Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases. Since cancer has highlighted the contribution to disease of aberrant DNA methylation patterns, such as the presence of promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and global DNA hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances in obtaining comprehensive DNA methylomes are hampered by the high cost and time-consuming aspects of the single nucleotide methods currently available for whole genome DNA methylation analyses. Following the success of the standard CpG methylation microarrays for 1,505 CpG sites and 27,000 CpG sites, we have validated in vivo the newly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500 bp, 5'-UTRs and exons 1) for coding genes, but also for the corresponding gene bodies and 3'-UTRs, in addition to intergenic regions derived from GWAS studies. Herein, we demonstrate that the 450K DNA methylation array can consistently and significantly detect CpG methylation changes in the HCT-116 colorectal cancer cell line in comparison with normal colon mucosa or HCT-116 cells with defective DNA methyltransferases (DKO). The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects.

[1]  M. Esteller,et al.  Cancer epigenetics reaches mainstream oncology , 2011, Nature Medicine.

[2]  M. Esteller,et al.  Aberrant epigenetic landscape in cancer: how cellular identity goes awry. , 2010, Developmental cell.

[3]  Huanming Yang,et al.  The DNA Methylome of Human Peripheral Blood Mononuclear Cells , 2010, PLoS biology.

[4]  M. Esteller,et al.  Epigenetic modifications and human disease , 2010, Nature Biotechnology.

[5]  Andrew P. Feinberg,et al.  Epigenomics Reveals a Functional Genome Anatomy and a New Approach to Common Disease , 2010, Nature Biotechnology.

[6]  J. Ordovás,et al.  Epigenetics and cardiovascular disease , 2010, Nature Reviews Cardiology.

[7]  M. Esteller,et al.  CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer , 2010, Oncogene.

[8]  D. Monk.  Deciphering the cancer imprintome. , 2010, Briefings in functional genomics.

[9]  Shinji Tanaka,et al.  miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma. , 2010, Carcinogenesis.

[10]  Owen T McCann,et al.  Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. , 2010, Genome research.

[11]  Wolfgang Wagner,et al.  Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. , 2010, Genome research.

[12]  A. Feinberg,et al.  Comprehensive High‐Throughput Arrays for Relative Methylation (CHARM) , 2010, Current protocols in human genetics.

[13]  B. Korn,et al.  DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells , 2010, Aging cell.

[14]  Hanna Göransson,et al.  Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. , 2010, Blood.

[15]  Kimberly D Siegmund,et al.  Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. , 2009, Human molecular genetics.

[16]  Jingqin Luo,et al.  Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer. , 2009, Cancer research.

[17]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[18]  Manel Esteller,et al.  Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies , 2009, The Lancet Neurology.

[19]  B. Christensen,et al.  Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context , 2009, PLoS genetics.

[20]  Miguel Alaminos,et al.  A microarray-based DNA methylation study of glioblastoma multiforme , 2009, Epigenetics.

[21]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[22]  A. Riggs,et al.  A human B cell methylome at 100−base pair resolution , 2009, Proceedings of the National Academy of Sciences.

[23]  S. Ropero,et al.  A microRNA DNA methylation signature for human cancer metastasis , 2008, Proceedings of the National Academy of Sciences.

[24]  Jennifer S. Yu,et al.  PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer , 2008, Oncogene.

[25]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[26]  R. Durbin,et al.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis , 2008, Nature Biotechnology.

[27]  M. Toyota,et al.  Epigenetic silencing of microRNA-34b/c and B-cell translocation gene 4 is associated with CpG island methylation in colorectal cancer. , 2008, Cancer research.

[28]  M. Herlyn,et al.  Cancer testis antigens in human melanoma stem cells: Expression, distribution, and methylation status , 2008, Journal of Cellular Physiology.

[29]  U. Lehmann,et al.  Epigenetic inactivation of microRNA gene hsa‐mir‐9‐1 in human breast cancer , 2008, The Journal of pathology.

[30]  E. Ballestar,et al.  Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. , 2007, Cancer research.

[31]  Wei Chen,et al.  Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer , 2007, PLoS genetics.

[32]  J. Lin,et al.  Methylation patterns of IGFBP7 in colon cancer cell lines are associated with levels of gene expression , 2007, The Journal of pathology.

[33]  Michael B. Stadler,et al.  Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome , 2007, Nature Genetics.

[34]  E. Li,et al.  Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells , 2007, Nature Genetics.

[35]  Peter A. Jones,et al.  The Epigenomics of Cancer , 2007, Cell.

[36]  M. Fraga,et al.  Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. , 2007, Cancer research.

[37]  Wei Jiang,et al.  High-throughput DNA methylation profiling using universal bead arrays. , 2006, Genome research.

[38]  I. Simon,et al.  Evidence for an instructive mechanism of de novo methylation in cancer cells , 2006, Nature Genetics.

[39]  W. Lam,et al.  Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.

[40]  Vincent Colot,et al.  Profiling DNA methylation patterns using genomic tiling microarrays , 2005, Nature Methods.

[41]  A. Jeltsch,et al.  Biochemistry and biology of mammalian DNA methyltransferases , 2004, Cellular and Molecular Life Sciences CMLS.

[42]  J. Herman,et al.  GATA-4 and GATA-5 Transcription Factor Genes and Potential Downstream Antitumor Target Genes Are Epigenetically Silenced in Colorectal and Gastric Cancer , 2003, Molecular and Cellular Biology.

[43]  Esteban Ballestar,et al.  Methyl‐CpG binding proteins identify novel sites of epigenetic inactivation in human cancer , 2003, The EMBO journal.

[44]  M. Paz,et al.  Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. , 2003, Human molecular genetics.

[45]  K. Schuebel,et al.  Epigenetic inactivation of CHFR in human tumors , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  M. Robert,et al.  DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells , 2003, Nature Genetics.

[47]  Matty P. Weijenberg,et al.  A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer , 2002, Nature Genetics.

[48]  Bert Vogelstein,et al.  DNMT1 and DNMT3b cooperate to silence genes in human cancer cells , 2002, Nature.

[49]  J. Sheu,et al.  Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily. , 2001, Cancer research.

[50]  J. Herman,et al.  CpG methylation is maintained in human cancer cells lacking DNMT1 , 2000, Nature.

[51]  J. Herman,et al.  Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.