Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes

Chuan Mu Chen, Hsiao Ling Chen, Timothy H.C. Hsiau, Andrew H.A. Hsiau, Huidong Shi, Graham J.R. Brock, Susan H. Wei, Charles W. Caldwell, Pearlly S. Yan, Tim Hui Ming Huang

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

Hypermethylation of multiple CpG islands is a common event in cancer. To assess the prognostic values of this epigenetic alteration, we developed Methylation Target Array (MTA), derived from the concept of tissue microarray, for simultaneous analysis of DNA hypermethylation in hundreds of tissue genomes. In MTA, linker-ligated CpG island fragments were digested with methylation-sensitive endonucleases and amplified with flanking primers. A panel of 468 MTA amplicons, which represented the whole repertoire of methylated CpG islands in 93 breast tumors, 20 normal breast tissues, and 4 breast cancer cell lines, were arrayed on nylon membrane for probe hybridization. Positive hybridization signals detected in tumor amplicons, but not in normal amplicons, were indicative of aberrant hypermethylation in tumor samples. This is attributed to aberrant sites that were protected from methylation-sensitive restriction and were amplified by PCR in tumor samples, while the same sites were restricted and could not be amplified in normal samples. Hypermethylation frequencies of the 10 genes tested in breast tumors and cancer cell lines were 60% for GPC3, 58% for RASSF1A, 32% for 30ST3B, 30% for HOXA5, 28% for uPA, 25% for WT1, 23% for BRCA1, 9% for DAPK1, and 0% for KL. Furthermore, hypermethylation of 5 to 7 loci of these genes was significantly correlated with hormone receptor status, clinical stages, and ages at diagnosis of the patients analyzed. This novel approach thus provides an additional avenue for assessing clinicopathological consequences of DNA hypermethylation in breast cancer.

Original languageEnglish (US)
Pages (from-to)37-45
Number of pages9
JournalAmerican Journal of Pathology
Volume163
Issue number1
DOIs
StatePublished - Jul 1 2003

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CpG Islands
Methylation
Genome
Breast Neoplasms
Neoplasms
Tissue Array Analysis
Endonucleases
DNA
Nylons
Tumor Cell Line
Gene Frequency
Epigenomics
Breast
Hormones
Cell Line
Polymerase Chain Reaction
Membranes
Genes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Chen, C. M., Chen, H. L., Hsiau, T. H. C., Hsiau, A. H. A., Shi, H., Brock, G. J. R., ... Huang, T. H. M. (2003). Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. American Journal of Pathology, 163(1), 37-45. https://doi.org/10.1016/S0002-9440(10)63628-0

Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. / Chen, Chuan Mu; Chen, Hsiao Ling; Hsiau, Timothy H.C.; Hsiau, Andrew H.A.; Shi, Huidong; Brock, Graham J.R.; Wei, Susan H.; Caldwell, Charles W.; Yan, Pearlly S.; Huang, Tim Hui Ming.

In: American Journal of Pathology, Vol. 163, No. 1, 01.07.2003, p. 37-45.

Research output: Contribution to journalArticle

Chen, CM, Chen, HL, Hsiau, THC, Hsiau, AHA, Shi, H, Brock, GJR, Wei, SH, Caldwell, CW, Yan, PS & Huang, THM 2003, 'Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes', American Journal of Pathology, vol. 163, no. 1, pp. 37-45. https://doi.org/10.1016/S0002-9440(10)63628-0
Chen, Chuan Mu ; Chen, Hsiao Ling ; Hsiau, Timothy H.C. ; Hsiau, Andrew H.A. ; Shi, Huidong ; Brock, Graham J.R. ; Wei, Susan H. ; Caldwell, Charles W. ; Yan, Pearlly S. ; Huang, Tim Hui Ming. / Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. In: American Journal of Pathology. 2003 ; Vol. 163, No. 1. pp. 37-45.
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AU - Shi, Huidong

AU - Brock, Graham J.R.

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