Cancer Research Grants Advances in Breast Cancer Research
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Cancer Research Clinical Cancer Research
Cancer Epidemiology Biomarkers & Prevention Molecular Cancer Therapeutics
Molecular Cancer Research Cancer Prevention Research
Cancer Prevention Journals Portal Cancer Reviews Online
Annual Meeting Education Book Meeting Abstracts Online
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yan, P. S.
Right arrow Articles by Huang, T. H.-M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yan, P. S.
Right arrow Articles by Huang, T. H.-M.
[Cancer Research 61, 8375-8380, December 1, 2001]
© 2001 American Association for Cancer Research

Advances in Brief

Dissecting Complex Epigenetic Alterations in Breast Cancer Using CpG Island Microarrays1

Pearlly S. Yan, Chuan-Mu Chen, Huidong Shi, Farahnaz Rahmatpanah, Susan H. Wei, Charles W. Caldwell and Tim Hui-Ming Huang2

Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65203 [P. S. Y., H. S., F. R., S. H. W., C. W. C., T. H-M. H.], and Department of Zoology, Life Science College, National Chung Hsing University, Taiwan, Republic of China [C-M. C.]

It is now clear that aberrant DNA methylation observed in cancer cells is not restricted to a few CpG islands, but affects multiple loci. When this epigenetic event occurs at the 5'-end of the regulatory region of genes, it is frequently associated with transcriptional silencing. To investigate further this widespread event in the tumor genome, we developed a novel microarray containing 7776 short GC-rich tags tethered to glass slide surfaces. This DNA chip was used to study 17 paired tissues of breast tumors and normal controls. Amplicons, representing differential pools of methylated DNA fragments between tumors and normal controls, were cohybridized to the microarray panel. Hypermethylation of multiple CpG island loci was then detected in a two-color fluorescence system. Approximately 1% (on average, 83 loci) of these CpG islands examined were hypermethylated in this patient group. Hierarchical clustering segregated these tumors based on their methylation profiles and identified a group of CpG island loci that corresponds to the hormone-receptor status of breast cancer. This observation was independently confirmed by examining a single locus, the promoter of the human glypican 3 gene, which was predominately hypermethylated in the hormone receptor-negative tumors. Our findings support the notion that hypermethylation of critical CpG island loci influences cancer development and produces distinct epigenetic signatures for particular tumor subtypes.




This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Oda, J. L. Glass, R. F. Thompson, Y. Mo, E. N. Olivier, M. E. Figueroa, R. R. Selzer, T. A. Richmond, X. Zhang, L. Dannenberg, et al.
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
Nucleic Acids Res., April 22, 2009; (2009) gkp260v1.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
X. Xu, M. D. Gammon, J. G. Wetmur, P. T. Bradshaw, S. L. Teitelbaum, A. I. Neugut, R. M. Santella, and J. Chen
B-Vitamin Intake, One-Carbon Metabolism, and Survival in a Population-Based Study of Women with Breast Cancer
Cancer Epidemiol. Biomarkers Prev., August 1, 2008; 17(8): 2109 - 2116.
[Abstract] [Full Text] [PDF]

Home page
 Neuro OncolHome page
J. A. Anderton, J. C. Lindsey, M. E. Lusher, R. J. Gilbertson, S. Bailey, D. W. Ellison, and S. C. Clifford
Global analysis of the medulloblastoma epigenome identifies disease-subgroup-specific inactivation of COL1A2
Neuro-oncol, January 1, 2008; 10(6): 981 - 994.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. R.H. Estecio, P. S. Yan, A. E.K. Ibrahim, C. S. Tellez, L. Shen, T. H.-M. Huang, and J.-P. J. Issa
High-throughput methylation profiling by MCA coupled to CpG island microarray
Genome Res., October 1, 2007; 17(10): 1529 - 1536.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
J. R. Pollack
A Perspective on DNA Microarrays in Pathology Research and Practice
Am. J. Pathol., August 1, 2007; 171(2): 375 - 385.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Z. Lin, S. Reierstad, C.-C. Huang, and S. E. Bulun
Novel Estrogen Receptor-{alpha} Binding Sites and Estradiol Target Genes Identified by Chromatin Immunoprecipitation Cloning in Breast Cancer
Cancer Res., May 15, 2007; 67(10): 5017 - 5024.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
I. Zighelboim, P. J. Goodfellow, A. P. Schmidt, K. C. Walls, M. A. Mallon, D. G. Mutch, P. S. Yan, T. H.-M. Huang, and M. A. Powell
Differential Methylation Hybridization Array of Endometrial Cancers Reveals Two Novel Cancer-Specific Methylation Markers
Clin. Cancer Res., May 15, 2007; 13(10): 2882 - 2889.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
R. M. Brena and J. F. Costello
Genome-epigenome interactions in cancer
Hum. Mol. Genet., April 15, 2007; 16(R1): R96 - R105.
[Abstract] [Full Text] [PDF]

Home page
 aacredbookHome page
C. Plass
Restriction Landmark Genomic Scanning
Am. Assoc. Cancer Res. Educ. Book, April 14, 2007; 2007(1): 185 - 188.
[Full Text] [PDF]

Home page
 aacredbookHome page
P. S. Yan and T. H.-M. Huang
Tools to Uncover Altered DNA Methylation in Cancer Genomes
Am. Assoc. Cancer Res. Educ. Book, April 14, 2007; 2007(1): 194 - 196.
[Full Text] [PDF]

Home page
 Cancer Res.Home page
K. H. Taylor, K. E. Pena-Hernandez, J. W. Davis, G. L. Arthur, D. J. Duff, H. Shi, F. B. Rahmatpanah, O. Sjahputera, and C. W. Caldwell
Large-Scale CpG Methylation Analysis Identifies Novel Candidate Genes and Reveals Methylation Hotspots in Acute Lymphoblastic Leukemia
Cancer Res., March 15, 2007; 67(6): 2617 - 2625.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
H. Shi, J. Guo, D. J. Duff, F. Rahmatpanah, R. Chitima-Matsiga, M. Al-Kuhlani, K. H. Taylor, O. Sjahputera, M. Andreski, J. E. Wooldridge, et al.
Discovery of novel epigenetic markers in non-Hodgkin's lymphoma
Carcinogenesis, January 1, 2007; 28(1): 60 - 70.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
J.M. Ordway, J.A. Bedell, R.W. Citek, A. Nunberg, A. Garrido, R. Kendall, J.R. Stevens, D. Cao, R.W. Doerge, Y. Korshunova, et al.
Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets
Carcinogenesis, December 1, 2006; 27(12): 2409 - 2423.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
P. S. Yan, C. Venkataramu, A. Ibrahim, J. C. Liu, R. Z. Shen, N. M. Diaz, B. Centeno, F. Weber, Y.-W. Leu, C. L. Shapiro, et al.
Mapping Geographic Zones of Cancer Risk with Epigenetic Biomarkers in Normal Breast Tissue.
Clin. Cancer Res., November 15, 2006; 12(22): 6626 - 6636.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. E. K. Ibrahim, N. P. Thorne, K. Baird, N. L. Barbosa-Morais, S. Tavare, V. P. Collins, A. H. Wyllie, M. J. Arends, and J. D. Brenton
MMASS: an optimized array-based method for assessing CpG island methylation
Nucleic Acids Res., November 6, 2006; 34(20): e136 - e136.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. Gebhard, L. Schwarzfischer, T.-H. Pham, E. Schilling, M. Klug, R. Andreesen, and M. Rehli
Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia.
Cancer Res., June 15, 2006; 66(12): 6118 - 6128.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
A. S Perry, R. Foley, K. Woodson, and M. Lawler
The emerging roles of DNA methylation in the clinical management of prostate cancer.
Endocr. Relat. Cancer, June 1, 2006; 13(2): 357 - 377.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
H. Fiegl, S. Millinger, G. Goebel, E. Muller-Holzner, C. Marth, P. W. Laird, and M. Widschwendter
Breast Cancer DNA Methylation Profiles in Cancer Cells and Tumor Stroma: Association with HER-2/neu Status in Primary Breast Cancer
Cancer Res., January 1, 2006; 66(1): 29 - 33.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
J. Ying, G. Srivastava, W.-S. Hsieh, Z. Gao, P. Murray, S.-K. Liao, R. Ambinder, and Q. Tao
The Stress-Responsive Gene GADD45G Is a Functional Tumor Suppressor, with Its Response to Environmental Stresses Frequently Disrupted Epigenetically in Multiple Tumors
Clin. Cancer Res., September 15, 2005; 11(18): 6442 - 6449.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
R. van Doorn, W. H. Zoutman, R. Dijkman, R. X. de Menezes, S. Commandeur, A. A. Mulder, P. A. van der Velden, M. H. Vermeer, R. Willemze, P. S. Yan, et al.
Epigenetic Profiling of Cutaneous T-Cell Lymphoma: Promoter Hypermethylation of Multiple Tumor Suppressor Genes Including BCL7a, PTPRG, and p73
J. Clin. Oncol., June 10, 2005; 23(17): 3886 - 3896.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. E. Heisler, D. Torti, P. C. Boutros, J. Watson, C. Chan, N. Winegarden, M. Takahashi, P. Yau, T. H.-M. Huang, P. J. Farnham, et al.
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome
Nucleic Acids Res., May 23, 2005; 33(9): 2952 - 2961.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kimura, T. Nagasaka, J. Murakami, H. Sasamoto, M. Murakami, N. Tanaka, and N. Matsubara
Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients
Nucleic Acids Res., March 10, 2005; 33(5): e46 - e46.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
Y. P. Yu, S. Paranjpe, J. Nelson, S. Finkelstein, B. Ren, D. Kokkinakis, G. Michalopoulos, and J.-H. Luo
High throughput screening of methylation status of genes in prostate cancer using an oligonucleotide methylation array
Carcinogenesis, February 1, 2005; 26(2): 471 - 479.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. X. Jin, Y.-W. Leu, S. Liyanarachchi, H. Sun, M. Fan, K. P. Nephew, T. H.-M. Huang, and R. V. Davuluri
Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray
Nucleic Acids Res., December 17, 2004; 32(22): 6627 - 6635.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Y.-W. Leu, P. S. Yan, M. Fan, V. X. Jin, J. C. Liu, E. M. Curran, W. V. Welshons, S. H. Wei, R. V. Davuluri, C. Plass, et al.
Loss of Estrogen Receptor Signaling Triggers Epigenetic Silencing of Downstream Targets in Breast Cancer
Cancer Res., November 15, 2004; 64(22): 8184 - 8192.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
N. P. Carter and D. Vetrie
Applications of genomic microarrays to explore human chromosome structure and function
Hum. Mol. Genet., October 1, 2004; 13(suppl_2): R297 - R302.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
M Lacroix, R-A Toillon, and G Leclercq
Stable 'portrait' of breast tumors during progression: data from biology, pathology and genetics
Endocr. Relat. Cancer, September 1, 2004; 11(3): 497 - 522.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
A. Bahar, D. J. Simpson, S. J. Cutty, J. E. Bicknell, P. R. Hoban, S. Holley, M. Mourtada-Maarabouni, G. T. Williams, R. N. Clayton, and W. E. Farrell
Isolation and Characterization of a Novel Pituitary Tumor Apoptosis Gene
Mol. Endocrinol., July 1, 2004; 18(7): 1827 - 1839.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
M. Widschwendter, K. D. Siegmund, H. M. Muller, H. Fiegl, C. Marth, E. Muller-Holzner, P. A. Jones, and P. W. Laird
Association of Breast Cancer DNA Methylation Profiles with Hormone Receptor Status and Response to Tamoxifen
Cancer Res., June 1, 2004; 64(11): 3807 - 3813.
[Abstract] [Full Text] [PDF]

Home page
 Toxicol PatholHome page
Diagnostic Arrays for Epigenetic Markers: YU-WEI LEU AND TIM H.-M. HUANG, Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Medical Research Facility, Columbus, Ohio 43210
Toxicol Pathol, January 1, 2004; 32(1): 139 - 139.
[PDF]

Home page
 Clin. Cancer Res.Home page
R. Krassenstein, E. Sauter, E. Dulaimi, C. Battagli, H. Ehya, A. Klein-Szanto, and P. Cairns
Detection of Breast Cancer in Nipple Aspirate Fluid by CpG Island Hypermethylation
Clin. Cancer Res., January 1, 2004; 10(1): 28 - 32.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Respir. Cell Mol. Bio.Home page
H. Kim, G.-L. Xu, A. C. Borczuk, S. Busch, J. Filmus, M. Capurro, J. S. Brody, J. Lange, J. M. D'Armiento, P. B. Rothman, et al.
The Heparan Sulfate Proteoglycan GPC3 Is a Potential Lung Tumor Suppressor
Am. J. Respir. Cell Mol. Biol., December 1, 2003; 29(6): 694 - 701.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. J. Oberley, D. R. Inman, and P. J. Farnham
E2F6 Negatively Regulates BRCA1 in Human Cancer Cells without Methylation of Histone H3 on Lysine 9
J. Biol. Chem., October 24, 2003; 278(43): 42466 - 42476.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
D. G. Albertson and D. Pinkel
Genomic microarrays in human genetic disease and cancer
Hum. Mol. Genet., October 15, 2003; 12(90002): R145 - 152.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
F. A. Feltus, E. K. Lee, J. F. Costello, C. Plass, and P. M. Vertino
Predicting aberrant CpG island methylation
PNAS, October 14, 2003; 100(21): 12253 - 12258.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Y.-W. Leu, F. Rahmatpanah, H. Shi, S. H. Wei, J. C. Liu, P. S. Yan, and T. H.-M. Huang
Double RNA Interference of DNMT3b and DNMT1 Enhances DNA Demethylation and Gene Reactivation
Cancer Res., October 1, 2003; 63(19): 6110 - 6115.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
M. F. Paz, S. Wei, J. C. Cigudosa, S. Rodriguez-Perales, M. A. Peinado, T. H.-M. Huang, and M. Esteller
Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases
Hum. Mol. Genet., September 1, 2003; 12(17): 2209 - 2219.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Matsuyama, M. T. Kimura, K. Koike, T. Abe, T. Nakano, T. Asami, T. Ebisuzaki, W. A. Held, S. Yoshida, and H. Nagase
Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS)
Nucleic Acids Res., August 1, 2003; 31(15): 4490 - 4496.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
W. A. Palmisano, K. P. Crume, M. J. Grimes, S. A. Winters, M. Toyota, M. Esteller, N. Joste, S. B. Baylin, and S. A. Belinsky
Aberrant Promoter Methylation of the Transcription Factor Genes PAX5 {alpha} and {beta} in Human Cancers
Cancer Res., August 1, 2003; 63(15): 4620 - 4625.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
C.-M. Chen, H.-L. Chen, T. H.-C. Hsiau, A. H.-A. Hsiau, H. Shi, G. J. R. Brock, S. H. Wei, C. W. Caldwell, P. S. Yan, and T. H.-M. Huang
Methylation Target Array for Rapid Analysis of CpG Island Hypermethylation in Multiple Tissue Genomes
Am. J. Pathol., July 1, 2003; 163(1): 37 - 45.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
H. Shi, S. H. Wei, Y.-W. Leu, F. Rahmatpanah, J. C. Liu, P. S. Yan, K. P. Nephew, and T. H.-M. Huang
Triple Analysis of the Cancer Epigenome: An Integrated Microarray System for Assessing Gene Expression, DNA Methylation, and Histone Acetylation
Cancer Res., May 1, 2003; 63(9): 2164 - 2171.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Li, A. Protopopov, F. Wang, V. Senchenko, V. Petushkov, O. Vorontsova, L. Petrenko, V. Zabarovska, O. Muravenko, E. Braga, et al.
NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes
PNAS, August 6, 2002; 99(16): 10724 - 10729.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
G. Garcia-Manero, J. Daniel, T. L. Smith, S. M. Kornblau, M.-S. Lee, H. M. Kantarjian, and J.-P. J. Issa
DNA Methylation of Multiple Promoter-associated CpG Islands in Adult Acute Lymphocytic Leukemia
Clin. Cancer Res., July 1, 2002; 8(7): 2217 - 2224.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
S. H. Wei, C.-M. Chen, G. Strathdee, J. Harnsomburana, C.-R. Shyu, F. Rahmatpanah, H. Shi, S.-W. Ng, P. S. Yan, K. P. Nephew, et al.
Methylation Microarray Analysis of Late-Stage Ovarian Carcinomas Distinguishes Progression-free Survival in Patients and Identifies Candidate Epigenetic Markers
Clin. Cancer Res., July 1, 2002; 8(7): 2246 - 2252.
[Abstract] [Full Text] [PDF]

Home page
 EndocrinologyHome page
D. Soulet and S. Rivest
Perspective: How to Make Microarray, Serial Analysis of Gene Expression, and Proteomic Relevant to Day-to-Day Endocrine Problems and Physiological Systems
Endocrinology, June 1, 2002; 143(6): 1995 - 2001.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
H. Shi, P. S. Yan, C.-M. Chen, F. Rahmatpanah, C. Lofton-Day, C. W. Caldwell, and T. H.-M. Huang
Expressed CpG Island Sequence Tag Microarray for Dual Screening of DNA Hypermethylation and Gene Silencing in Cancer Cells
Cancer Res., June 1, 2002; 62(11): 3214 - 3220.
[Abstract] [Full Text] [PDF]

Home page
 Cell Growth Differ.Home page
J. M. Ordway and T. Curran
Methylation Matters: Modeling a Manageable Genome
Cell Growth Differ., April 1, 2002; 13(4): 149 - 162.
[Full Text] [PDF]

Home page
 Genome ResHome page
R. Ohlsson and C. Kanduri
New Twists on the Epigenetics of CpG Islands
Genome Res., April 1, 2002; 12(4): 525 - 526.
[Full Text] [PDF]

Home page
 Genes Dev.Home page
A. S. Weinmann, P. S. Yan, M. J. Oberley, T. H.-M. Huang, and P. J. Farnham
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
Genes & Dev., January 15, 2002; 16(2): 235 - 244.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Cancer Research Clinical Cancer Research
Cancer Epidemiology Biomarkers & Prevention Molecular Cancer Therapeutics
Molecular Cancer Research Cancer Prevention Research
Cancer Prevention Journals Portal Cancer Reviews Online
Annual Meeting Education Book Meeting Abstracts Online
Copyright © 2001 by the American Association for Cancer Research.