CPG METHYLATION AND MUTATION

Summary

Principal Investigator: Gerd P Pfeifer
Abstract: Transcriptional gene silencing by hypermethylation of CpG islands spanning the promoter regions of genes is a common and important mechanism in carcinogenesis. Hypermethylation leads to inactivation of gene expression, and this epigenetic alteration is considered a key mechanism for long-term gene silencing. Despite of thousands of reports in the literature describing hypermethylation of specific genes in almost every type of human cancer, the mechanisms of CpG island hypermethylation have remained obscure. This application will focus on mechanistic studies that will investigate the molecular pathways leading to DNA methylation changes in tumors with emphasis on DNA hypermethylation. As a key technology to accomplish these goals, we have recently developed a method that enables the precise genome-wide analysis of DNA cytosine methylation patterns in mammalian DNA. Using genome-wide methylation profiling, we will analyze the extent by which chemical carcinogens can induce DNA methylation changes. Using cell culture models, we will expose non-transformed human cells (fibroblasts, bronchial epithelial cells and mammary epithelial cells) to several chemical carcinogens. We will analyze DNA methylation changes within 27,800 CpG islands and along the entire short arms of chromosomes 3, 7, and 9. DNA methylation changes will be analyzed in a mouse skin carcinogenesis model in order to determine if epigenetic changes arise during the initiation or promotion of stages of carcinogenesis. We will also analyze if the same carcinogens can induce changes in histone modification patterns that may subsequently predispose the CpG islands to de novo DNA methylation. In another Specific Aim, we will analyze the hypothesis that DNA methylation changes can be induced by endogenous mechanisms including inflammation and oxidative DNA damage. We will investigate inflammation-induced DNA methylation changes using a mouse model in which inflammation is associated with cancer susceptibility. It has been hypothesized that the Polycomb repression complex present in stem cells at specific gene loci accelerates or facilitates recruitment of DNA methyltransferases and de novo methylation of CpG-rich sequences during the process of cell transformation. We will test this hypothesis using a neural stem cell and brain tumor model, which includes neural stem cells, stem cell-like glioma cells, and DNA samples from glioma tumors. Finally, the connection between Ras transformation, the Polycomb complex and DNA hypermethylation will be analyzed. NIH3T3 cells and immortalized epithelial cells will be transformed with the activated K-ras oncogene. We will determine if K-ras-induced transformation operates through the Polycomb complex to promote de novo methylation of CpG islands. PUBLIC HEALTH RELEVANCE: Despite of thousands of reports in the literature describing hypermethylation of specific genes in almost every type of human cancer, the mechanisms of tumor-associated CpG island hypermethylation have remained obscure. This application will focus on mechanistic studies that will investigate the molecular pathways leading to DNA methylation changes in tumors with emphasis on DNA hypermethylation. We will investigate if chemical carcinogens, or endogenous processes such as inflammation and oxidative stress can induce changes in DNA methylation. In parallel, we will study molecular pathways involving the Polycomb repression complex that might operate during tumor progression to promote hypermethylation of CpG islands in malignant tissue.
Funding Period: 1999-10-01 - 2015-02-28
more information: NIH RePORT

Top Publications

  1. ncbi Investigating human cancer etiology by DNA lesion footprinting and mutagenicity analysis
    Ahmad Besaratinia
    Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
    Carcinogenesis 27:1526-37. 2006
  2. pmc CpG island hypermethylation in human astrocytomas
    Xiwei Wu
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
    Cancer Res 70:2718-27. 2010
  3. pmc DNA methylation profiling using the methylated-CpG island recovery assay (MIRA)
    Tibor A Rauch
    Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA
    Methods 52:213-7. 2010
  4. pmc Applications of the human p53 knock-in (Hupki) mouse model for human carcinogen testing
    Ahmad Besaratinia
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA
    FASEB J 24:2612-9. 2010
  5. pmc Investigating the epigenetic effects of a prototype smoke-derived carcinogen in human cells
    Stella Tommasi
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
    PLoS ONE 5:e10594. 2010
  6. pmc Identification of driver and passenger DNA methylation in cancer by epigenomic analysis
    Satish Kalari
    Department of Cancer Biology, Beckman Research Institute of the Cityof Hope, Duarte, CA, USA
    Adv Genet 70:277-308. 2010
  7. pmc Unveiling the methylation status of CpG dinucleotides in the substituted segment of the human p53 knock-in (Hupki) mouse genome
    Sang In Kim
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, USA
    Mol Carcinog 49:999-1006. 2010
  8. pmc Genomic mapping of 5-hydroxymethylcytosine in the human brain
    Seung Gi Jin
    Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
    Nucleic Acids Res 39:5015-24. 2011
  9. pmc Fen1 mutations that specifically disrupt its interaction with PCNA cause aneuploidy-associated cancer
    Li Zheng
    Department of Cancer Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
    Cell Res 21:1052-67. 2011
  10. pmc Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks
    Maria A Hahn
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
    PLoS ONE 6:e18844. 2011

Research Grants

Detail Information

Publications29

  1. ncbi Investigating human cancer etiology by DNA lesion footprinting and mutagenicity analysis
    Ahmad Besaratinia
    Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
    Carcinogenesis 27:1526-37. 2006
    ..We present examples of application of each of these methodologies to human cancer etiology, and provide prospective views on investigations using these technologies for carcinogenicity testing...
  2. pmc CpG island hypermethylation in human astrocytomas
    Xiwei Wu
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
    Cancer Res 70:2718-27. 2010
    ....
  3. pmc DNA methylation profiling using the methylated-CpG island recovery assay (MIRA)
    Tibor A Rauch
    Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA
    Methods 52:213-7. 2010
    ..The MIRA method is compatible with microarray and next generation DNA sequencing approaches. We describe the principles and details of this method applied for methylation profiling of genomes containing methylated CpG sequences...
  4. pmc Applications of the human p53 knock-in (Hupki) mouse model for human carcinogen testing
    Ahmad Besaratinia
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA
    FASEB J 24:2612-9. 2010
    ..We summarize the salient findings of the respective studies and discuss their relevance to human cancer etiology...
  5. pmc Investigating the epigenetic effects of a prototype smoke-derived carcinogen in human cells
    Stella Tommasi
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
    PLoS ONE 5:e10594. 2010
    ..Unveiling the initiating events that cause aberrant DNA methylation in lung cancer has tremendous public health relevance, as it can help define future strategies for early detection and prevention of this highly lethal disease...
  6. pmc Identification of driver and passenger DNA methylation in cancer by epigenomic analysis
    Satish Kalari
    Department of Cancer Biology, Beckman Research Institute of the Cityof Hope, Duarte, CA, USA
    Adv Genet 70:277-308. 2010
    ....
  7. pmc Unveiling the methylation status of CpG dinucleotides in the substituted segment of the human p53 knock-in (Hupki) mouse genome
    Sang In Kim
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, USA
    Mol Carcinog 49:999-1006. 2010
    ....
  8. pmc Genomic mapping of 5-hydroxymethylcytosine in the human brain
    Seung Gi Jin
    Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
    Nucleic Acids Res 39:5015-24. 2011
    ..Our data provide an overview of the genomic distribution of 5hmC in human brain and will set the stage for further functional characterization of this novel DNA modification...
  9. pmc Fen1 mutations that specifically disrupt its interaction with PCNA cause aneuploidy-associated cancer
    Li Zheng
    Department of Cancer Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
    Cell Res 21:1052-67. 2011
    ..Thus, this study establishes an exemplary case for investigating the biological significance of protein-protein interactions by knock-in of a point mutation rather than knock-out of a whole gene...
  10. pmc Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks
    Maria A Hahn
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
    PLoS ONE 6:e18844. 2011
    ....
  11. pmc 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations
    Seung Gi Jin
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
    Cancer Res 71:7360-5. 2011
    ..In addition, a lack of 5hmC may become a useful biomarker for cancer diagnosis...
  12. ncbi DNA methylation biomarkers for lung cancer
    Tibor A Rauch
    Division of Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
    Tumour Biol 33:287-96. 2012
    ..Many of these newly discovered methylated CpG islands hold promise for becoming biomarkers for the early detection of lung cancer...
  13. pmc The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells
    S Kalari
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
    Oncogene 32:3559-68. 2013
    ....
  14. pmc Methods for genome-wide analysis of DNA methylation in intestinal tumors
    Maria A Hahn
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
    Mutat Res 693:77-83. 2010
    ..In this review, we discuss the role of DNA methylation in intestinal carcinogenesis as well as the different methodological approaches that are currently being used for methylation analysis on a genome-wide scale...
  15. pmc In vitro recapitulating of TP53 mutagenesis in hepatocellular carcinoma associated with dietary aflatoxin B1 exposure
    Ahmad Besaratinia
    Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California 91010, USA
    Gastroenterology 137:1127-37, 1137.e1-5. 2009
    ..HCCs from AFB(1)-exposed individuals frequently have distinct TP53 mutations, such as G to T transversions in the second guanine of codon 249 (AGG to AGT), and a characteristic mutational spectrum predominated by G:C to T:A mutations...
  16. pmc Human RIF1 encodes an anti-apoptotic factor required for DNA repair
    Haibo Wang
    Laboratory of Cancer Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
    Carcinogenesis 30:1314-9. 2009
    ..Our results suggest that RIF1 encodes an anti-apoptotic factor required for DNA repair and is a potential target for cancer treatment...
  17. ncbi Mutagenesis at methylated CpG sequences
    G P Pfeifer
    Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
    Curr Top Microbiol Immunol 301:259-81. 2006
    ..Certain polycyclic aromatic hydrocarbons form guanine adducts and induce G to T transversion mutations with high selectivity at mCpG sequences...
  18. ncbi Mutation accumulation in the intestine and colon of mice deficient in two intracellular glutathione peroxidases
    Dong Hyun Lee
    Department of Biology and Department of Radiation Biology, City of Hope Cancer Center, Duarte, California 91010, USA
    Cancer Res 66:9845-51. 2006
    ..0% versus 40.1%; P < 0.001). Our results suggest that inflammation drives gene mutations, which leads to neoplastic transformation of intestinal epithelium in the B6.129 Gpx1/2-DKO mice but rarely in the B6 Gpx1/2-DKO mice...
  19. ncbi Mutagenesis induced by the nitric oxide donor sodium nitroprusside in mouse cells
    Dong Hyun Lee
    Division of Biology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
    Mutagenesis 22:63-7. 2007
    ..003) but the proportion of transition mutations was not increased. We discuss the potential origin of the G-->T mutations induced by this compound in mammalian cells...
  20. ncbi A review of mechanisms of acrylamide carcinogenicity
    Ahmad Besaratinia
    Division of Biology, Beckman Research Institute of the City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010, USA
    Carcinogenesis 28:519-28. 2007
    ..Future directions for research on acrylamide and cancer are outlined, and potential challenges are underscored...
  21. ncbi Lack of mutagenicity of acrolein-induced DNA adducts in mouse and human cells
    Sang In Kim
    Division of Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California 91010 3000, USA
    Cancer Res 67:11640-7. 2007
    ..We conclude that acrolein is not mutagenic to mouse and human fibroblasts, regardless of DNA repair capacity or methylation status of CpGs, possibly because of a highly accurate replication bypass of the induced lesions...
  22. pmc Second-hand smoke and human lung cancer
    Ahmad Besaratinia
    Division of Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, CA 91010, USA
    Lancet Oncol 9:657-66. 2008
    ..This Review is a synopsis of research on SHS and lung cancer, with special focus on hypothetical modes of action of SHS for carcinogenesis, including genotoxic and epigenetic effects...
  23. pmc Methylation of polycomb target genes in intestinal cancer is mediated by inflammation
    Maria A Hahn
    Division of Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
    Cancer Res 68:10280-9. 2008
    ..In summary, inflammation creates a signature of aberrant DNA methylation, which is observed later in the malignant tissue and is directed by the PcG complex...
  24. pmc A human B cell methylome at 100-base pair resolution
    Tibor A Rauch
    Department of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
    Proc Natl Acad Sci U S A 106:671-8. 2009
    ..Our data provide a valuable resource for the analysis of CpG methylation patterns in a differentiated human cell type and provide new clues regarding the function of mammalian DNA methylation...
  25. pmc DNA-lesion mapping in mammalian cells
    Ahmad Besaratinia
    Division of Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, CA 91010, USA
    Methods 48:35-9. 2009
    ..Here, we describe an updated protocol for LM-PCR analysis of the mammalian genome. This protocol can routinely be used for DNA-lesion footprinting of a variety of chemical and/or physical carcinogens in mammalian cells...
  26. pmc Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer
    Stella Tommasi
    Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
    Breast Cancer Res 11:R14. 2009
    ....
  27. pmc Mutational spectra of human cancer
    Gerd P Pfeifer
    Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
    Hum Genet 125:493-506. 2009
    ..Unraveling the origin of these G to C mutations will be of importance for understanding cancer etiology...
  28. pmc DNA methylation patterns in lung carcinomas
    Gerd P Pfeifer
    Department of Biology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
    Semin Cancer Biol 19:181-7. 2009
    ..Since these epigenetic changes are found in early stage tumors, their contribution to tumor etiology as well as their potential usefulness as diagnostic or prognostic biomarkers of the disease should be considered...
  29. pmc Loss of the polycomb mark from bivalent promoters leads to activation of cancer-promoting genes in colorectal tumors
    Maria A Hahn
    Authors Affiliations Departments of Cancer Biology
    Cancer Res 74:3617-29. 2014
    ..Based on our findings, we propose that a loss of Polycomb repression at bivalent genes combined with an ensuing selection for tumor-driving events plays a major role in cancer progression...

Research Grants30

  1. MicroRNAs in the Progression and Metastisis of Prostate Cancer
    Rajvir Dahiya; Fiscal Year: 2013
    ..In the future, these results may provide better strategies for the management of prostate cancer. ..