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Seminar

Transcriptome Profiling of Epigenetic Modifying Drugs in Prostate Cancer

Shabana Shabbeer
Albert Einstein School of Medicine

Date: Wednesday, November 11th, 2009
Location CII (LOW) 3116 - 4:00 p.m. to 5:00 p.m.

Abstract:

50 years after the deciphering of the genetic code, attention has now turned to epigenetic mechanisms like DNA methylation, histone modifications, chromatin modification, and RNA interference. There is now sufficient evidence to implicate epigenetic mechanisms in regulating gene activation and inactivation in order to define the normal phenotype. The cancer phenotype too is not immune to epigenetic changes. In many cancer types, the cancer cell has hijacked its own normally functioning epigenetic machinery to result in epigenetic alterations that may further fuel the carcinogeneic process. This knowledge has led to an increasing interest in cancer drugs that interfere with the epigenetic machinery. Common drugs that act epigenetically are the DNA Methyl Transferase (DNMT) Inhibitors (DNMTi) like 5-aza-2'-deoxycytidine, and the Histone Deacetylase Inhibitors (HDACi) like Valproic acid (VPA). Like their names suggest, the former class of drugs alter the methylation state of the DNA while the latter alter the acetylation state of chromatin. However, these drugs are not "clean", resulting in pleiotropic effects other than the ones suggested. Hence, it is still an open question as to what functions these drugs ultimately result in the desired phenotypic change that they are being used for. In order to understand if drug resistant and sensitive phenotypes are a consequence of the epigenetic states, prostate cancer cell lines, DU145 and PC3, were treated with HDACi and the changed gene expression pattern studied by cDNA microarray analysis. In order to study the effect of different HDACis (vorinostat and VPA) and incubation periods (48h and 96h) on two prostate cancer cell lines, DU145 and PC3, a novel "multiple-loop, double-cube" cDNA microarray experiment was designed. With this design, 16 conditions could be tested on 22 microarrays. The microarrays consist of 21,073 60-mer probes printed at random on a glass slide. Although microarray technology has been widely adopted by the scientific community, analysis of the ensuing data remains challenging. All analyses in this study were done using the software Bioconductor limma and marray packages for R. The analysis revealed that a different expression caused by HDACi treatment of 2.8% to 10% (P < 0.001) in the relatively resistant PC3 cells and more sensitive DU145 cells respectively had occurred. The extent of differential expression was associated with cell line, DU145 > PC3 - shedding light on why the former is more sensitive to HDACi than the latter, HDACi, VPA > vorinostat - identifying the more potent HDACi, and duration of treatment (96h > 48h). The microarray analysis also identified known and new treatment targets involving in cell cycle and apoptosis.

Further studies with HDACis revealed that VPA caused changes that are a hallmark of the DNMTi class of drugs. This includes demethylation of the Androgen Receptor in the DU145 cells. At least one of the mechanisms by which VPA modulates methylation is by inhibiting the anchoring of DNMT to the chromatin via a decrease in the levels of PCNA, its DNA anchoring partner. Thus if HDACi treatment results in (de)methylation changes, then there may be similarities in gene (re)expression patterns between the two different classes of drugs. Such similarities may be identified by analyzing microarray data of DNMTi and HDACi treated cells. Like in the case of the resistant and sensitive cells above, such analysis may be computationally challenging. Knowledge generated from this analysis will provide further insight into the mechanisms of acction of these two classes of drugs.

Bio:

Shabana Shabbeer obtained her PhD in Biochemistry from the Cancer Research Institute in Mumbai, India in 2003. Soon after, she had a short stint as an editor of a science magazine. Research beckoned again and she left her editorial duties to pursue a postdoctoral fellowship at the Johns Hopkins Medical Institution, Baltimore. Here she studied the mechanism of action of epigenetic drugs. Her preclinical studies there led the way to clinical trials for epigenetic drugs for solid tumors.

Currently she is a Research Associate at the Einstein School of Medicine, NY where as part of her research interests in the chemoprevention of cancer, she is working on discovering biomarkers of prognosis of breast cancer.

Last updated: September 29, 2009