High throughput screening of methylation status of genes in prostate cancer using an oligonucleotide methylation array

Carcinogenesis

Volumn 26, Issue 2, 2005, Pages 471-479

  Yu, Yan Ping ^a   Paranjpe, Shirish ^a   Nelson, Joel ^a   Finkelstein, Sydney ^a   Ren, Baoguo ^a   Kokkinakis, Demetrius ^a   Michalopoulos, George ^a   Luo, Jian Hua ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CELL CULTURE; CARCINOGENESIS; CONTROLLED STUDY; CORRELATION FUNCTION; DNA HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; DOWN REGULATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; HUMAN TISSUE; LABELING INDEX; PRIORITY JOURNAL; PROSTATE CANCER;

ACETYLATION; CPG ISLANDS; DNA METHYLATION; EXONS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES; HISTONES; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); PROSTATIC NEOPLASMS; TUMOR CELLS, CULTURED;

EID: 13844254856     PISSN: 01433334     EISSN: None     Source Type: Journal    
DOI: 10.1093/carcin/bgh310     Document Type: Article

References (24)

1. Li,E., Beard,C. and Jaenisch,R. (1993) Role for DNA methylation in genomic imprinting. Nature, 366, 362-365.
2. Tremblay,K.D., Saam,J.R., Ingram,R.S., Tilghman,S.M. and Bartolomei,M.S. (1995) A paternal-specific methylation imprint marks the alleles of the mouse H19 gene. Nature Genet., 9, 407-413.
3. Pfeifer,G.P., Steigerwald,S.D., Mueller,P.R., Wold,B. and Riggs,A.D. (1989) Genomic sequencing and methylation analysis by ligation mediated PCR. Science, 246, 810-813.
4. Riggs,A.D. and Pfeifer,G.P. (1992) X-chromosome inactivation and cell memory. Trends Genet., 8, 169-174.
5. Fan,X., Inda,M.M., Tunon,T. and Castresana,J.S. (2002) Improvement of the methylation specific PCR technical conditions for the detection of p16 promoter hypermethylation in small amounts of tumor DNA. Oncol. Rep., 9, 181-183.
6. Vanaja,D.K., Cheville,J.C., Iturria,S.J. and Young,C.Y. (2003) Transcriptional silencing of zinc finger protein 185 identified by expression profiling is associated with prostate cancer progression. Cancer Res., 63, 3877-3882.
7. Golub,T.R. (2001) Genome-wide views of cancer. N. Engl. J. Med., 344, 601-602.
8. Jones,P.A. and Takai,D. (2001) The role of DNA methylation in mammalian epigenetics. Science, 293, 1068-1070.
9. Clark,S.J., Harrison,J., Paul,C.L. and Frommer,M. (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res., 22, 2990-2997.
10. Zhang,L., Cui,X., Schmitt,K., Hubert,R., Navidi,W. and Arnheim,N. (94) Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl Acad. Sci. USA, 89 5847-5851.
11. Lage,J.M., Leamon,J.H., Pejovic,T. et al. (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res., 13, 294-307.
12. Yu,Y.P., Landsittel,D.L., Jing,L. et al. (2004) Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J. Clin. Oncol., 22, 2790-2799.
13. Lee,W.H., Morton,R.A., Epstein,J.I., Brooks,J.D., Campbell,P.A., Bova,G.S., Hsieh,W.S., Isaacs,W.B. and Nelson,W.G. (1994) Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc. Natl Acad. Sci. USA, 91, 1173-11737.
14. Chetcuti,A., Margan,S.H., Russell,P., Mann,S., Millar,D.S., Clark,S.J., Rogers,J., Handelsman,D.J. and Dong,Q. (2001) Loss of annexin II heavy and light chains in prostate cancer and its precursors. Cancer Res., 61, 6331-6334.
15. Yan,P.S., Chen,C.M., Shi,H., Rahmatpanah,F., Wei,S.H., Caldwell,C.W. and Huang,T.H. (2001) Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res. 61, 8375-8380.
16. Gitan,R.S., Shi,H., Chen,C.M., Yan,P.S. and Huang,T.H. (2002) Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res., 12, 158-164.
17. Shi,H., Maier,S., Nimmrich,I., Yan,P.S., Caldwell,C.W., Olek,A. and Huang,T.H. (2003) Oligonucleotide-based microarray for DNA methylation analysis: principles and applications. J. Cell. Biochem. 88, 138-143.
18. Yamamoto,F. and Yamamoto,M. (2004) A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses. Mol. Genet. Genomics, 271, 678-686.
19. Luo,J.H., Yu,Y.P., Cieply,K., Lin,F., Deflavia,P., Dhir,R., Finkelstein,S., Michalopoulos,G. and Becich,M. (2002) Gene expression analysis of prostate cancers. Mol. Carcinog., 33, 25-35.
20. Dhanasekaran,S.M., Barrette,T.R., Ghosh,D., Shah,R., Varambally,S., Kurachi,K., Pienta,K.J., Rubin,M.A. and Chinnaiyan,A.M. (2001) Delineation of prognostic biomarkers in prostate cancer. Nature 412, 822-826.
21. Luo,J., Duggan,D.J., Chen,Y., Sauvageot,J., Ewing,C.M., Bittner,M.L., Trent,J.M. and Isaacs,W.B. (2001) Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Res., 61, 4683-4688.
22. Singh,D., Febbo,P.G., Ros,K. et al. (2002) Gene expression correlates of clinical prostate cancer behavior. Cancer Cell, 1, 203-209.
23. Luo,J.H. and Yu,Y.P. (2003) Genetic factors underlying prostate cancer. Expert Rev. Mol. Med., 5, 1-26.
24. Yegnasubramanian,S., Kowalski,J., Gonzalgo,M.L. et al. (2004) Hypermethylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res., 64, 1975-1986.