Global gene methylation profiling of CLL patients and its implication in therapy Free

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Aberrant DNA methylation of multiple promoter associated CpG islands is a very prevalent phenomenon in human leukemias. Data from our laboratory indicates that methylation profiling allows us to identify patients with leukemia at different risk and develop molecular tools to determine minimal residual disease at the time of initial remission. Despite the advances in the understanding of the molecular biology of CLL, very few studies on DNA methylation have been performed in CLL. In the current study, we investigated the global gene methylation profile of CLL patients using novel MCA/promoter array technique. We found around 280 gene-associated promoter CpG islands are differentially methylated in CLL patients as compared with normal controls. We further investigated 11 of these genes (LHX1, GALGT2, TFAP2C, ING1, SOX11, SALL1, LTBP2, APP, DXL1, GPS1 and MLL1) in a cohort of 78 CLL patients and 10 healthy control. Our results indicate that most of these genes (except SALL1 and MLL1) are frequently hypermethylated in CLL patients compared with healthy controls. Expression analysis of four selected genes (LHX1, GALGT2, TFAP2C and Prima1) in CLL cell lines (MEC1 and EHBH) and CLL patient samples by real-time PCR further confirmed methylation associated gene silencing, and treatment of these cell lines with demethylating agents resulted in gene re-expression. Further analysis showed that methylation status of some of these genes are associated with patient survival and prognosis. Our studies indicate that MCA/promoter array technique allows us to identify global aberrantly methylated CGIs in CLL and also identify novel biomarkers that could be useful in profiling of CLL and other cancers.