Quantitative PCR identifies a minimal deleted region of 120 kb extending from the Philadelphia chromosome ABL translocation breakpoint in chronic myeloid leukemia with poor outcome

Abstract

Fluorescence in situ hybridization (FISH) analysis has shown previously that 10-15% of chronic myeloid leukemias (CML) have hemizygous deletions of variable sizes affecting regions that flank the ABL and BCR translocation breakpoints on the derivative chromosome 9, and these patients have a poor outcome. FISH studies using large commercial genomic probes have previously suggested that haploinsufficiency of sequences flanking either ABL or BCR modify the disease process of CML and lead to an unfavorable prognosis. In this present study, real-time quantitative PCR (Q-PCR) analysis was used to identify and map much smaller hemizygous microdeletions in a subset of CML patients that were not deleted using large genomic FISH probes. Microdeletions were identified by Q-PCR in 25 of 71 patients selected based on less favorable outcome (chronic phase duration of less than 96 months and a survival time of less than 84 months). In contrast, no microdeletion was detected in any of 18 CML samples selected from a group with a more favorable outcome. Detailed mapping of the 25 Q-PCR microdeletions showed that the minimal deleted region extended approximately 120 kb from the 5' end of the ABL gene in the centromeric direction on the derivative chromosome 9, and the region 3' to BCR on chromosome 22 was excluded. Of the four ESTs and/or genes that map to the 120 kb region, the putative tumor suppressor PRDM12 is the strongest candidate gene. The potential role for each sequence in modifying the clinical behavior of CML is presented.

Genomic segmental duplications on the basis of the t(9;22) rearrangement in chronic myeloid leukemia

“…resulting in variable deletions size as a consequence of a nonrecurrent event (Sinclair et al, 2000;Storlazzi et al, 2002;Kolomietz et al, 2003;Fourouclas et al, 2006;Kreil et al, 2007). The deletions on der(9) have been associated with an adverse prognosis in relation to the efficacy of interferon-a therapy, whereas controversial data are available about their influence on the response to imatinib.…”

Derivative chromosome 9 deletions are a significant feature of childhood Philadelphia chromosome positive acute lymphoblastic leukaemia

“…8,27 Such submicroscopic deletions, below the level of detection by FISH, have been identified in a small series of patients whose prognosis was poor. 9 A candidate tumour suppressor gene, PRDM12, was identified in these cases 32 and subsequently shown to be deleted in a case of Ph-positive CML with a variant translocation. 33 No association with survival has yet been established for deletions of der(9) in ALL.…”

A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion

“…Several groups, including our laboratory, have investigated this marker on CLL B cells and found that greater than 30% CD38 expression within a CLL leukemic population correlates to an overall shorter time to progression and, in general, a poor clinical outcome. [1][2][3][4][5] However, another study suggests that scoring CLL B-cell CD38 expression using both percent-positive and mean fluorescence intensity (MFI) is a more accurate prognostic tool for B-CLL patients. 6 Recently, Ghia et al 7 found that even a small distinct population of CD38 pos cells, displayed as a small peak in a bimodal CD38-staining profile, was associated with progressive disease.…”

“…2 The PRMD12 gene warrants further attention in order to elucidate its role in the pathogenesis of CML.…”

“…1 The deletions, detected by fluorescent in situ hybridisation (FISH) using large commercial contig probes, were associated with rapid progression to blast crisis and short survival. A recent study by Kolomietz et al 2 used quantitative PCR to demonstrate that a further subset of der (9) deletions exist beyond the resolution of large commercial FISH probes. Subsequent mapping of the microdeletions identified a minimal commonly deleted region (CDR) of 120 kb, associated with short survival.…”