Abstract 4677: Integrated molecular profiles and guadecitabine response in relapsed/refractory acute myeloid leukemia

• Published in: Cancer research (Chicago, Ill.) Ill.), 2017-07, Vol.77 (13_Supplement), p.4677-4677
• Main Authors: Chung, Woonbok, Kelly, Andrew D., Kropf, Patricia, Taverna, Pietro, Naim, Sue, Azab, Mohammad, Jelinek, Jaroslav, Kantarjian, Hagop M., Issa, Jean-Pierre J.
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2017-4677

Epigenetic patterns of DNA methylation are frequently altered in acute myeloid leukemia (AML). Guadecitabine is a novel next generation hypomethylating drug with a demonstrated clinical activity in elderly AML. In our previous study of guadecitabine, we identified in relapsed/refractory (r/r) AML patients a gene expression signature (high DNMT3B, low P15, and low CDA) associated with reduced LINE-1 demethylation and resistance to the drug. Since pharmacodynamics only explains a small portion of the variability in response to guadecitabine, we suggest that intrinsic genetic and epigenetic characteristics can distinguish responders from non-responders. We analyzed genome-wide methylation patterns and screened 54 genes frequently mutated in leukemia in DNA from pre-treatment blood or bone marrow from 119 patients with r/r AML enrolled in guadecitabine phase I/II trials. Blood samples from 49 healthy donors were used as controls. We also examined expression of a panel of genes (CDA, P15, P21, DNMT3B, DNMT3A, DNMT1, and CTCF) at baseline by quantitative RT-PCR. Global DNA methylation at pre/post treatment was estimated by bisulfite-pyrosequencing of the LINE-1 repetitive sequence. For comparing methylation profiles at CpG islands (CGI), we performed hierarchical clustering analysis of differentially methylated 2794 CGI sites in 119 r/r AML and 49 healthy controls. Hierarchical clustering split them into 3 main groups of normal-like cluster (n=36), intermediate (n=41) and CpG island methylator phenotype (CIMP) like cluster (n=42). Normal-like cluster had a higher response rate (39 %) compared to intermediate (17%) and CIMP- like cluster (15%) (p=0.025, Fisher’s exact test). Demethylation rate of LINE-1 was lower in CIMP-like cluster than in normal-like and intermediate cluster (average demethylation -19 ± 2 % in CIMP-like cluster vs. -31 ± 2 % in normal-like vs. -23 ± 2 % in intermediate cluster, p=0.0007, One-way ANOVA). Mutation screening revealed frequent alterations affecting signaling pathways (CSF3R, KIT, KRAS, NRAS and FLT3) in the CIMP-like cluster (62%) compared to normal-like (11%) and intermediate cluster (13%) (p