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Abstract
Chromatin immunoprecipitation, commonly referred to as ChIP, is a powerful technique for the evaluation of in vivo interactions of proteins with specific regions of genomic DNA. Formaldehyde is used in this technique to cross-link proteins to DNA in vivo, followed by the extraction of chromatin from cross-linked cells and tissues. Harvested chromatin is sheared and subsequently used in an immunoprecipitation incorporating antibodies specific to protein(s) of interest and thus coprecipitating and enriching the cross-linked, protein-associated DNA. The cross-linking process can be reversed, and protein-bound DNA fragments of optimal length ranging from 200 to 1000 base pairs (bp) can subsequently be purified and measured or sequenced by numerous analytical methods. In this protocol, two different fixation methods are described in detail. The first involves the standard fixation of cells and tissue by formaldehyde if the target antigen is highly abundant. The dual cross-linking procedure presented at the end includes an additional preformaldehyde cross-linking step and can be especially useful when the target protein is in low abundance or if it is indirectly associated with chromatin DNA through another protein.
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Keverne J, Binder EB. A Review of epigenetics in psychiatry: focus on environmental risk factors. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Epigenetic modifications play a key role in development and cell type specificity. These modifications seem to be particularly critical for brain development, where mutations in epigenetic enzymes have been associated with neurodevelopmental disorders as well as with the function of post-mitotic neurons. Epigenetic modifications can be influenced by genetic and environmental factors, both known major risk factors for psychiatric disorders. Epigenetic modifications may thus be an important mediator of the effects of genetic and environmental risk factors on cell function.
This review summarizes the different types of epigenetic regulation and then focuses on the mechanisms transducing environmental signals, especially adverse life events that are major risk factors for psychiatric disorders, into lasting epigenetic changes. This is followed by examples of how the environment can induce epigenetic changes that relate to the risk of psychiatric disorders.
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Affiliation(s)
| | - Elisabeth B. Binder
- Dept. of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Kraepelinstr. 2-10 , Munich , Germany
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Choukrallah MA, Sewer A, Talikka M, Sierro N, Peitsch MC, Hoeng J, Ivanov NV. Epigenomics in tobacco risk assessment: Opportunities for integrated new approaches. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Liu Y, Song C, Ladas I, Fitarelli-Kiehl M, Makrigiorgos GM. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res 2017; 45:e39. [PMID: 27903892 PMCID: PMC5389605 DOI: 10.1093/nar/gkw1166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes.
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Affiliation(s)
- Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed. Tel: +1 617 525 7122; Fax: +1 617 582 6037;
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Teh AL, Pan H, Lin X, Lim YI, Patro CPK, Cheong CY, Gong M, MacIsaac JL, Kwoh CK, Meaney MJ, Kobor MS, Chong YS, Gluckman PD, Holbrook JD, Karnani N. Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples. Epigenetics 2016; 11:36-48. [PMID: 26786415 PMCID: PMC4846133 DOI: 10.1080/15592294.2015.1132136] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Interindividual variability in the epigenome has gained tremendous attention for its potential in pathophysiological investigation, disease diagnosis, and evaluation of clinical intervention. DNA methylation is the most studied epigenetic mark in epigenome-wide association studies (EWAS) as it can be detected from limited starting material. Infinium 450K methylation array is the most popular platform for high-throughput profiling of this mark in clinical samples, as it is cost-effective and requires small amounts of DNA. However, this method suffers from low genome coverage and errors introduced by probe cross-hybridization. Whole-genome bisulfite sequencing can overcome these limitations but elevates the costs tremendously. Methyl-Capture Sequencing (MC Seq) is an attractive intermediate solution to increase the methylome coverage in large sample sets. Here we first demonstrate that MC Seq can be employed using DNA amounts comparable to the amounts used for Infinium 450K. Second, to provide guidance when choosing between the 2 platforms for EWAS, we evaluate and compare MC Seq and Infinium 450K in terms of coverage, technical variation, and concordance of methylation calls in clinical samples. Last, since the focus in EWAS is to study interindividual variation, we demonstrate the utility of MC Seq in studying interindividual variation in subjects from different ethnicities.
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Affiliation(s)
- Ai Ling Teh
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore
| | - Hong Pan
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,b School of Computer Engineering, Nanyang Technological University , Singapore
| | - Xinyi Lin
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore
| | - Yubin Ives Lim
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,c Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | | | | | - Min Gong
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore
| | - Julia L MacIsaac
- e Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute , Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
| | - Chee-Keong Kwoh
- b School of Computer Engineering, Nanyang Technological University , Singapore
| | - Michael J Meaney
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,d Ludmer Center for Neuroinformatics & Mental Health, Douglas University Mental Health Institute, McGill University , Montreal , Quebec Canada
| | - Michael S Kobor
- e Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute , Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
| | - Yap-Seng Chong
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,c Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Peter D Gluckman
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,f Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland , Auckland , New Zealand
| | | | - Neerja Karnani
- a Singapore Institute for Clinical Sciences, A*STAR , Singapore.,c Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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Udali S, Guarini P, Ruzzenente A, Ferrarini A, Guglielmi A, Lotto V, Tononi P, Pattini P, Moruzzi S, Campagnaro T, Conci S, Olivieri O, Corrocher R, Delledonne M, Choi SW, Friso S. DNA methylation and gene expression profiles show novel regulatory pathways in hepatocellular carcinoma. Clin Epigenetics 2015; 7:43. [PMID: 25945129 PMCID: PMC4419480 DOI: 10.1186/s13148-015-0077-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 12/30/2022] Open
Abstract
Background Alcohol is a well-known risk factor for hepatocellular carcinoma (HCC), but the mechanisms underlying the alcohol-related hepatocarcinogenesis are still poorly understood. Alcohol alters the provision of methyl groups within the hepatic one-carbon metabolism, possibly inducing aberrant DNA methylation. Whether specific pathways are epigenetically regulated in alcohol-associated HCC is, however, unknown. The aim of the present study was to investigate the genome-wide promoter DNA methylation and gene expression profiles in non-viral, alcohol-associated HCC. From eight HCC patients undergoing curative surgery, array-based DNA methylation and gene expression data of all annotated genes were analyzed by comparing HCC tissue and homologous cancer-free liver tissue. Results After merging the DNA methylation with gene expression data, we identified 159 hypermethylated-repressed, 30 hypomethylated-induced, 49 hypermethylated-induced, and 56 hypomethylated-repressed genes. Notably, promoter DNA methylation emerged as a novel regulatory mechanism for the transcriptional repression of genes controlling the retinol metabolism (ADH1A, ADH1B, ADH6, CYP3A43, CYP4A22, RDH16), iron homeostasis (HAMP), one-carbon metabolism (SHMT1), and genes with a putative, newly identified function as tumor suppressors (FAM107A, IGFALS, MT1G, MT1H, RNF180). Conclusions A genome-wide DNA methylation approach merged with array-based gene expression profiles allowed identifying a number of novel, epigenetically regulated candidate tumor-suppressor genes in alcohol-associated hepatocarcinogenesis. Retinol metabolism genes and SHMT1 are also epigenetically regulated through promoter DNA methylation in alcohol-associated HCC. Due to the reversibility of epigenetic mechanisms by environmental/nutritional factors, these findings may open up to novel interventional strategies for hepatocarcinogenesis prevention in HCC related to alcohol, a modifiable dietary component. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0077-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Udali
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Patrizia Guarini
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Andrea Ruzzenente
- Department of Surgery, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Alberto Ferrarini
- Department of Biotechnology, Genetics and Heredity Section, University of Verona School of Agroindustrial Biotechnology, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alfredo Guglielmi
- Department of Surgery, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Valentina Lotto
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Paola Tononi
- Department of Biotechnology, Genetics and Heredity Section, University of Verona School of Agroindustrial Biotechnology, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Patrizia Pattini
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Sara Moruzzi
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Tommaso Campagnaro
- Department of Surgery, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Simone Conci
- Department of Surgery, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Oliviero Olivieri
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Roberto Corrocher
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, Genetics and Heredity Section, University of Verona School of Agroindustrial Biotechnology, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Sang-Woon Choi
- Friedman School of Nutrition Science and Policy Tufts University, 150 Harrison Ave, Boston, MA 02111 USA ; Chaum Life Center, CHA University, 4-1, Cheongdam-dong, Gangnam-gu, 135-948 Seoul, Korea
| | - Simonetta Friso
- Department of Medicine, University of Verona School of Medicine, Policlinico 'G.B. Rossi', P.le L.A. Scuro, 10, 37134 Verona, Italy
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Bracht JR, Perlman DH, Landweber LF. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biol 2012; 13:R99. [PMID: 23075511 PMCID: PMC3491425 DOI: 10.1186/gb-2012-13-10-r99] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 10/17/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells. RESULTS Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells. CONCLUSIONS These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.
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Doehring A, Geisslinger G, Lötsch J. Epigenetics in pain and analgesia: An imminent research field. Eur J Pain 2012; 15:11-6. [DOI: 10.1016/j.ejpain.2010.06.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 04/15/2010] [Accepted: 06/01/2010] [Indexed: 01/13/2023]
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Wang L, Sun J, Wu H, Liu S, Wang J, Wu B, Huang S, Li N, Wang J, Zhang X. Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies. J Biotechnol 2011; 157:1-6. [PMID: 21763364 DOI: 10.1016/j.jbiotec.2011.06.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/23/2011] [Accepted: 06/29/2011] [Indexed: 12/22/2022]
Abstract
Complementary to the time- and cost-intensive direct bisulfite sequencing, we applied reduced representation bisulfite sequencing (RRBS) to the human peripheral blood mononuclear cells (PBMC) from YH, the Asian individual whose genome and epigenome has been deciphered in the YH project and systematically assessed the genomic coverage, coverage depth and reproducibility of this technology as well as the concordance of DNA methylation levels measured by RRBS and direct bisulfite sequencing for the detected CpG sites. Our result suggests that RRBS can cover more than half of CpG islands and promoter regions with a good coverage depth and the proportion of the CpG sites covered by the biological replicates reaches 80-90%, indicating good reproducibility. Given a smaller data quantity, RRBS enjoys much better coverage depth than direct bisulfite sequencing and the concordance of DNA methylation levels between the two methods is high. It can be concluded that RRBS is a time and cost-effective sequencing method for unbiased DNA methylation profiling of CpG islands and promoter regions in a genome-wide scale and it is the method of choice to assay certain genomic regions for multiple samples in a rapid way.
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Affiliation(s)
- Li Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
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Pälmke N, Santacruz D, Walter J. Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip. Methods 2010; 53:175-84. [PMID: 20638478 DOI: 10.1016/j.ymeth.2010.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 07/12/2010] [Indexed: 01/28/2023] Open
Abstract
Genome-wide mapping of epigenetic changes is essential for understanding the mechanisms involved in gene regulation during cell differentiation and embryonic development. DNA-methylation is one of these key epigenetic marks that is directly linked to gene expression is. Methylated DNA immunoprecipitation (MeDIP) is a recently devised method used to determine the distribution of DNA-methylation within functional regions (e.g., promoters) or in the entire genome robustly and cost-efficiently. This approach is based on the enrichment of methylated DNA with an antibody that specifically binds to 5-methyl-cytosine and can be combined with PCR, microarrays or high-throughput sequencing. This article outlines the experimental procedure of MeDIP-chip and provides a comprehensive summary of quality control strategies and primary data analysis.
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Affiliation(s)
- Nina Pälmke
- Institut für Genetik, FB Biowissenschaften, Universität des Saarlandes, Saarbrücken, Germany
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Thu KL, Pikor LA, Kennett JY, Alvarez CE, Lam WL. Methylation analysis by DNA immunoprecipitation. J Cell Physiol 2010; 222:522-31. [PMID: 20020444 DOI: 10.1002/jcp.22009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methylation regulates gene expression primarily through modification of chromatin structure. Global methylation studies have revealed biologically relevant patterns of DNA methylation in the human genome affecting sequences such as gene promoters, gene bodies, and repetitive elements. Disruption of normal methylation patterns and subsequent gene expression changes have been observed in several diseases especially in human cancers. Immunoprecipitation (IP)-based methods to evaluate methylation status of DNA have been instrumental in such genome-wide methylation studies. This review describes techniques commonly used to identify and quantify methylated DNA with emphasis on IP based platforms. In an effort to consolidate the wealth of information and highlight critical aspects of methylated DNA analysis, sample considerations, experimental and bioinformatic approaches for analyzing genome-wide methylation profiles, and the benefit of integrating DNA methylation data with complementary dimensions of genomic data are discussed.
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Affiliation(s)
- Kelsie L Thu
- Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
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