Abstract 5430: Analysis of genome-wide DNA methylation in CCRF-CEM cells confirms hypermethylation at reported epigenetic markers of T-cell lymphoblastic leukemia and identifies novel therapeutic targets with reduced methylation upon treatment with dietary indoles

Abstract

Abstract Acute lymphoblastic leukemia/lymphoma (ALL) is the most common class of malignancies among children and cases of T-cell origin are less responsive to therapy than their B-cell counterparts. Cruciferous vegetables have been demonstrated to be chemoprotective in a number of cancer cell types due to their high content of indoles and isothiocyanates. Previously, we demonstrated that indole-3-carbinol (I3C) is an effective transplacental chemopreventive agent in a dibenzo[def, p]chrysene (DBC)-induced model of murine T-ALL. We further confirmed that treatment of human T-ALL cell lines with I3C and diindolylmethane (DIM), the primary product of I3C condensation, reduces cell proliferation, viability, and expression of cell-cycle proteins. Aberrant DNA methylation is a recognized event in the development of cancer and pharmacological demethylation of promoter-associated CpG islands is of therapeutic interest to restore expression of epigenetically silenced genes. We utilized genome-wide DNA methylation analysis to identify potential epigenetic therapeutic targets of I3C and DIM in a model of T-ALL. By differential methylation region (DMR) analysis with stringent bonferroni multiple testing correction, 1,699 DMR probes were identified which mapped to 298 unique transcripts. The differential degree of hypomethylation by I3C, compared with DIM, is consistent with previous findings that DIM is a more potent therapeutic in this model. I3C (60 µM) significantly reduced methylation in 53% of DMRs yet increased methylation in the remaining 173 gene-mapped DMRs. DIM treatment with the consumer available supplement formulation known as Bioresponse-DIM (BR-DIM; 5 µM), or with the pure crystalline form (C-DIM; 5 µM or 15 µM), reduced methylation in over 500 probes and more than 200 genes. Functional annotation of differentially hypomethylated genes revealed that homeobox genes and transcription factors were most commonly represented with negative regulators of apoptosis and Wnt/Frizzled families also among the top gene clusters. Many identified genes have been previously recognized as being frequently hypermethylated in hematological malignancies and our results support demethylation of these critical cancer survival pathways by dietary indoles derived from cruciferous vegetables. These and novel genes from our analysis are currently being validated and examined at the level of transcription. Supported by P01CA90890, P42ES016465, CA135523 and The Linus Pauling Institute. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5430. doi:1538-7445.AM2012-5430