 1998-07-01 - 2015-04-30
more information: NIH RePORT

Top Publications

  1. pmc Epigenetic downregulation of the DNA repair gene MED1/MBD4 in colorectal and ovarian cancer
    J Harrison Howard
    Department of Surgery at The University of Alabama at Birmingham, USA
    Cancer Biol Ther 8:94-100. 2009
  2. pmc Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations
    Alfonso Bellacosa
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cancer Prev Res (Phila) 3:48-61. 2010
  3. ncbi Che-1 promotes tumor cell survival by sustaining mutant p53 transcription and inhibiting DNA damage response activation
    Tiziana Bruno
    Department of Therapeutic Programs Development, Regina Elena Cancer Institute, Rome, Italy
    Cancer Cell 18:122-34. 2010
  4. pmc APC +/- alters colonic fibroblast proteome in FAP
    Bhavinkumar B Patel
    Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    Oncotarget 2:197-208. 2011
  5. pmc Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair
    Salvatore Cortellino
    Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cell 146:67-79. 2011
  6. pmc Beta-catenin inhibits melanocyte migration but induces melanoma metastasis
    S J Gallagher
    Centre de Recherche, Developmental Genetics of Melanocytes, Institut Curie, Orsay, France
    Oncogene 32:2230-8. 2013
  7. pmc Dose dependent effects on cell cycle checkpoints and DNA repair by bendamustine
    Neil Beeharry
    Basic Science Division, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 7:e40342. 2012
  8. pmc DNA demethylation by TDG
    Shannon R Dalton
    Cancer Biology Program, Epigenetics and Progenitor Cells Program, Fox Chase Cancer Center, PA 19111, USA
    Epigenomics 4:459-67. 2012
  9. pmc BCR-ABL1 kinase inhibits uracil DNA glycosylase UNG2 to enhance oxidative DNA damage and stimulate genomic instability
    A Slupianek
    Department of Microbiology and Immunology, Temple University, Philadelphia, PA, USA
    Leukemia 27:629-34. 2013

Research Grants

Detail Information

Publications9

  1. pmc Epigenetic downregulation of the DNA repair gene MED1/MBD4 in colorectal and ovarian cancer
    J Harrison Howard
    Department of Surgery at The University of Alabama at Birmingham, USA
    Cancer Biol Ther 8:94-100. 2009
    ..Detection of MED1 methylation and gene suppression in normal colon mucosa may contribute to identifying patients at higher risk of developing CRC during screening procedures...
  2. pmc Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations
    Alfonso Bellacosa
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cancer Prev Res (Phila) 3:48-61. 2010
    ....
  3. ncbi Che-1 promotes tumor cell survival by sustaining mutant p53 transcription and inhibiting DNA damage response activation
    Tiziana Bruno
    Department of Therapeutic Programs Development, Regina Elena Cancer Institute, Rome, Italy
    Cancer Cell 18:122-34. 2010
    ..Notably, loss of Che-1 activates DNA damage checkpoint response and induces transactivation of p73. Therefore, these findings underline the important role that Che-1 has in survival of cells expressing mutant p53...
  4. pmc APC +/- alters colonic fibroblast proteome in FAP
    Bhavinkumar B Patel
    Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    Oncotarget 2:197-208. 2011
    ..The results indicate that heterozygosity for a mutant APC tumor suppressor gene alters the proteomes of both colon-derived normal fibroblasts in a gene-specific manner, consistent with a "one-hit" effect...
  5. pmc Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair
    Salvatore Cortellino
    Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Cell 146:67-79. 2011
    ....
  6. pmc Beta-catenin inhibits melanocyte migration but induces melanoma metastasis
    S J Gallagher
    Centre de Recherche, Developmental Genetics of Melanocytes, Institut Curie, Orsay, France
    Oncogene 32:2230-8. 2013
    ..These results highlight that metastasis formation requires a series of successful cellular processes, any one of which may not be optimally efficient...
  7. pmc Dose dependent effects on cell cycle checkpoints and DNA repair by bendamustine
    Neil Beeharry
    Basic Science Division, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 7:e40342. 2012
    ..Sensitizing cells to killing by BDM can be achieved by inhibiting base-excision repair or disrupting the DNA damage checkpoint pathway...
  8. pmc DNA demethylation by TDG
    Shannon R Dalton
    Cancer Biology Program, Epigenetics and Progenitor Cells Program, Fox Chase Cancer Center, PA 19111, USA
    Epigenomics 4:459-67. 2012
    ..In this article, we review the recent literature highlighting the prominent role played in active DNA demethylation by base excision repair and especially by TDG...
  9. pmc BCR-ABL1 kinase inhibits uracil DNA glycosylase UNG2 to enhance oxidative DNA damage and stimulate genomic instability
    A Slupianek
    Department of Microbiology and Immunology, Temple University, Philadelphia, PA, USA
    Leukemia 27:629-34. 2013
    ....

Research Grants30

  1. Genetics of DNA methylation patterning of arabidopsis.
    Steven E Jacobsen; Fiscal Year: 2013
    ..Thus a further understanding of the DNA methylation may someday lead to methods for correcting DNA methylation patterning defects. ..
  2. Functional Analysis of the Embryonic Epigenome in a Non-rodent Model
    Mark E Westhusin; Fiscal Year: 2013
    ....
  3. Frontotemporal Dementias: Genotypes and Phenotypes
    Virginia M Lee; Fiscal Year: 2013
    ..elegans and transgenic mouse models. The proposed studies will provide important insights into mechanisms of FTLD and the diagnosis and treatment of these disorders. ..