A standardized microarray assay for the independent gene expression markers in AML: EVI1 and BAALC

Jaap Brand,Erik H Van Beers,Bob Löwenberg,Leonie De Best,Henk E Viëtor,Peter Jm Valk,Martin H Van Vliet

doi:10.1186/2162-3619-2-7

Jaap Brand, Erik H Van Beers + Show 5 more

Open Access

https://doi.org/10.1186/2162-3619-2-7

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Abstract

High levels of BAALC, ERG, EVI1 and MN1 expression have been associated with shorter overall survival in AML but standardized and clinically validated assays are lacking. We have therefore developed and optimized an assay for standardized detection of these prognostic genes for patients with intermediate cytogenetic risk AML. In a training set of 147 intermediate cytogenetic risk cases we performed cross validations at 5 percentile steps of expression level and observed a bimodal significance profile for BAALC expression level and unimodal significance profiles for ERG and MN1 levels with no statistically significant cutoff points near the median expression level of BAALC, ERG or MN1. Of the possible cutoff points for expression levels of BAALC, ERG and MN1, just the 30th and 75th percentile of BAALC expression level and the 30th percentile of MN1 expression level cutoff points showed clinical significance. Of these only the 30th percentile of BAALC expression level reproduced in an independent verification (extended training) data set of 242 cytogenetically normal AML cases and successfully validated in an external cohort of 215 intermediate cytogenetic risk AML cases. Finally, we show independent prognostic value for high EVI1 and low BAALC in multivariate analysis with other clinically relevant molecular AML markers. We have developed a highly standardized molecular assay for the independent gene expression markers EVI1 and BAALC.

Highlights

Overexpressions of Ecotropic Viral Integration 1 (EVI1), Brain and acute leukemia cytoplasmic (BAALC), ETS-related gene (ERG), and Meningioma 1 (MN1) have been reported to be prognostically relevant in Acute myeloid leukemia (AML) [1-9]
overall survival (OS) prognostic assay for BAALC, ERG, and MN1 BAALC, ERG and MN1 gene expression levels were determined in a standardized assay suitable for single case analysis in a training set, an independent verification set and one independent validation set of AML patients
We have developed a standardized assay for BAALC and EVI1 gene expression markers with prognostic value for patients with AML

Summary

Introduction

Overexpressions of EVI1, BAALC, ERG, and MN1 have been reported to be prognostically relevant in AML [1-9]. The prognostic value of EVI1 overexpression was discovered and reproduced in intermediate cytogenetic risk AML [4,9-13], while the prognostic value of BAALC, ERG and MN1 mRNA values were demonstrated in normal karyotype AML [1,6,8]. These studies selected univariate cutoff points for BAALC, ERG, and MN1 continuous expression levels based on cohort quartiles, while the EVI1 expression cutoff point was chosen to discriminate between undetectable or low levels versus high expression levels. Translation to the clinic has been proposed [14-20] but lack of standardized assays has hampered their

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