A Pathway-focused GSEA Platform In AML That Interrogates Interaction of Flt3ITD and tMLL with Their Epigenetic Targets (p16INK4a, DAPK1, and RUNX3), While Accurately Reporting Broad-based AML Prognosis and Targeting-agent Sensitivity.
Authors: Baghdadi Tareq Al , Goswami Chirayu , Sayar Hamid , Sargent Katie J. , Cripe Larry , Li Lang , Shanmugam Rajasubramaniam , Boswell H. Scott 
Published: October 2019

Abstract
Abstract 1660
GSEA (gene-set enrichment array) analysis for expression levels in acute myeloid leukemia (AML) blasts of hoxA9/meis1, has afforded additional prognostic capacity to cytogenetically-defined subtypes. Signaling pathway (KEGG, GO, Ingenuity) analysis of Affymetrix gene expression data has also been used to predict prognosis of AML patients, identifying an adverse high MAPK gene signature. Genome-wide epigenetic (DNA methylation) profiling has added to AML prognostication. We analyzed patient prognosis and in vitro sensitivity for blasts by pathway-targeting agents, in relation to expression clusters defined by the results of GSEA profiling. Blast cell sensitivity was assayed using the agents: (Tyrosine kinase inhibitors for: Flt3: Sorafenib (Onyx/Bayer) and Syk/Flt3: R406 (AstraZeneca); Bortezomib (Millenium), a proteasome- and NFkB- inhibitor, inducer of endoplasmic reticulum (ER) stress; or the pan-histone deacetylase (HDAC) inhibitor, SBHA, Vorinostat analogue). A group of 70 AML cases was studied. GSEA's (Taqman/RQ-PCR, ABI) were performed on two different 31-gene platforms interrogating the interaction of tyrosine kinase survival pathways (eg. Flt3) with downstream epigenetic targets: tumor suppressor genes DAPK1, p16INK4a/CDKN2A, and RUNX3. Expression levels of these are responsive to input from c-jun/AP-1, non-canonical NFkB isoforms/HDAC's, polycomb genes, and ets/ERG, which were monitored. Analysis of overall patient survival (OS) by Kaplan-Meier plots revealed conformity with established outcomes for conventional cytogenetic categories. Also, poor-risk categories defined by normal karyotype Flt3ITD mutation, as well as high hoxA9 and meis1 expressions were recognized. Classification categories involving NKFlt3ITD/high hoxA9/meis1 or complex cytogenetics/high MAPK were most strictly separated by Kaplan-Meier curves, and by representation on the GSEA heatmaps, vs. CBF/PML-RAR translocations. Specific association, between repression of the tumor suppressor DAPK1 (normalized to c-jun, a transcriptional activator) with high expressions of hoxA9 and DAPK1-repressive, non-canonical NFkB/relB, was apparent in most NKFlt3ITD and tMLL cases. Also, a known functional interaction implicating high Id1 expression with its repression of p16INK4a(CDKN2A) was linked by their expression levels on GSEA. The DAPK1/CDKN2A clusters demonstrated significant overlap, often with additional RUNX3 repression. The DAPK1-repressed(R) clusters demonstrated independent prognostic importance. There was median OS for DAPK1-R cluster #1(lower MAPK signature) of 17 months vs. for DAPK1-R cluster #2 of 6 months. This latter cluster was described by higher MAPK signature evidenced by heightened transcript levels of BRCA1 [Bullinger et al. Blood, 2007], FoxM1, bcl-2, IL-1b. The dominant cytogenetic/molecularly-defined phenotypes represented in these DAPK1-R clusters were NKFlt3ITD+ve and tMLL. A very-high MAPK/complex cluster, evidenced median OS 4.5 months vs. good prognosis (low MAPK/DAPK1, and low hoxA9/meis1) group: median OS> 3 years. Interestingly, in vitro activity for the dual inhibitor R406 on blasts was greatest in the category with strongest repression of both p16INK4a/CDKN2A and DAPK1, and with lowest expression of syk transcripts (10-fold compared with high patient values), with a median IC50 of between 10 nM (tMLL)-100nM (Flt3ITD). By contrast, Sorafenib demonstrated its greatest activity in a high MAPK phenotype, including but not restricted to Flt3ITD+ve status. Bortezomib demonstrated median IC50 40 nM. However, high expression levels of FoxM1, putative Bortezomib target, were negatively-associated with its activity. SBHA, the HDAC inhibitor, demonstrated lower activity on a molar basis, but had important synergy with tyrosine kinase inhibitors, a property that was optimal in the context of Id1 hyperexpression. Bortezomib was strongly synergistic with Flt3/syk inhibitors, particularly on FltITD+ve blasts. Indeed, both Bortezomib and the HDAC inhibitor demonstrated by correlation analysis (coefficients=63.3 and 13.4, respectively) optimal activities with Id1 hyperexpression. In conclusion, a pathway-focused genetic and epigenetic prognostic classification that also reports targeting agent sensitivity was established and further validated in a phase I (Sorafenib/Vorinostat) trial in AML (H Sayar, these abstracts).

Disclosures:
Sayar: Onyx/Bayer: Research Funding.