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Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization

Abstract

Chromosomal abnormalities are important for the classification and risk stratification of patients with acute lymphoblastic leukemia (ALL). However, approximately 30% of childhood and 50% of adult patients lack abnormalities with clinical relevance. Here, we describe the use of array-based comparative genomic hybridization (aCGH) to identify copy number alterations (CNA) in 58 ALL patients. CNA were identified in 83% of cases, and most frequently involved chromosomes 21 (n=42), 9 (n=21), 6 (n=16), 12 (n=11), 15 (n=11), 8 (n=10) and 17 (n=10). Deletions of 6q (del(6q)) were heterogeneous in size, in agreement with previous data, demonstrating the sensitivity of aCGH to measure CNA. Although 9p deletions showed considerable variability in both the extent and location, all encompassed the CDKN2A locus. Six patients showed del(12p), with a common region encompassing the ETV6 gene. Complex CNA were observed involving chromosomes 6 (n=2), 15 (n=2) and 21 (n=11) with multiple regions of loss and gain along each chromosome. Chromosome 21 CNA shared a common region of gain, with associated subtelomeric deletions. Other recurrent findings included dim(13q), dim(16q) and enh(17q). This is the first report of genome-wide detection of CNA in ALL patients using aCGH, and it has demonstrated a higher level of karyotype complexity than anticipated from conventional cytogenetic analysis.

Introduction

The detection of chromosomal abnormalities by conventional cytogenetic analysis is an essential component of the multidisciplinary approach to the diagnosis, classification and risk-stratification of patients with acute leukemia (Mrozek et al., 2004). The development of fluorescence in situ hybridization (FISH) has expanded the utility of cytogenetics. It has identified a number of clinically relevant chromosomal abnormalities (Romana et al., 1994; Berger et al., 2003), and allowed the detection of these alterations in patients with failed cytogenetic results, normal, complex or ill-defined karyotypes (Harrison et al., 2005). In spite of its limited resolution, chromosome-based comparative genomic hybridization (cCGH) (Kallioniemi et al., 1992) has provided additional genomic information in some groups of patients (Haas et al., 1998; Larramendy et al., 1998).

Ever since cCGH was first reported, significant advances in our knowledge of the human genome sequence, and the ability to spot DNA sequences onto microarray slides at high density, have allowed the conventional metaphase chromosome template to be superseded by array-based methods (Pinkel et al., 1998). Array-based CGH (aCGH), using large-insert genomic clones, offers a high-resolution analysis of copy number alterations (CNA) that can be directly related to sequence information (Snijders et al., 2001). This approach has been widely applied to the study of the malignant genome, including the characterization of CNA in a range of hematological malignancies (Martinez- Ramirez et al., 2005; Nakashima et al., 2005; Rubio-Moscardo et al., 2005; Hosoya et al., 2006; Horsley et al., 2006; Paulsson et al., 2006; Rucker et al., 2006, Tyybakinoja et al., 2006; van Vlierberghe et al., 2006).

An established chromosomal change with prognostic significance accounts for two-thirds of childhood and half of adult acute lymphoblastic leukemia (ALL), with the remainder being unclassified, including those with a normal karyotype (Faderl et al., 1998; Pui and Evans, 2006). In this report, we describe the use of aCGH in the definition of ALL karyotypes, with particular focus on those from the unclassified group. Here, we demonstrate that aCGH, at high resolution, accurately defines chromosomal changes and identifies new recurring abnormalities.

Results

Copy number alterations are a common feature of acute lymphoblastic leukemia

CNA were observed in 48 patients (83%), as shown in detail in Table 1 and represented diagrammatically in Figure 1. Regions of high-level gain/amplification and homozygous loss/deletion were detected, as well as regions showing low-level CNA. In total, 188 CNA were observed, with sub-chromosome CNA (n=148) being more frequent than whole chromosome CNA (n=40). Based on the total cohort, an average of 3.24 (±2.76) CNA per patient was observed, with sub-chromosome CNA and whole chromosome CNA being found at frequencies of 2.55 and 0.69 per patient, respectively. The average size of the sub-chromosome CNA was 19.7 Mb, with losses (CNL) (98/148) occurring twice as frequently as gains (CNG) (50/148).

Table 1 ISCN, FISH and aCGH data from 58 patients with acute lymphoblastic leukemia
Figure 1
figure1

CNAs detected in 58 ALL patients. To the left and right of each chromosome, idiograms are red and green vertical lines showing copy number loss and gain, respectively. Each vertical line shows the extent and position of each copy number change and represents a single change in a single patient. Amplifications are shown in dark green.

aCGH alterations correlate with results from classical and molecular cytogenetic analysis

From Table 1, a comparison can be made between the karyotype determined by conventional cytogenetics (CC) and the aCGH results. Among the 57 whole chromosome gains and losses detected by CC, 37 (65%) were confirmed by aCGH. Twenty occurred in patients with high hyperdiploidy, which corresponded to the same chromosome gain detected by CC. Among the 20 non-concordant cases, the abnormality was not detected by aCGH owing to normal cell contamination (n=14) (mean % normal cells=73%, range 55–95%), or only a sub-chromosome CNA was identified for the chromosome in question (n=6), which was owing to the inability of CC to detect the abnormality. CC detected 40 deletions or duplications, of which 33 were identified by aCGH. Normal cell contamination was responsible for the non-detection of the seven abnormalities. In two patients (3597, 5073) with unbalanced translocations involving chromosome 15, CNA were observed for the partner chromosome only (chromosomes 1 and 12 in cases 3597 and 5073, respectively). A further 35 abnormalities, described from CC as either additional undefined material (add) or marker chromosomes, were characterized by aCGH. Besides defining the breakpoints of chromosomal changes detected by CC, aCGH detected 29 gains and losses that were beyond the resolution of the light microscope (<5 Mb in size). In addition, a further 16 larger CNA were identified by aCGH alone. Five of the 12 patients with a normal karyotype showed eight sub-microscopic deletions by aCGH, whereas seven cases showed no abnormality by CC or aCGH. In total, 20 alterations were detected in four cases with failed CC.

A total of 229 CNA observed by aCGH were confirmed using a series of BAC clones from the arrays labeled for FISH. The aCGH and FISH results were concordant for 206 clones (90%). The 23 cases of discordant loci were attributed to the presence of a significant proportion of normal cells.

CNA involve recurrent genomic regions

The CNA most frequently involved chromosomes 21 (n=42), 9 (n=21), 6 (n=16), 12 (n=11), 15 (n=11), 8 (n=10) and 17 (n=10) and rarely chromosomes 2 (n=2), 3 (n=2), 14 (n=3) and 19 (n=3) (Figure 1). Recurrent CNA are shown in Table 2.

Table 2 Recurrent CNA in 58 ALL patients detected by aCGH

The majority of CNA involving chromosome 9 were deletions of the short arm, with 19 CNL observed in 18 patients. The extent of these deletions ranged from 0.7 (n=4) to 36.7 Mb (n=4). All cases showed a common region of deletion (genomic position 22.2–22.9), involving clones RP11–408N14 to AL341117 and encompassing the DMRTA1, CDKN2A, CDKN2B and MTAP genes. One of these patients (7104) showed two separate regions of CNL on 9p (genomic position 22.2–29.5 and 35.4–36.7 Mb), although only one breakpoint was implicated from CC. Two patients (3507, 6789) with large terminal deletions also had CNL involving 20q, of 32.2 (genomic position 31.4–63.6 Mb) and 36.2 Mb (genomic position 33.2–69.4) in size, respectively. Both patients showed a dic(9;20)(p1113;q11) by FISH (Figure 2). Two patients CNG were identified involving the long arm of chromosome 9, genomic position 86.5–87.8 and 129.3–134.3 Mb in patients 6789 and 6843, respectively.

Figure 2
figure2

aCGH analysis of patient 3507 for chromosome 20 (a) and 9 (b) with FISH confirmation (c). Profiles are shown for each chromosome horizontally from the p- to q-telomere. For each chromosome, the Log2 ratio for both dye swap experiments is shown, along with cutoff values for loss and gain displayed as red and green horizontal lines, respectively. Below each profile is a ruler showing the genomic position and an idiogram for the chromosome in question. Below each idiogram is a red line showing the position and extent of the deleted region. Below (c) is the FISH confirmation of four DNA clones numbered (i), (ii), (iii) and (iv), corresponding to the genomic clones on the profile with the same numeral.

Deletions accounted for 69% (11/16) of the chromosome 6 CNA in nine patients. Nine CNL involved the long arm and ranged in size from 34.5 to 91.1 Mb. With the exception of patient 3771, they shared a common region of CNL of 1.8 Mb (genomic position 104.2–106 Mb). Several expressed sequences, including the GRIK2, HACE1, POPDC3, PREP, PRDM1 and APG5L genes, are located in this region.

Eight patients showed loss of regions of 12p, ranging from 0.7 to 20.9 Mb in size. They showed a common region of deletion between genomic positions 10.9 and 11.6 Mb, representing the CNL in patient 6022, which encompassed 22 expressed sequences, including the ETV6 gene. In four patients, the 12p CNL accompanied the ETV6-RUNX1 fusion.

Of the six patients who had 11 CNA of chromosome 15, three shared a 6.4 Mb deletion close to the telomere (genomic position 87.4–94.0 Mb). Ten CNA involving chromosome 17 were observed in eight patients. In addition to two patients (7060, 7141) with whole chromosome gain, two (2835, 5895) had large deletions of 17p, including the TP53 gene. Five cases had CNG of 17q, involving a minimal region of 12 Mb. The CNA involving chromosome 5 (n=5) were deletions, which varied in size from 7.4 to 32.6 Mb, with different genomic locations. With the exception of a single CNG, all CNA affecting chromosome 7 were deletions. Two patients shared a commonly deleted region on the short arm (13.8 Mb, position 37.0–50.8 Mb), whereas another two patients shared a commonly deleted region of 5.0 Mb (genomic position 133.4–138.4 Mb) on the long arm. Four cases had deletions of 13q, three of which shared a common region of deletion between 48.8 and 56.7 Mb, containing a large number of expressed sequences including the RB1 gene.

In addition to the presence of 12p deletions, three ETV6-RUNX1 positive cases showed gain of an entire chromosome 21 (3428, 5053, 6834). Two cases with complex abnormalities of chromosome 6 (3428, 7019) also harbored an ETV6–RUNX1 fusion. Single cases showed deletions of chromosomes 4, 5, 8, 10, 18 and gains of 8q. Only one BCR-ABL positive case was included in this study (7134), which was also high hyperdiploid and showed a cryptic gain of 3q. Patient 7141, also high hyperdiploid, showed the same cryptic CNG of 3q, with a common region between genomic positions 173.1 and 204.4 Mb.

Genome complexity in ALL patients

Fourteen patients exhibited complex chromosome profiles that were not evident from the CC analysis, examples of which are shown in Figure 3. Eighteen single chromosome changes described by CC were redefined as 49 CNA by aCGH, particularly involving chromosomes 6, 15 and 21. Of the 42 CNA involving chromosome 21, 26 occurred in 10 patients with intrachromosomal amplification of chromosome 21 (iAMP21). Each patient harbored at least one chromosome 21 CNA, whereas a complex pattern of four distinct CNA was observed in patient 5898. This patient showed loss of 6.1 and 3.2 Mb regions, as well as 5.7 Mb (genomic position 22.1–27.8 Mb) and 12.3 Mb (29.4–41.7 Mb) regions of gain and amplification, respectively. The remaining nine patients were less complex, with a common region of chromosome 21 CNG between genomic position 31.5 and 40.1 Mb (clones RP11–191I6 to RP5–206A10). In addition, seven patients showed deletions of chromosome 21. With the exception of a single deletion close to the centromere (patient 5898), all CNL included a subtelomeric region. Three patients showed CNA of chromosome 21 in the absence of iAMP21. Patient 186 showed a 24.8 Mb CNG (genomic position 22.1–46.9) and patient 4247 exhibited a gain between 21.1 and 46.9 Mb, whereas patient 4746 displayed a complex series of loss (0.6 Mb), gain (1.6 Mb), loss (1.7 Mb) and amplification (22.9 Mb) along chromosome 21 (Figure 3a).

Figure 3
figure3

Complex CNA involving chromosomes 21, 6 and 15 in three patients with ALL. Chromosomes are positioned as in Figure 2. The red and green lines positioned below and above the chromosome idiograms represent areas of CNL and CNG, respectively. (ac) CNA profiles for chromosomes 21, 6 and 15 for patients 4746, 3428 and 6783, respectively are shown.

In two patients (3428 and 6956), the 6q CNL were part of a more complex series of gains and losses along the length of the chromosome, which in both cases corresponded to ring chromosomes by CC. Patient 3428 showed a complex series of copy number changes along chromosome 6, from a 3.8 Mb deletion on 6p, a gain of a pericentric region and a deletion of a large 91.1 Mb region on 6q (Figure 3b). Surprising complexity was observed in two patients (4414 and 6783) with monosomy 15 detected by CC, where they showed patterns of CNL and CNG along this chromosome. Patient 6783 showed five regions of CNA (Table 1 and Figure 3c).

Discussion

This is the first report of genome wide detection of DNA copy number changes in both B- and T-ALL using aCGH at 1 Mb resolution. The aim of the study was to find new recurring chromosomal abnormalities among patients without known established chromosomal rearrangements. Among 58 patients analysed, novel regions of genomic imbalance were identified, and breakpoints of previously reported chromosomal abnormalities were more accurately defined.

We demonstrated that aCGH detection of chromosomal abnormalities in ALL is accurate, as there was a strong correlation between those abnormalities detected by CC and aCGH. When discrepancies arose, they were mostly explained as a lack of detection by aCGH resulting from a high level contaminating normal population or the presence of balanced rearrangements. According to previously published data, the proportion of leukemic cells in a DNA sample needs to be more than 40% for accurate detection (Hosoya et al., 2006). The lack of detection by CC compared with aCGH usually resulted from the low resolution of CC with the inability to detect small aberrations or incorrect cytogenetic interpretation. aCGH, as a complementary tool to CC, accurately characterized markers and unidentified chromosomal regions.

In our patient series, the use of aCGH resulted in the detection of 128 additional CNA, many of which were either classified incompletely, or missed by CC. These findings compared well with previously published chromosome-based CGH (cCGH) studies in the detection of recurrent abnormalities, such as del(9p) and del(12p) (Scholz et al., 2001). We confirmed heterogeneous deletions of 6q as recurrent events in ALL. These findings concurred with a number of studies using FISH and loss of heterozygosity (LOH), which demonstrated several common regions of deletion involving 6q21–q23 (Jackson et al., 2000; Foroni et al., 2003; Sinclair et al., 2004), further highlighting the importance of this region in ALL pathogenesis while demonstrating that aCGH can be used to accurately delineate regions of CNA in ALL.

Even though the cases in this study were highly selected for the absence of established chromosomal abnormalities, a small number were included from other patient subgroups, such as high hyperdiploid and ETV6–RUNX1 positive patients. The analysis of these patients contributed to the high frequency of chromosome 21 CNA. The majority of the remaining patients with chromosome 21 CNA belonged to a newly identified poor-risk cytogenetic sub-group in ALL (Harewood et al., 2003; Robinson et al., 2003), which we have defined as iAMP21 (Strefford et al., 2006). This study corroborated our earlier findings and confirmed the variable nature of this chromosomal abnormality. Two patients (4247, 4746), with multiple small chromosomes derived from chromosome 21, showed similar genomic profiles to iAMP21. However, they were not defined as such because their cytogenetic profile did not conform to the current definition assigned to the iAMP21 subgroup. It may be that by aCGH analysis of more cases, a more accurate definition may emerge from the genomic profile, rather than from the cytogenetic one.

Deletions of 9p occur in approximately 10% of children with ALL and usually target two tandemly linked cyclin-dependent kinase inhibitor genes at 9p21: CDKN2A and CDKN2B (Bertin et al., 2003). Cytogenetically visible 9p abnormalities have been reported to confer an adverse clinical outcome (Hann et al., 2001), whereas recent data on specific loss of CDKN2A showed no link with outcome (van Zutven et al., 2005; Mirebeau et al., 2006;). All 9p deletions in our series encompassed the CDKN2A locus. At the same time, they showed considerable heterogeneity in both the extent and location of the deletion, resulting in more than 10 different regions of CNL. The association with prognosis may be dependent on the size of the deletion and the loss of other genes in cooperation with CDKN2A.

The formation of dicentric chromosomes involving chromosome 9 usually leads to loss of 9p and 7p, 12p or 20q (Behrendt et al., 1995; Clark et al., 2000). Two patients with a dic(9;20)(p1113;q11) were included in this study. They showed different breakpoints for both chromosomes 9 and 20. The gene fusion, PAX5–ETV6, has been found in patients with a dic(9;12)(p13;p13) (Strehl et al., 2003). Although based on only two patients, the heterogeneity of breakpoints is likely to preclude a consistent gene rearrangement being associated with dic(9;20).

A number of other chromosomal regions have emerged as recurrent abnormalities in this study. This applies in particular to deletions of 7p, 13q and 16q, and gains of 17q, most of which have been described in other types of hematological malignancy (Fioretos et al., 1999; Scheurlen et al., 1999), including ALL (Chung et al., 2000; Heerema et al., 2000; Heerema et al., 2004). Although deletions of 16q are recurrent events in several hematological malignancies, including AML and multiple myeloma, they have not been previously identified in ALL. Although 17q LOH has been demonstrated in children with ALL (Takeuchi et al., 2003), more recent studies have shown that LOH may arise from acquired isodisomy, with no overall loss of genomic DNA (Raghavan et al., 2005). Further studies will determine if these are polymorphic or pathogenic chromosomal regions.

We have investigated the utility of aCGH in the detection of secondary chromosomal changes in a number of patients with known established chromosomal abnormalities. The detected abnormalities reflected previously published data, for example gain of chromosome 21 and deletions of 12p in ETV6–RUNX1 positive patients (Attarbaschi et al., 2004) and loss of 9p in patients with high hyperdiploidy (Pui et al., 1989; Moorman et al., 2003). In addition, further CNA were identified, including two patients with high hyperdiploidy and gain of a common genomic region on 3q. Previous reports suggest that approximately 15–20% of patients with a high-hyperdiploid karyotype relapse (Moorman et al., 2003), and thus it may be that as yet unidentified additional genomic alterations in these patients, such as gain of 3q, confer this adverse clinical outcome.

Unlike solid tumors, the genomic alterations of patients with leukemia were assumed to be considerably less complex. Here, we show that several chromosomes, in particular 6, 15 and 21, harbor multiple regions of CNA, demonstrating unexpectedly complex abnormalities, not seen at the cytogenetic level. We showed that chromosomes 6 and 21 aberrations might be more frequent than previously thought, owing to their involvement in such complex genomic alterations. In particular, this study has provided further support to the pivotal role of chromosome 21 in the initiation and maintenance of the leukemic process. This is the first report of complex CNA of chromosome 15 in ALL, which may reflect an important genetic event involving this chromosome in leukemogenesis.

In this study, aCGH has provided accurate molecular characterization of recurrent chromosomal regions and evidence of new abnormalities in ALL. This approach has provided further insight into the size, genomic position, gene content and high-resolution characterization of the breakpoints producing these abnormalities, demonstrating that the genomic changes in ALL patients are often more complex than anticipated. Such precise descriptions of the genetic alterations in ALL may lead to improved molecular diagnosis and prediction of outcome. Concurrent single nucleotide polymorphism and expression array studies will determine the presence of LOH in the absence of CNA, and allow accurate correlations between genomic copy number and gene expression to be made. The submicroscopic alterations described here may facilitate the identification of novel molecular targets implicated in the pathogenesis of ALL.

Materials and Methods

Patients and cytogenetic analysis

DNA from diagnostic bone marrow samples was obtained from patients identified among those enrolled on the UK ALL treatment trials: ALL97/99 or ALL2003 for children aged 1–18 years (n=49), or UKALLXII for adults aged 15–55 years (n=9). Cytogenetic and FISH details of these 58 patients are provided in Table 1. Those with no known established chromosomal abnormalities were preferentially selected (n=39), although samples from well-defined (n=9) and emerging (n=10) cytogenetic subgroups were included. Chromosomal analysis was performed in the UK regional cytogenetics laboratories, and described according to the International System for Human Cytogenetic Nomenclature (ISCN, 2005). FISH analysis was performed for the presence of established rearrangements using a range of commercially available probes (Abbott Diagnostics, Maidenhead, UK; DakoCytomation, Glostrup, Denmark) according to the manufacturers' instructions.

BAC aCGH processing and analysis

Changes in genomic copy number were assessed using two commercially available BAC aCGH systems (Spectral Genomics and IntegraGen, Genosystems, Paris, France). They comprised 2621 and 3172 genomic clones positioned at approximately 1 and 0.85 Mb intervals throughout the genome, respectively. The position of genes and BAC clones were determined using the National Center for Biotechnology Information (NCBI) MapViewer for Homo Sapiens, Build 35.1.

Pooled DNA extracted from peripheral blood of 10 healthy donors, sex mismatched to the test sample, was used as the reference (Promega, Southampton, UK), and array experiments were processed according to the manufacturers' instructions. Cy3 and Cy5 images were scanned independently using a GenePix 4000B scanner (Axon Instruments Inc., Union City, USA). Grid placement, spot quality, data normalization, fluorescence quantification and post-processing of the array image was performed with BlueFuse software (BlueGnome, Cambridge, UK). Array spot data showing low signal to background intensity ratios (Signal <5 times the background) or low quality replicate measurements (elimination of spot replicates differing by >0.3 standard deviation (s.d.) in the log2 ratio) were excluded from the analysis. Abnormal clones were defined as averaged log ratios of −2s.d. and +2s.d., where the ratios were outside the threshold values of −0.1 and +0.1 in both dye-swap experiments for CNG and CNL, respectively. Chromosomal regions of copy number change were identified as a minimum of three adjacent clones simultaneously deviating beyond the threshold values in both dye-swap experiments. Data smoothing and breakpoint recognition was performed as described previously (Jong et al., 2004). Copy number variations were excluded from this study by comparison with previous data (Iafrate et al., 2004; Sebat et al., 2004).

Fluorescence in situ hybridization

Where material was available, the CNA detected by aCGH were confirmed with FISH using the same BAC clones as spotted onto the arrays (Sanger Institute, Cambridge, UK; BACPAC Resources, Oakland, USA). Clones were cultured, extracted, labeled and hybridized using standard methodologies (Qiagen, Crawley, UK; Abbott Diagnostics, Maidenhead, UK). FISH analysis was performed on 200 interphase cells using standard fluorescent microscopy.

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Acknowledgements

This study could not have been performed without the dedication of the MRC Childhood and Adult Leukaemia Working Parties and their members, who have designed and coordinated the clinical trials through which these patients were identified and treated. We thank the UK Cancer Cytogenetics Group laboratories for the contribution of fixed cell suspensions, other members of the Leukaemia Research Cytogenetics Group for technical help and discussion, and Leukaemia Research for financial support.

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Correspondence to J C Strefford.

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Strefford, J., Worley, H., Barber, K. et al. Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization. Oncogene 26, 4306–4318 (2007). https://doi.org/10.1038/sj.onc.1210190

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Keywords

  • array
  • CGH
  • acute lymphoblastic leukemia
  • copy number

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