Identification of Two Critically Deleted Regions within Chromosome Segment 7q35-q36 in EVI1 Deregulated Myeloid Leukemia Cell Lines

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

Genes located in the 1.33 Mb SRO on 7q35−q36.

<p>Genes located in the 1.33 Mb SRO on 7q35−q36.</p

Name and position of FISH probes.

*<p>UCSC genome browser database (<a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>).</p

Array CGH results of chromosome 7 deletions.

<p>Bold formatting indicates deletions on the 7q arm.</p>*<p>Based upon the UCSC genome browser (<a href="http://genome.ucsc.edu/cgi-bin/hgGateway" target="_blank">http://genome.ucsc.edu/cgi-bin/hgGateway</a>, NCBI Build 36.1).</p>†<p>Between brackets is the total number of genes residing in the deleted area.</p>‡<p>Homozygous deletion.</p

Patient and cell line characteristics: diagnosis, karyotype and <i>EVI1</i> FISH and RT-qPCR results.

<p>Bold formatting indicates the 3q26 rearrangement.</p>*<p>AML = acute myeloid leukemia and MDS = myelodysplastic syndrome.</p>†<p>The chromosomal aberration implicating the <i>EVI1</i> locus is indicated with bold formatting.</p>‡<p>Positive for <i>EVI1</i> FISH/qRT-PCR = +and negative for <i>EVI1</i> FISH/qRT-PCR = −.</p

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

<p>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 (<a href="http://projects.tcag.ca/variation/" target="_blank">http://projects.tcag.ca/variation/</a>). 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, <a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>) shows an overview of the known RefSeq genes in the 1.33 Mb critical region.</p

Overview of deletions in cell lines and patients.

<p>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.</p