Identification of Histone Epigenetic Modifications with Chromatin Immunoprecipitation PCR Array in Chronic Lymphocytic Leukemia Specimens

Histone epigenetic modifications are one of the frequently observed epigenetic alterations in leukemic cells. To efficiently identify histone acetylation status of a number of gene promoters in chronic lymphocytic leukemia (CLL) specimens, we performed a combination of chromatin immunoprecipitation (ChIP) and PCR array. ChIP by an antipan acetylated H4 histone antibody was followed by a PCR amplification of gene promoters (n=84) to determine their histone acetylation status. A subset of genes with differential histone acetylation status was identified in CLL specimens, and their RNA expression level was correlated with real time quantitative RT-PCR analysis (qRT-PCR). Globally CLL specimens have more hypo-acetylated or epigenetically silenced gene promoters as compared to normal peripheral-blood mononuclear cells. Promoters of E-cadherin, Fos, CDKN2B, c-Jun, BAX genes were found to be histone hypo-acetylated while the promoters of cyclin D1, CDK4, Myc, and TGF beta were hyper-acetylated. The histone acetylation status correlated well with qRT-PCR analysis of a number of CLL specimens. Based on the ChIP-PCR array epigenetically silenced genes and transcriptionaly active genes can be identified. Histone deacetylase inhibitors (HDACi) induce apoptosis in CLL specimens and to determine changes in gene transcription induced by HDACi the ChIP-PCR array was performed with HDACi treatment. Interestingly the HDACi exposure resulted in histone hyper-acetylation of a subset of genes with increased expression of CDKN2B, c-Jun and BAX RNA while promoters of pro-growth and survival genes such as BCL-2, NFKB1, beta-catenin and CDK4 underwent promoter histone hypo-acetylation and downregulation of their RNA expression. The ChIP-PCR array assay can be utilized to detect histone modifications in the genome of leukemic cells and reflects the transcriptional status of the genes. Journal of Cancer Science & Therapy J o u r na l o f C anc er ence & Tera p y