Acute myeloid leukemia with complex karyotypes and abnormal chromosome 21: Amplification discloses overexpression of APP, ETS2, and ERG genes

Abstract

Molecular mechanisms of leukemogenesis have been successfully unraveled by studying genes involved in simple rearrangements including balanced translocations and inversions. In contrast, little is known about genes altered in complex karyotypic abnormalities. We studied acute myeloid leukemia (AML) patients with complex karyotypes and abnormal chromosome 21. High-resolution bacterial artificial chromosome (BAC) array-based comparative genomic hybridization disclosed amplification predominantly in the 25- to 30-megabase (MB) region that harbors the APP gene (26.3 MB) and at position 38.7-39.1 MB that harbors the transcription factors ERG and ETS2. Using oligonucleotide arrays, APP was by far the most overexpressed gene (mean fold change 19.74, P = 0.0003) compared to a control group of AML with normal cytogenetics; ERG and ETS2 also ranked among the most highly expressed chromosome 21 genes. Overexpression of APP and ETS2 correlated with genomic amplification, but high APP expression occurred even in a subset of AML patients with normal cytogenetics (10 of 64, 16%). APP encodes a glycoprotein of unknown function previously implicated in Alzheimer's disease, but not in AML. We hypothesize that APP and the transcription factors ERG and ETS2 are altered by yet unknown molecular mechanisms involved in leukemogenesis. Our results highlight the value of molecularly dissecting leukemic cells with complex karyotypes.

Fig. 1.

Gains (red) and losses (green) of 21q material detected by BAC array CGH in 12 AML patients with complex karyotype. Genes appearing in boldface are contained in the corresponding BAC clone; the remaining genes are located in the vicinity of the BAC clone used here but are not present in this BAC. The asterisk indicates cases studied for gene expression by oligonucleotide array.

Fig. 2.

Ratios of DNA copy number of chromosome 21 clones (red dots connected with red line) and array-derived gene expression estimates (black dots) of 230 probe sets for AML patient 5 (A) and for a representative AML case with a normal karyotype (B) (expression ratios for the AML CN case in B were obtained by the comparison to the four remaining AML CN of the control group). (C) DNA copy number ratios for the clones from chromosomes other than chromosome 21 are shown for patient 11 (dots) and the reference DNA (× for normal blood), illustrating loss of material from chromosomes 7 and 16 and gain of material from chromosomes 8 and 11 in patient 11. These changes were confirmed by cytogenetic analyses. The ratios for the X and Y chromosomes are typical for males. Ratios were calculated as described in Materials and Methods and were plotted as a function of their position; SD for each clone in reference DNA is depicted.

Fig. 3.

APP mRNA expression determined by real-time RT-PCR in AML. Bracket indicates samples that were included in gene expression studies using oligonucleotide arrays.