Abstract
A pharmacological-based global screen for epigenetically silenced tumor suppressor genes was performed in MCF-7 and MDA-MB-231 breast cancer cells. Eighty-one genes in MCF-7 cells and 131 in MDA-MB-231 cells were identified, that had low basal expression and were significantly upregulated following treatment. Eighteen genes were studied for methylation and/or expression in breast cancer; PTCH, the receptor for the hedgehog (Hh) pathway and a known tumor suppressor gene, was selected for further analysis. Methylation of the PTCH promoter was found in MCF-7 cells and in breast cancer samples, and correlated with low PTCH expression. Immunohistochemical analysis of breast tissue arrays revealed high expression of PTCH in normal breast compared to ductal carcinomas in situ (DCIS) and invasive ductal carcinomas; furthermore, association was found between PTCH expression and favorable prognostic factors. PTCH is an inhibitor of the Hh pathway, and its silencing activates the pathway and promotes growth. Indeed, high activity of the Hh pathway was identified in MCF-7 cells and overexpression of PTCH inhibited the pathway. Moreover, treatment with cyclopamine, an inhibitor of the pathway, reduced cell growth and slowed the cell cycle in these cells. Thus, unmasking of epigenetic silencing in breast cancer enabled us to discover a large number of candidate tumor suppressor genes. Further analysis suggested a role of one of these genes, PTCH, in breast cancer tumorigenesis.
Similar content being viewed by others
References
Widschwendter M, Jones PA (2002) DNA methylation and breast carcinogenesis. Oncogene 21:5462–5482
Szyf M, Pakneshan P, Rabbani SA (2004) DNA methylation and breast cancer. Biochem Pharmacol 68:1187–1197
Ottaviano YL, Issa JP, Parl FF, Smith HS, Baylin SB, Davidson NE (1994) Methylation of the estrogen receptor gene CpG island marks loss of estrogen receptor expression in human breast cancer cells. Cancer Res 54:2552–2555
Christman JK (2002) 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene 21:5483–5485
Villar-Garea A, Esteller M (2004) Histone deacetylase inhibitors: understanding a new wave of anticancer agents. Int J Cancer 112:171–178
Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB (1999) Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 21:103–107
Suzuki H, Gabrielson E, Chen W, Anbazhagan R, van Engeland M, Weijenberg MP et al (2002) A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31:141–149
Yamashita K, Upadhyay S, Osada M, Hoque MO, Xiao Y, Mori M et al (2002) Pharmacologic unmasking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma. Cancer Cell 2:485–495
Tokumaru Y, Yamashita K, Osada M, Nomoto S, Sun DI, Xiao Y et al (2004) Inverse correlation between cyclin A1 hypermethylation and p53 mutation in head and neck cancer identified by reversal of epigenetic silencing. Cancer Res 64:5982–5987
Lodygin D, Epanchintsev A, Menssen A, Diebold J, Hermeking H (2005) Functional epigenomics identifies genes frequently silenced in prostate cancer. Cancer Res 65:4218–4227
Takai N, Kawamata N, Walsh CS, Gery S, Desmond JC, Whittaker S et al (2005) Discovery of epigenetically masked tumor suppressor genes in endometrial cancer. Mol Cancer Res 3:261–269
Lacroix M, Leclercq G (2004) Relevance of breast cancer cell lines as models for breast tumours: an update. Breast Cancer Res Treat 83:249–289
Beachy PA, Karhadkar SS, Berman DM (2004) Tissue repair and stem cell renewal in carcinogenesis. Nature 432:324–331
Lewis MT, Veltmaat JM (2004) Next stop, the twilight zone: hedgehog network regulation of mammary gland development. J Mammary Gland Biol Neoplasia 9:165–181
Cohen MM Jr (2005) The hedgehog signaling network. Am J Med Genet 123:5–28
Hahn H, Wicking C, Zaphiropoulous PG, Gailani MR, Shanley S, Chidambaram A et al (1996) Mutations of the human homolog of Drosophila patched in the nevoid basal cell carcinoma syndrome. Cell 1996:841–851
Denef N, Neubuser D, Perez L, Cohen SM (2000) Hedgehog induces opposite changes in turnover and subcellular localization of patched and smoothened. Cell 102:521–531
Taipale J, Cooper MK, Maiti T, Beachy PA (2002) Patched acts catalytically to suppress the activity of Smoothened. Nature 418:892–897
Berman DM, Karhadkar SS, Hallahan AR, Pritchard JI, Eberhart CG, Watkins DN et al (2002) Medulloblastoma growth inhibition by hedgehog pathway blockade. Science 297:1559–1561
Watkins DN, Berman DM, Burkholder SG, Wang B, Beachy PA, Baylin SB (2003) Hedgehog signalling within airway epithelial progenitors and in small-cell lung cancer. Nature 422:313–317
Thayer SP, di Magliano MP, Heiser PW, Nielsen CM, Roberts DJ, Lauwers GY et al (2003) Hedgehog is an early and late mediator of pancreatic cancer tumorigenesis. Nature 425:851–856
Berman DM, Karhadkar SS, Maitra A, Montes De Oca R, Gerstenblith MR, Briggs K et al (2003) Widespread requirement for Hedgehog ligand stimulation in growth of digestive tract tumours. Nature 425:846–851
Oniscu A, James RM, Morris RG, Bader S, Malcomson RD, Harrison DJ (2004) Expression of Sonic hedgehog pathway genes is altered in colonic neoplasia. J Pathol 203:909–917
Sanchez P, Hernandez AM, Stecca B, Kahler AJ, DeGueme AM, Barrett A et al (2004) Inhibition of prostate cancer proliferation by interference with Sonic Hedgehog-Gli1 signaling. Proc Natl Acad Sci U S A 101:12561–12566
Karhadkar SS, Bova GS, Abdallah N, Dhara S, Gardner D, Maitra A et al (2004) Hedgehog signalling in prostate regeneration, neoplasia and metastasis. Nature 431:707–712
Sheng T, Li C, Zhang X, Chi S, He N, Chen K et al (2004) Activation of the hedgehog pathway in advanced prostate cancer. Mol Cancer 3:29
Calzada-Wack J, Kappler R, Schnitzbauer U, Richter T, Nathrath M, Rosemann M et al (2002) Unbalanced overexpression of the mutant allele in murine Patched mutants. Carcinogenesis 23:727–733
Uhmann A, Ferch U, Bauer R, Tauber S, Arziman Z, Chen C et al (2005) A model for PTCH1/Ptch1-associated tumors comprising mutational inactivation, gene silencing. Int J Oncol 27:1567–1575
Toyota M, Kopecky KJ, Toyota MO, Jair KW, Willman CL, Issa JP (2001) Methylation profiling in acute myeloid leukemia. Blood 97:2823–2829
Lewis MT, Ross S, Strickland PA, Sugnet CW, Jimenez E, Scott MP et al (1999) Defects in mouse mammary gland development caused by conditional haploinsufficiency of Patched-1. Development 126:5181–5193
Lewis MT, Ross S, Strickland PA, Sugnet CW, Jimenez E, Hui C et al (2001) The Gli2 transcription factor is required for normal mouse mammary gland development. Dev Biol 238:133–144
Chang-Claude J, Dunning A, Schnitzbauer U, Galmbacher P, Tee L, Wjst M et al (2003) The patched polymorphism Pro1315Leu (C3944T) may modulate the association between use of oral contraceptives and breast cancer risk. Int J Cancer 103:779–783
Xie J, Johnson RL, Zhang X, Bare JW, Waldman FM, Cogen PH et al (1997) Mutations of the PATCHED gene in several types of sporadic extracutaneous tumors. Cancer Res 57:2369–2372
Oro AE, Higgins KM, Hu Z, Bonifas JM, Epstein EH Jr, Scott MP (1997) Basal cell carcinomas in mice overexpressing sonic hedgehog. Science 276:817–821
Kubo M, Nakamura M, Tasaki A, Yamanaka N, Nakashima H, Nomura M et al (2004) Hedgehog signaling pathway is a new therapeutic target for patients with breast cancer. Cancer Res 64:6071–6074
Hu Z, Bonifas JM, Aragon G, Kopelovich L, Liang Y, Ohta S et al (2003) Evidence for lack of enhanced hedgehog target gene expression in common extracutaneous tumors. Cancer Res 63:923–928
Mukherjee S, Frolova N, Sadlonova A, Novak Z, Steg A, Page GP et al (2006) Hedgehog signaling, response to cyclopamine differ in epithelial, stromal cells in benign breast, breast cancer. Cancer Biol Ther 5:674–683
Wolf I, O’Kelly J, Rubinek T, Tong M, Nguyen A, Lin BT et al (2006) 15-hydroxyprostaglandin dehydrogenase is a tumor suppressor of human breast cancer. Cancer Res 66:7818–7823
Munster PN, Troso-Sandoval T, Rosen N, Rifkind R, Marks PA, Richon VM (2001) The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells. Cancer Res 61:8492–8497
Domann FE, Rice JC, Hendrix MJ, Futscher BW (2000) Epigenetic silencing of maspin gene expression in human breast cancers. Int J Cancer 85:805–810
Gagnon J, Shaker S, Primeau M, Hurtubise A, Momparler RL (2003) Interaction of 5-aza-2′-deoxycytidine and depsipeptide on antineoplastic activity and activation of 14–3-3sigma, E-cadherin and tissue inhibitor of metalloproteinase 3 expression in human breast carcinoma cells. Anticancer Drugs 14:193–202
Taipale J, Chen JK, Cooper MK, Wang B, Mann RK, Milenkovic L et al (2000) Effects of oncogenic mutations in Smoothened and Patched can be reversed by cyclopamine. Nature 406:1005–1009
Futscher BW, O’Meara MM, Kim CJ, Rennels MA, Lu D, Gruman LM et al (2004) Aberrant methylation of the maspin promoter is an early event in human breast cancer. Neoplasia 6:380–9
Grothey A, Hashizume R, Sahin AA, McCrea PD (2000) Fascin, an actin-bundling protein associated with cell motility, is upregulated in hormone receptor negative breast cancer. Br J Cancer 83:870–873
Spychala J, Lazarowski E, Ostapkowicz A, Ayscue LH, Jin A, Mitchell BS (2004) Role of estrogen receptor in the regulation of ecto-5′-nucleotidase and adenosine in breast cancer. Clin Cancer Res 10:708–717
Maesawa C, Tamura G, Iwaya T, Ogasawara S, Ishida K, Sato N et al (1998) Mutations in the human homologue of the Drosophila patched gene in esophageal squamous cell carcinoma. Genes Chromosomes Cancer 21:276–279
McGarvey TW, Maruta Y, Tomaszewski JE, Linnenbach AJ, Malkowicz SB (1998) PTCH gene mutations in invasive transitional cell carcinoma of the bladder. Oncogene 17:1167–1172
Kogerman P, Krause D, Rahnama F, Kogerman L, Unden AB, Zaphiropoulos PG et al (2002) Alternative first exons of PTCH1 are differentially regulated in vivo and may confer different functions to the PTCH1 protein. Oncogene 21:6007–6016
Nagao K, Toyoda M, Takeuchi-Inoue K, Fujii K, Yamada M, Miyashita T (2005) Identification and characterization of multiple isoforms of a murine and human tumor suppressor, patched, having distinct first exons. Genomics 85:462–471
Raffel C, Jenkins RB, Frederick L, Hebrink D, Alderete B, Fults DW et al (1997) Sporadic medulloblastomas contain PTCH mutations. Cancer Res 57:842–845
Minobe K, Onda M, Iida A, Kasumi F, Sakamoto G, Nakamura Y et al (1998) Allelic loss on chromosome 9q is associated with lymph node metastasis of primary breast cancer. Jpn J Cancer Res 89:916–922
Katayam M, Yoshida K, Ishimori H, Katayama M, Kawase T, Motoyama J et al (2002) Patched and smoothened mRNA expression in human astrocytic tumors inversely correlates with histological malignancy. J Neurooncol 59:107–115
Acknowledgments
This work was supported in part by the Inger Fund, Alec Borden Trust, Rountree Trust and the Mary Barry Foundation and by grants from the Women’s Cancer Research Institute, Samuel Oschin Comprehensive Cancer Institute at Cedars-Sinai Medical Center. HPK is a member of the Molecular Biology Institute and Jonsson Comprehensive Cancer Center at UCLA, and holds the endowed Mark Goodson Chair of Oncology Research at Cedars-Sinai Medical Center/UCLA School of Medicine. IW is the Mary Barry Medical Bridges Foundation Fellow. We thank PA Beachy (Johns Hopkins University School of Medicine, MD) for the PTCH and Gli-luciferase expression vectors.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Supplemental Table 1
ESM1 (XLS 135 KB)
Supplemental Table 2
ESM2 (XLS 168 KB)
Supplemental Table 3
ESM3 (DOC 32KB)
Rights and permissions
About this article
Cite this article
Wolf, I., Bose, S., Desmond, J.C. et al. Unmasking of epigenetically silenced genes reveals DNA promoter methylation and reduced expression of PTCH in breast cancer. Breast Cancer Res Treat 105, 139–155 (2007). https://doi.org/10.1007/s10549-006-9440-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10549-006-9440-4