DNA copy number alterations mark disease progression in paediatric chronic myeloid leukaemia

Authors

  • Naomi E. van der Sligte,

    1. Division of Paediatric Oncology/Haematology, Department of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
    Search for more papers by this author
    • These authors contributed equally.
  • Manuela Krumbholz,

    1. Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
    Search for more papers by this author
    • These authors contributed equally.
  • Agata Pastorczak,

    1. Laboratory of Paediatric Oncology, Radboud University Medical centre, Nijmegen, The Netherlands
    Search for more papers by this author
    • These authors contributed equally.
  • Blanca Scheijen,

    1. Laboratory of Paediatric Oncology, Radboud University Medical centre, Nijmegen, The Netherlands
    Search for more papers by this author
  • Josephine T. Tauer,

    1. Department of Paediatrics, University Hospital “Carl Gustav Carus”, Dresden, Germany
    Search for more papers by this author
  • Christina Nowasz,

    1. Department of Paediatrics, University Hospital “Carl Gustav Carus”, Dresden, Germany
    Search for more papers by this author
  • Edwin Sonneveld,

    1. Dutch Childhood Oncology Group, The Hague, The Netherlands
    Search for more papers by this author
  • Geertruida H. de Bock,

    1. Department of Epidemiology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
    Search for more papers by this author
  • Tiny G. J. Meeuwsen-de Boer,

    1. Division of Paediatric Oncology/Haematology, Department of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
    Search for more papers by this author
  • Simon van Reijmersdal,

    1. Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
    Search for more papers by this author
  • Roland P. Kuiper,

    1. Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
    Search for more papers by this author
  • Jutta Bradtke,

    1. Oncogenetic laboratory, Institute of Pathology, University Hospital Giessen and Marburg, Giessen and Marburg, Germany
    Search for more papers by this author
  • Markus Metzler,

    1. Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
    Search for more papers by this author
    • Contributed equally as senior authors.
  • Meinolf Suttorp,

    1. Department of Paediatrics, University Hospital “Carl Gustav Carus”, Dresden, Germany
    Search for more papers by this author
    • Contributed equally as senior authors.
  • Evelina S. J. M. de Bont,

    Corresponding author
    1. Division of Paediatric Oncology/Haematology, Department of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
    • Correspondence: Evelina S. J. M. de Bont MD, PhD, Division of Paediatric Oncology/Haematology, Department of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, University of Groningen, PO Box 30.001, Groningen 9700 RB, The Netherlands. E-mail: e.s.j.m.de.bont@umcg.nl

    Search for more papers by this author
    • Contributed equally as senior authors.
  • Frank N. van Leeuwen

    1. Laboratory of Paediatric Oncology, Radboud University Medical centre, Nijmegen, The Netherlands
    Search for more papers by this author
    • Contributed equally as senior authors.

Errata

This article is corrected by:

  1. Errata: Erratum Volume 167, Issue 4, 584, Article first published online: 27 October 2014

Summary

Early recognition of children with chronic phase chronic myeloid leukaemia (CML-CP) at risk for developing a lymphoid blast crisis (LyBC) is desirable, because therapy options in CML-LyBC are limited. We used Multiplex Ligation-dependent Probe Amplification to determine whether B-cell lymphoid leukaemia-specific copy number alterations (CNAs) (e.g. IKZF1, PAX5, CDKN2A deletions) could be detected in CML-CP and may be used to predict disease progression to LyBC. CNAs were detected in all patients with CML-LyBC, but in none of the 77 patients with CML-CP. Based on this study we conclude that CNAs remain a hallmark of disease progression.

Chronic myeloid leukaemia (CML) is a clonal myeloproliferative expansion of transformed, primitive haematopoietic progenitor cells. The BCR-ABL1 fusion gene, resulting from the Philadelphia chromosome translocation t(9;22)(q34;q11), is found in up to 95% of all CML patients (Faderl et al, 1999). Clinical and laboratory studies demonstrate that the BCR-ABL1 fusion protein plays an essential role in the initiation, maintenance and progression of CML (Hehlmann et al, 2007).

With the introduction of tyrosine kinase inhibitors (TKIs), CML has transformed from a fatal disease to a leukaemia subtype with a favourable prognosis (Hehlmann et al, 2007). Estimated progression-free survival rates at 36 months are 98% in children with chronic phase CML (CML-CP) (Suttorp et al, 2012; Millot et al, 2011). However, once a blast crisis (BC) has occurred, treatment options are limited with a median overall survival of approximately 5·3 months in adult lymphoid BC (CML-LyBC) patients (Cortes et al, 2008). Therefore, early recognition of patients at risk of developing a BC seems important.

There is accumulating evidence that specific gene abnormalities contribute to the transformation from CML-CP to CML-BC in adults (Mullighan et al, 2008; Alpar et al, 2012). In addition to the BCR-ABL1 translocation t(9;22)(q34;q11), deletions in IKZF1, PAX5, and/or CDKN2A have been frequently reported in CML-LyBC (Mullighan et al, 2008; Alpar et al, 2012). Similar deletions in IKZF1, PAX5, and CDKN2A are also frequently observed in B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) (Mullighan et al, 2007, 2008; Kuiper et al, 2007, 2010).

In the present study we used Multiplex Ligation-dependent Probe Amplification (MLPA) analysis to screen for the presence of copy number alterations (CNAs) in a large cohort of 77 children with CML-CP, two patients with accelerated phase CML (CML-AP), and one patient with CML-LyBC, to investigate whether deletions in IKZF1 and other genes are detectable in paediatric CML and if they could be used to predict disease progression in CML-CP.

Material and methods

Patient characteristics

A total of 80 children with newly diagnosed CML were included: 51 patients from Germany and 29 patients from the Netherlands. Disease stage was determined at time of diagnosis following standard World Health Organization criteria [% blast cells in peripheral blood (PB) or bone marrow (BM), % blast cells plus promyelocytes in PB, % basophils in PB, persistent thrombocytopenia unrelated to therapy and presence of extramedullary blast involvement].

DNA isolation

Genomic DNA was isolated according to manufacturer's protocol from whole peripheral blood or bone marrow using the QIAamp DNA Blood Mini Kit or from mononuclear cells using the QIAamp DNA easy kit (Qiagen, Hilden, Germany) for the German and Dutch samples, respectively. All isolated DNA was quantified by NanoDrop spectrophotometry (NanoDrop, Wilmington, DE, USA).

Multiplex ligation-dependent probe amplification (MLPA)

Targeted copy number screening of eight selected loci (IKZF1, BTG1, CDKN2A/B, EBF1, ETV6, PAX5, RB1, and the PAR1 region) was performed in the cohort by means of MLPA using the P335-B2 SALSA MLPA kit (MRC-Holland, Amsterdam, the Netherlands) as described previously (Kuiper et al, 2010). All samples contained >50% BCR-ABL1 positive cells, as MLPA analysis is sufficient to detect copy number alterations when they are present in more than 50% of the cells (MRC-Holland).

Direct sequencing for detection of point mutations in IKZF1 gene

To search for IKZF1 point mutations, direct sequencing was performed on material from patients who experienced CML-BC but were negative for IKZF1 deletions by MLPA. Primers for polymerase chain reaction (PCR) reactions were designed in all coding regions of IKZF1. The sequences of designed primers are listed in Table SI. Amplification was carried out using an Eppendorf Mastercycler (Eppendorf, Hamburg, Germany). After the PCR products were verified by electrophoresis, direct DNA sequencing was performed on an ABI 3730 DNA analyser (Applied Biosystems, Foster City, CA, USA) following the manufacturer's instructions. Sequences were analysed using vector nti® software (Life Technologies, Carlsbad, CA, USA) and aligned against a reference sequence obtained from USCS Genome Bioinformatics (NM_006060) (University of California, Santa Cruz, CA, USA).

Results

A cohort of 80 children with newly diagnosed CML was analysed. Patients' characteristics are listed in Table SII. Of the 80 patients, 77 were diagnosed with CML-CP, 2 with CML-AP and 1 with CML-LyBC. Four patients diagnosed with CML-CP experienced progression to a BC (two myeloid BC (MyBC) and two LyBC). Both patients diagnosed with CML-AP (Patients 58, 67) experienced progression to LyBC at 6·5 and 8·1 months after diagnosis, respectively. Patient 22, diagnosed with CML-LyBC, also experienced a LyBC relapse.

CNAs in BTG1, CDKN2A/B, EBF1, ETV6, IKZF1, PAX5 and RB1 were determined using MLPA analysis. An IKZF1 deletion involving exons 4 to 7 (del 4–7) was identified in one patient diagnosed with CML-AP (Patient 58, Table 1). In the patient diagnosed with CML-LyBC an IKZF1 del 4–7 and an EBF1 deletion were identified (Patient 22, Table 1). No CNAs were identified in the 77 patients diagnosed with CML-CP (Table 1). Patients who experienced disease progression were further analysed. There was no material available for the two patients that progressed to MyBC at this time point. In all of the four patients that showed progression to LyBC, CNAs were detected at BC (Table 2). Patient 62, diagnosed with CML-CP, experienced LyBC 4·1 months after diagnosis. At the time of LyBC, a new IKZF1 del 1–8 and a PAX5 deletion were detected (Table 2). Patient 64, diagnosed with CML-CP, experienced LyBC 5·4 months after diagnosis. At the time of LyBC, a new CDKN2A/B deletion was detected (Table 2). Sanger sequencing was performed, screening all exons of IKZF1 using material from patients 18 and 32, at the time of CML-CP, and patient 64, at LyBC onset. However, no IKZF1 mutations were found. Both patients diagnosed with CML-AP experienced LyBC at 6·5 and 8·1 months after diagnosis, respectively. An IKZF1 deletion encompassing exons 4–7 was found in patient 58 at the time of diagnosis (Table 2); at time of LyBC, this IKZF1 4–7 deletion, but no other CNAs were found. No CNAs or point mutations could be detected in patient 67 at time of diagnosis, although at the time of LyBC, novel IKZF1 del 1–8 and PAX5 deletions were detected (Table 2).

Table 1. Copy number alterations detected in paediatric CML at diagnosis.
Disease stage at diagnosisGene IKZF1, CDKN2A/B, PAX5, ETV6, BTG1, RB1, CRLF2, EBF1
Chronic phase
 N = 77None
Accelerated phase
Patient 58IKZF1 del 4–7
Patient 67None
Lymphoid blast crisis
Patient 22IKZF1 del 4–7, EBF1 del
Table 2. Copy number alterations detected in CML patients with disease progression.
PatientDisease stageTime of progression (months after diagnosis)Copy number alterations
  1. CML, chronic myeloid leukaemia; CP, chronic phase; MyBC, myeloid blast crisis; LyBC, lymphoid blast crisis; AP, accelerated phase; CNA, copy number alterations.

18CP No CNAs
MyBC7·79No material available
32CP No CNAs
MyBC5·69No material available
58AP IKZF1 del 4–7
LyBC6·54IKZF1 del 4–7
62CP No CNAs
LyBC4·08IKZF1 del 1–8, PAX5
64CP No CNAs
LyBC5·42 CDKN2A/B
67AP No CNAs
LyBC8·12IKZF1 del 1–8, PAX5

Discussion

This study characterized copy number alterations using MLPA analysis in the largest paediatric CML cohort to date. MLPA analysis was used to screen for deletions in eight different genes that are frequently deleted in CML-LyBC and BCP-ALL (Mullighan et al, 2007, 2008; Kuiper et al, 2007, 2010). CNAs were detectable in material from one of the CML-AP and in all of the CML-LyBC patients, while no CNAs were found in any of the 77 CML-CP samples.

The samples from all of the 77 analysed CML-CP cases contained ≥63% BCR-ABL1 positive cells, which should allow detection of clonal deletions by MLPA. CNAs were restricted to patients experiencing progressive disease. In one patient, presenting with a CML-AP, an IKZF1 exon 4–7 deletion was detected at time of diagnosis. Recurrent deletions at time of CML-LyBC were found in IKZF1, PAX5, and the CDKN2A/B locus. Recently, a comparable study was performed on a smaller cohort of mainly adult CML patients (= 39, 30 CML-CP (3 paediatric and 27 adult patients) and 9 CML-LyBC (all adults)) (Alpar et al, 2012). CNAs were found in material of only two imatinib-resistant adult patients at the time of CML-CP, but several CNAs were detected during CML-LyBC (Alpar et al, 2012).

Our results in paediatric CML are also in accordance with studies performed in adults (Mullighan et al, 2008; Nacheva et al, 2010; Nadarajan et al, 2011; Wang et al, 2013). Mullighan et al used single nucleotide polymorphism arrays on 34 adult CML cases and described a mean of 0·47 CNAs per CML-CP whereas in CML-AP and CML-LyBC the mean was 1·14 and 7·8, respectively (Mullighan et al, 2008). In a more recent study, no IKZF1 deletions were detected in CML-CP or CML-AP (= 104) (Wang et al, 2013). Therefore, we conclude that clonal CNAs are rare or even absent in CML-CP, but are relatively common at progressed stages, which is consistent with the notion that the BCR-ABL1 fusion protein is sufficient to induce CML, but additional genomic changes are required for disease progression (Mullighan et al, 2008; Nacheva et al, 2010; Nadarajan et al, 2011; Wang et al, 2013).

In vitro long-term cultures suggest that loss of IKZF1 and the presence of the BCR-ABL1 fusion protein synergistically contribute to leukemogenesis, resulting in aggressive lymphoid leukemogenesis as observed in CML-LyBC (Suzuki et al, 2012). IKZF1, PAX5, and CDKN2A deletions are also recurrently found in both diagnosis and relapsed BCP-ALL, as shown previously (Kuiper et al, 2007, 2010). Our results not only support the notion that BCR-ABL1 synergizes with these specific genetic events, but also suggest that there are intriguing similarities in the development of CML-LyBC and relapsed BCP-ALL. In addition, based on the type of CNAs found both in children and adults with CML, there appear to be no large changes in disease mechanism with age.

In summary, we conclude that, using MLPA analysis, clonal CNAs could not be detected in paediatric CML-CP but remain a hallmark of disease progression.

Authorship contribution

NEvdS, MK, AP, BS, MM, MS, ESJMdB, and FNvL were responsible for the study design. MK, AP, JTT, CN, TGJMdB, and SvR collected the experimental data. NEvdS, ES, JB, MM, and MS collected the samples and clinical data. NEvdS, MK, AP, BS, SvR, RPK, MM, MS, ESJMdB, and FNvL analysed, interpreted the data and wrote and supervised the paper. GHdB supervised statistical analysis. This manuscript was reviewed and approved by all authors.

Financial support

This work was performed without any financial support.

Competing interest

The authors have no competing interests.

Ancillary