Abstract 4677: Integrated molecular profiles and guadecitabine response in relapsed/refractory acute myeloid leukemia
Authors: Woonbok Chung, Andrew D. Kelly, Patricia Kropf, Pietro Taverna, Sue Naim, Mohammad Azab, Jaroslav Jelinek, Hagop M. Kantarjian, Jean-Pierre J. Issa
Journal: Cancer Research (2017)

Abstract 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&amp;lt;0.0001, Fisher’s exact test). High number of hypermethylated sites per patient was prominent in the CIMP-like cluster and associated with a four gene expression classifier z-score (low CDA, low P15, low CTCF and high DNMT3B) (R=-0.637, p&amp;lt;0.0001) as well as resistance to guadecitabine (mean of 4 gene z-score 0.54 in non-responders vs. 2.31 in responders, p=0.001). We propose that DNA hypermethylation at CpG islands, mutations in signaling pathways and unfavorable gene expression signature can be developed as biomarkers predicting resistance to guadecitabine in r/r AML. This trials were registered at www.clinicaltrials.gov as NCT02293993 (Phase I) and NCT02197676 (Phase II). Citation Format: Woonbok Chung, Andrew D. Kelly, Patricia Kropf, Pietro Taverna, Sue Naim, Mohammad Azab, Jaroslav Jelinek, Hagop M. Kantarjian, Jean-Pierre J. Issa. Integrated molecular profiles and guadecitabine response in relapsed/refractory acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4677. doi:10.1158/1538-7445.AM2017-4677