Genomes and Genes
Regulation of Genomic and Epigenomic Stability at CpG Sites
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
- Epigenetic downregulation of the DNA repair gene MED1/MBD4 in colorectal and ovarian cancerJ 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...
- Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutationsAlfonso Bellacosa
Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Cancer Prev Res (Phila) 3:48-61. 2010....
- Che-1 promotes tumor cell survival by sustaining mutant p53 transcription and inhibiting DNA damage response activationTiziana 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...
- APC +/- alters colonic fibroblast proteome in FAPBhavinkumar 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...
- Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repairSalvatore Cortellino
Cancer Biology Program and Epigenetics and Progenitor Cells Keystone Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Cell 146:67-79. 2011....
- Beta-catenin inhibits melanocyte migration but induces melanoma metastasisS 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...
- Dose dependent effects on cell cycle checkpoints and DNA repair by bendamustineNeil 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...
- DNA demethylation by TDGShannon 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...
- BCR-ABL1 kinase inhibits uracil DNA glycosylase UNG2 to enhance oxidative DNA damage and stimulate genomic instabilityA Slupianek
Department of Microbiology and Immunology, Temple University, Philadelphia, PA, USA
Leukemia 27:629-34. 2013....
- 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. ..
- Functional Analysis of the Embryonic Epigenome in a Non-rodent ModelMark E Westhusin; Fiscal Year: 2013....
- Frontotemporal Dementias: Genotypes and PhenotypesVirginia 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. ..