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Blood, Vol. 95 No. 3 (February 1), 2000:
pp. 738-743
PLENARY PAPER
From the University of Cambridge, Department of Hematology, MRC
Centre, Cambridge, United Kingdom (UK); the Department of Hematology,
Addenbrooke's Hospital, Cambridge, UK; the Sanger Centre, Wellcome
Trust Genome Campus, Hinxton, Cambridge, UK; and the Department of
Hematology and Cytogenetics, Christie's Hospital, Manchester, UK.
The hallmark of chronic myeloid leukemia (CML) is the
BCR-ABL fusion gene, which is usually formed as a result of the
t(9;22) translocation. Patients with CML show considerable
heterogeneity both in their presenting clinical features and in the
time taken for evolution to blast crisis. In this study, metaphase
fluorescence in situ hybridization showed that a substantial minority
of patients with CML had large deletions adjacent to the translocation
breakpoint on the derivative 9 chromosome, on the additional partner
chromosome in variant translocations, or on both. The
deletions spanned up to several megabases, had variable
breakpoints, and could be detected by microsatellite polymerase
chain reaction in unfractionated bone marrow and purified peripheral
blood granulocytes. The deletions were likely to occur early and
possibly at the time of the Philadelphia (Ph) chromosome translocation:
deletions were detected at diagnosis in 11 patients, were found
in all Ph-positive metaphases, and were more prevalent in
patients with variant Ph chromosomes. Kaplan-Meier analysis showed a
median survival time of 36 months in patients with a deletion; patients
without a detectable deletion survived > 90 months. The survival-time
difference was significant on log-rank analysis (P = .006).
Multivariate analysis demonstrated that the prognostic importance of
deletion status was independent of age, sex, percentage of peripheral
blood blasts, and platelet count. Our data therefore suggest that an
apparently simple, balanced translocation may result not only in the
generation of a dominantly acting fusion oncogene but also in the loss
of one or more genes that influence disease progression.
(Blood. 2000;95:738-743)
Chronic myeloid leukemia (CML) is a clonal hematologic
malignant disease arising in the stem-cell compartment.1-3
The hallmark of CML is the formation of a BCR-ABL fusion gene,
usually as a result of the Philadelphia (Ph) chromosome translocation.
The BCR-ABL fusion gene is thought to play a central role in
the pathogenesis of CML. This concept is strongly supported by
retroviral transduction experiments in which p210 BCR-ABL was
expressed in murine bone marrow cells and resulted in a
myeloproliferative disorder resembling CML.4-9
CML is a biphasic disease with an initial chronic phase during which
the disorder is readily controlled. However, chronic-phase CML is
followed by a terminal blastic phase that resembles acute leukemia and
is usually refractory to treatment. Transformation of chronic phase to
blast crisis is accompanied by secondary cytogenetic changes in
approximately 85% of cases.10 However, the genetic events
responsible for the transformation of CML are poorly understood. Homozygous deletions in the p16Ink gene have been reported
in lymphoid blast crisis.11,12 Mutations in the p53 and
N-ras genes have been reported but are rare.13,14
Allelotype analysis has identified loss of heterozygosity at multiple
genomic regions in a varying proportion of patients in blast
crisis.15 Some of these regions may contain tumor
suppressor genes that influence the evolution to CML blast crisis.
Current options for treatment of patients with CML include hydroxyurea,
The first of these possibilities has been investigated in considerable
detail over the past 10 years and was reviewed by Melo.17 The position of the translocation breakpoint in the BCR gene
alters the amount of BCR protein in the BCR-ABL fusion
protein. This in turn influences the phenotype of the associated
leukemia, with p190, p210, and p230 proteins usually accompanying acute
lymphoblastic leukemia, CML, and chronic neutrophilic
leukemia (CNL), respectively. It was also reported that
the position of the breakpoint within the M-bcr region may
influence prognosis,18 although larger studies failed to
confirm this idea.19-22 The position of the breakpoint relative to the ABL coding sequence is less variable. The few cases with fusions to the a3 exon seem indistinguishable from those
with the more usual a2 fusion.17 The ABL-BCR fusion
gene is expressed in only about two thirds of patients with
CML,23 and the presence of the ABL-BCR transcript
does not influence cytogenetic response to interferon.24
We here present the first evidence of a previously unrecognized form of
genetic heterogeneity among patients with CML. We found that a
substantial minority of patients with CML had large acquired genomic
deletions resulting in loss of chromosome 9 and 22 sequences flanking
the translocation breakpoint on the derivative 9, on additional partner
chromosomes, or on both. Furthermore, such deletions were associated
with a worse prognosis. Our results suggest that the loss of genes
adjacent to the translocation breakpoint may influence the progression
of CML.
Patients' clinical and laboratory data
Fluorescence in situ (FISH) probes and detection systems
Triple-probe/3-color system.
This system is based on the following 3 probes (Figure
1): ASS probe, a 350-kilobase (kb)
cosmid contig that contains the ASS gene, the gene 8604 Met
(which maps to a region about 20 kb proximal to ABL exon 1b),
and the most centromeric breakpoints reported in patients with
CML25; ABL probe (Vysis Inc, Downer's Grove, IL),
a 300-kb cosmid contig that contains the 3' region of the
ABL gene (ABL exon 3 to the last exon of ABL);
and BCR probe (Vysis Inc), an approximately 300-kb contig that
begins between BCR exon 13 and 14 and extends well beyond the
M-bcr region.
D-FISH BCR-ABL detection system.
This system is available commercially (Appligene Oncor, UK) and
consists of the following 2 probes (Figure 1): ABL probe, a
600-kb contig spanning the breakpoint region on ABL labeled with a green fluorochrome (fluorescein isothiocyanate, conjugated [FITC]); and BCR probe, a 500-kb contig containing the major
and minor breakpoint regions of BCR labeled with a red
fluorochrome (Texas red). Images were captured and analyzed using a
Smart Capture View Point multicolor imaging station (Digital
Scientific, Cambridge, UK), as with the triple-probe/3-color system.
Chromosome 22 and 9 locus-specific probes.
The cosmid C106G1220, isolated from the telomeric region of chromosome
22, was provided by D. Ledbetter (University of Chicago). All
other locus-specific probes (cosmids) were obtained from the Sanger
Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
(Figure 5). Approximate distances between the
locus-specific probes, the BCR gene, and the 22q telomere are
given in Figure 5.27 Distances between the locus-specific
probes from chromosome 9 used in this study (Figure 5) were based on a
physical map of the 9q34 region.28 C106G1220 and D9S60 were
labeled with Spectrum Orange by using a Vysis
nick-translation kit (catalogue 32-801 300). All other
locus-specific probes were labeled with biotin by using a Gibco-BRL
(Life Technologies, Inc, Gaithersburg, MD) BioNick
labeling system (catalogue 18 247-015). The 2 probes labeled with
Spectrum Orange were used to mark the position of 9q and 22q in
metaphase cells. Combinations of either C106G1220 or D9S60 and each of
the biotinylated probes were applied to cytogenetic preparations from
patients known to have deletions of the region between ABL and
ASS. For these experiments, the biotinylated probe was detected
with an avidin/FITC detection system. After capture, Spectrum Orange
signals were pseudocolored in red and FITC signals in green.
Hybridization and detection procedures
Microsatellite polymerase chain reaction (PCR) Granulocytes and T cells were prepared from peripheral blood as previously described.31 Microsatellite PCR amplification was performed as previously described31 by using primers corresponding to a sequenced tagged site (STS) within intron 14 of the ASS gene32 or to D9S159 (described at http://www.gdb.org).Statistical analysis All calculations were performed with the SPSS statistical package (SPSS Inc, Chicago, IL). Means and SDs were calculated for age, sex, and clinical and laboratory findings at diagnosis for patients with and without deletions and tested for significance with the Mann-Whitney U test (continuous variables) or 2 analysis and
Fisher's exact tests (categorical variables). Survival time was
calculated from month of presentation to month of death, with a median
follow-up of 23 months (range, 4-90 months). Two patients who died from
transplantation-related complications and one who died in chronic phase
for reasons unrelated to CML were censored at date of death. Survival
time in patients with deletions was compared with that in patients
without deletions. Survival data were available for a total of 55 patients. Values were calculated with the Kaplan-Meier estimator;
significance was tested with the log-rank test. The analysis was
performed both by time censoring at the time of transplantation and
also by excluding patients who underwent transplantation. Survival data
from the 2 groups of patients were also used to construct a Cox
proportional hazard model from which significance by 2
analysis, hazard ratio, and 95% confidence intervals (CI) was derived.
Possible confounding effects of age, sex, percentage of peripheral
blood blasts, and platelet count on the prognostic importance of
deletion status were assessed with logistic regression analysis.
Deletion of chromosome 9 sequences on the derivative 9 chromosome We previously described a triple-probe/3-color FISH system for detection of BCR-ABL-positive cells.26 The introduction of a probe for the ASS locus, which lies upstream of ABL, permits identification of the derivative 9 chromosome in Ph-positive cells (Figure 1) and thus allows highly sensitive detection of residual disease.
Deletion of chromosome 22 sequences from the derivative 9 chromosome
Detection of deletions by microsatellite PCR analysis of peripheral blood granulocytes The Ph chromosome is present in peripheral blood granulocytes in most patients with chronic-phase CML although, in some, the percentage of BCR-ABL-positive granulocytes may be significantly lower than the percentage of BCR-ABL-positive bone marrow cells.26 We confirmed the existence of the deletion by using a polymorphic STS that lies within the ASS gene. Loss of heterozygosity could clearly be seen in bone marrow from a patient with a deletion (Figure 3A). To investigate whether the deletion was detectable in peripheral blood cells, we purified granulocytes and T cells from 2 other patients, one with and one without a deletion. Microsatellite PCR using primers for the D9S159 locus, which lies between D9S115 and D9S63, clearly showed loss of heterozygosity in granulocytes from the patient in whom our FISH studies detected a deletion (Figure 3B and Figure 3C).
Size of and variations in deletion breakpoints To assess the extent of the deletion of chromosome 9 and 22 sequences, we used a panel of locus-specific FISH probes to map the deletions in 16 patients found to lack the ASS signal (Figure 4 and Figure 5). For each probe, a minimum of 10 Ph-positive metaphases were analyzed. For each patient, all metaphases showed the same hybridization pattern; in no instance did we find clonal variation (ie, some metaphases carrying a deletion and others lacking a deletion) within the population of Ph-positive metaphases.
Deletion of the derivative 9 chromosome and a poor prognosis To assess the possible biologic importance of the chromosomal deletions, we collected data on clinical features, treatment history, and survival of the patients. Survival data were available for 55 patients (16 with and 39 without detectable deletions). As shown in Table 1, the clinical and laboratory features at presentation in patients with and without deletions were not significantly different. However, the median survival time was 36 months (95% CI, 13-60 months) in patients with a deletion and could not be calculated in patients without a deletion because too many are still alive. The median follow-up time was similar in patients with and without a deletion (23.5 months compared with 23 months), as was the range (4-90 months compared with 7-90 months). The difference in survival time was significant on log-rank analysis (P = .006) (Figure 6). If patients who received a bone marrow transplantation were excluded, the significance level increased (P = .004). Significance was also obtained with Cox proportional hazard analysis, with a hazard ratio of 3.81 (95% CI, 1.36-10.73) calculated for patients with a deletion compared with those without a deletion. Multivariate analysis showed that the prognostic importance of deletion status was independent of age, sex, percentage of peripheral blood blasts, or platelet count. The only possible confounding variable was treatment with interferon only: 5 of 16 patients with deletions but 28 of 40 patients without deletions received this agent. It seems unlikely that this could have accounted for the marked survival difference observed here, particularly because randomized trials have shown only a moderate benefit, at best, with interferon.33-36 Furthermore, if our Kaplan-Meier analysis is restricted to patients treated with interferon, although the numbers are small, patients with deletions have a significantly worse survival time (P = .04). Taken together, our results suggest that large genomic deletions at the translocation breakpoint on the derivative 9 chromosome are associated with a worse prognosis.
We found that a substantial minority of patients with CML had large deletions adjacent to the translocation breakpoint of the derivative 9 chromosome. These data show the existence of previously unsuspected genetic heterogeneity among patients with CML. We also found evidence suggesting that the large deletions are associated with a poor prognosis. Our results raise the possibility that an apparently simple, balanced translocation may result not only in generation of a dominantly acting fusion oncogene but also in loss of one or more tumor suppressor genes adjacent to the translocation breakpoint.
We are grateful to Toby Prevot, Brian Tom, and Sue Richards for statistical advice and to John Proffit and Kim Wieber from Vysis, Inc, Downer's Grove, IL, for preparing the ASS contig.
Submitted May 13, 1999; accepted September 11, 1999.
Reprints: A.R. Green, Department of Hematology, MRC Centre, Hills Road, Cambridge CB2 2QH, UK; e-mail: arg1000{at}cam.ac.uk.
The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked "advertisement" in accordance with 18 U.S.C. section 1734.
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G. Saglio, C. T. Storlazzi, E. Giugliano, C. Surace, L. Anelli, G. Rege-Cambrin, A. Zagaria, A. J. Velasco, A. Heiniger, P. Scaravaglio, et al. A 76-kb duplicon maps close to the BCR gene on chromosome 22 and the ABL gene on chromosome 9: Possible involvement in the genesis of the Philadelphia chromosome translocation PNAS, July 23, 2002; 99(15): 9882 - 9887. [Abstract] [Full Text] [PDF] |
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B. J. P. Huntly, A. J. Bench, E. Delabesse, A. G. Reid, J. Li, M. A. Scott, L. Campbell, J. Byrne, E. Pinto, A. Brizard, et al. Derivative chromosome 9 deletions in chronic myeloid leukemia: poor prognosis is not associated with loss of ABL-BCR expression, elevated BCR-ABL levels, or karyotypic instability Blood, May 29, 2002; 99(12): 4547 - 4553. [Abstract] [Full Text] [PDF] |
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A. G. Reid, B. J. P. Huntly, E. Hennig, D. Niederwieser, L. J. Campbell, N. Bown, N. Telford, H. Walker, C. D. Grace, M. W. Deininger, et al. Deletions of the derivative chromosome 9 do not account for the poor prognosis associated with Philadelphia-positive acute lymphoblastic leukemia Blood, March 15, 2002; 99(6): 2274 - 2275. [Full Text] [PDF] |
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J. de la Fuente, K. Merx, E. J. Steer, M. Muller, R. M. Szydlo, O. Maywald, U. Berger, R. Hehlmann, J. M. Goldman, N. C. P. Cross, et al. ABL-BCR expression does not correlate with deletions on the derivative chromosome 9 or survival in chronic myeloid leukemia Blood, November 1, 2001; 98(9): 2879 - 2880. [Full Text] [PDF] |
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J. M. Goldman and B. J. Druker Chronic myeloid leukemia: current treatment options Blood, October 1, 2001; 98(7): 2039 - 2042. [Abstract] [Full Text] [PDF] |
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B. J. P. Huntly, A. G. Reid, A. J. Bench, L. J. Campbell, N. Telford, P. Shepherd, J. Szer, H. M. Prince, P. Turner, C. Grace, et al. Deletions of the derivative chromosome 9 occur at the time of the Philadelphia translocation and provide a powerful and independent prognostic indicator in chronic myeloid leukemia Blood, September 15, 2001; 98(6): 1732 - 1738. [Abstract] [Full Text] [PDF] |
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E. Kolomietz, J. Al-Maghrabi, S. Brennan, J. Karaskova, S. Minkin, J. Lipton, and J. A. Squire Primary chromosomal rearrangements of leukemia are frequently accompanied by extensive submicroscopic deletions and may lead to altered prognosis Blood, June 1, 2001; 97(11): 3581 - 3588. [Abstract] [Full Text] [PDF] |
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B. J. Druker, C. L. Sawyers, R. Capdeville, J. M. Ford, M. Baccarani, and J. M. Goldman Chronic Myelogenous Leukemia Hematology, January 1, 2001; 2001(1): 87 - 112. [Abstract] [Full Text] [PDF] |
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