Research Topics
Genomes and GenesSpecies | CPG METHYLATION AND MUTATIONSummaryPrincipal 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
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Publications
Investigating human cancer etiology by DNA lesion footprinting and mutagenicity analysisAhmad 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...
CpG island hypermethylation in human astrocytomasXiwei Wu
Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
Cancer Res 70:2718-27. 2010....- 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... - Applications of the human p53 knock-in (Hupki) mouse model for human carcinogen testingAhmad 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... - Investigating the epigenetic effects of a prototype smoke-derived carcinogen in human cellsStella 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... - Identification of driver and passenger DNA methylation in cancer by epigenomic analysisSatish Kalari
Department of Cancer Biology, Beckman Research Institute of the Cityof Hope, Duarte, CA, USA
Adv Genet 70:277-308. 2010.... - Unveiling the methylation status of CpG dinucleotides in the substituted segment of the human p53 knock-in (Hupki) mouse genomeSang 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.... - Genomic mapping of 5-hydroxymethylcytosine in the human brainSeung 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... - Fen1 mutations that specifically disrupt its interaction with PCNA cause aneuploidy-associated cancerLi 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... - Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marksMaria 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.... - 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutationsSeung 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... - DNA methylation biomarkers for lung cancerTibor 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... - The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cellsS Kalari
Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
Oncogene 32:3559-68. 2013.... - Methods for genome-wide analysis of DNA methylation in intestinal tumorsMaria 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... - In vitro recapitulating of TP53 mutagenesis in hepatocellular carcinoma associated with dietary aflatoxin B1 exposureAhmad 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... - Human RIF1 encodes an anti-apoptotic factor required for DNA repairHaibo 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... - Mutagenesis at methylated CpG sequencesG 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... - Mutation accumulation in the intestine and colon of mice deficient in two intracellular glutathione peroxidasesDong 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... - Mutagenesis induced by the nitric oxide donor sodium nitroprusside in mouse cellsDong 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... - A review of mechanisms of acrylamide carcinogenicityAhmad 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... - Lack of mutagenicity of acrolein-induced DNA adducts in mouse and human cellsSang 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... - Second-hand smoke and human lung cancerAhmad 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... - Methylation of polycomb target genes in intestinal cancer is mediated by inflammationMaria 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... - A human B cell methylome at 100-base pair resolutionTibor 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... - DNA-lesion mapping in mammalian cellsAhmad 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... - Methylation of homeobox genes is a frequent and early epigenetic event in breast cancerStella Tommasi
Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
Breast Cancer Res 11:R14. 2009.... - Mutational spectra of human cancerGerd 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... - DNA methylation patterns in lung carcinomasGerd 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... - Loss of the polycomb mark from bivalent promoters leads to activation of cancer-promoting genes in colorectal tumorsMaria 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 Grants
- MicroRNAs in the Progression and Metastisis of Prostate CancerRajvir Dahiya; Fiscal Year: 2013..In the future, these results may provide better strategies for the management of prostate cancer. ..