Abstract 3647: Gene expression analysis in AML cell line MV4-11 following treatment with the anti-cancer aptamer AS1411
Authors: Senderovich Shai , Ajami Alfred , Doran Ben , McLaughlin Fiona , Jones David 
Published: February 2011

AS1411 is a 26-base DNA aptamer which is shortly due to enter a phase IIb clinical trial in acute myeloid leukaemia (AML). In an initial phase II trial in AML, combination of AS1411 with cytarabine produced an increased response rate compared to cytarabine alone, and AS1411 was well tolerated. When cells in culture are exposed to AS1411, a cytostatic effect is observed initially, followed by cell death after 72 to 96 hours. Several mechanisms have been described by which AS1411 exerts these effects; we performed a gene expression microarray analysis to evaluate which cellular pathways and functions were modulated by AS1411 treatment. We also sought to identify biomarkers for drug activity which could be translated to use in the clinic in the forthcoming phase IIb trial.

The AML cell line MV4-11 was exposed to AS1411 at two concentrations; these approximated concentrations observed in patient plasma following two different doses of AS1411 in the prior phase II trial. mRNA was isolated from cells at 24 and 72 hours, time points associated with cytostatic and cytotoxic effects, respectively. Controls at time zero and in the absence of drug were also analysed. The Affymetrix plus 2™ arrays were processed and the raw data were normalised according to the Rosetta Resolver model. The gene lists for each time point (4 replicates) were then clustered non-hierarchically and distributed into pathways using MetaCore™.

Gene clusters were separately generated to identify specific genes which were up- or down-regulated at different doses and different time-points. These were then compared to identify those that were regulated by a common pathway. Pathways and regulatory networks that were either up- or down-regulated after exposure to AS1411 included nuclear import/export, nucleotide biosynthesis/metabolism, DNA damage response and pathways related to cell cycle control and cell death (including genes in the p53 signalling pathway). While some of these activities had been shown previously to be modified upon AS1411 exposure, other findings are novel.

A number of genes showed marked changes in expression following AS1411 exposure; these are undergoing validation by quantitative PCR as potential biomarkers. They include upregulated genes TP53i3 and p21 (p53 signalling pathway), RDM1 (DNA damage), YPEL3 and DAPK1 (proliferation and apoptosis) as well as individual genes such as GNG7. Several genes, including INO80C, exhibited a marked dose-dependent down regulation.

This work demonstrates that a number of cellular activities are modulated by AS1411, and provides important information for the future clinical development of AS1411, including pointers to the selection of biomarkers for analysis of blood and bone marrow samples from patients in the forthcoming phase IIb study in AML.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3647.