Identification of two critically deleted regions within chromosome segment 7q35-q36 in EVI1 deregulated myeloid leukemia cell lines

Abstract

Chromosomal rearrangements involving the EVI1 proto-oncogene are a recurrent finding in myeloid leukemias and are indicative of a poor prognosis. Rearrangements of the EVI1 locus are often associated with monosomy 7 or cytogenetic detectable deletions of part of 7q. As EVI1 overexpression alone is not sufficient to induce leukemia, loss of a 7q tumour suppressor gene might be a required cooperating event. To test this hypothesis, we performed high-resolution array comparative genomic hybridization analysis of twelve EVI1 overexpressing patients and three EVI1 deregulated cell lines to search for 7q submicroscopic deletions. This analysis lead to the delineation of two critical regions, one of 0.39 Mb on 7q35 containing the CNTNAP2 gene and one of 1.33 Mb on chromosome bands 7q35-q36 comprising nine genes in EVI1 deregulated cell lines. These findings open the way to further studies aimed at identifying the culprit EVI1 implicated tumour suppressor genes on 7q.

Figure 1. Overview of deletions in cell lines and patients.

Chromosome view of chromosome 7 deletions in the cell lines Kasumi-3, MUTZ-3 and UCSD-AML1 and in cases 2, 3 and 9. Deletions are indicated using grey bars.

Figure 2. FISH analysis of the 7q35–q36 deletions in cell lines.

A), D) and G) FISH analysis on cytogenetically normal controls with probes located within the 7q35–q36 deleted regions. B), E) and H) FISH analysis with probes located within the 7q35–q36 deleted regions on the cell lines Kasumi-3 (B), UCSD-AML1 (E) and MUTZ-3 (H). C), F) and I) FISH analysis with probes just outside of the 7q35–q36 deleted regions on the cell lines Kasumi-3 (C), UCSD-AML1 (F) and MUTZ-3 (I).

Figure 3. Array CGH profile of chromosome 7 (141 Mb–153 Mb) for Kasumi-3, MUTZ-3 and UCSD-AML1.

A) Array CGH profile of Kasumi-3, B) MUTZ-3 and C) UCSD-AML1 indicating the 0.39 Mb SRO on 7q35 and the 1.33 Mb SRO on chromosome bands 7q35–q36. Log₂-ratios of the clones are depicted by vertical dots corresponding to the respective genomic position (NCBI build 36). Deletions are shown in red. The SROs are indicated with a purple box. The bottom of the figure shows the genomic position with an indication of known CNVs as present in the Database of Genomic Variants (http://projects.tcag.ca/variation/). Regions of segmental duplication are displayed using black and grey boxes indicating identical genomic regions. A screenshot of the UCSC Genome Browser (NCBI build 36, http://genome.ucsc.edu) shows an overview of the known RefSeq genes in the 1.33 Mb critical region.