Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia
Recurrent deletions of the CDKN2A/ARF/CDKN2B genes encoded at chromosome 9p21 have been described in both pediatric and adult acute lymphoblastic leukemia (ALL), but their prognostic value remains controversial, with limited data on adult T-ALL. Here, we investigated the presence of homozygous and heterozygous deletions of the CDKN2A/ARF and CDKN2B genes in 64 adult T-ALL patients enrolled in two consecutive trials from the Spanish PETHEMA group. Alterations in CDKN2A/ARF/CDKN2B were detected in 35/64 patients (55%). Most of them consisted of 9p21 losses involving homozygous deletions of the CDKNA/ARF gene (26/64), as confirmed by single nucleotide polymorphism (SNP) arrays and interphase fluorescence in situ hybridization (iFISH). Deletions involving the CDKN2A/ARF/CDKN2B locus correlated with a higher frequency of cortical T cell phenotype and a better clearance of minimal residual disease (MRD) after induction therapy. Moreover, the combination of an altered copy-number-value (CNV) involving the CDKN2A/ARF/CDKN2B gene locus and undetectable MRD (≤ 0.01%) values allowed the identification of a subset of T-ALL with better overall survival in the absence of hematopoietic stem cell transplantation.
KeywordsT-ALL CDKN2A/ARF CDKN2B Prognosis MRD
Acute lymphoblastic leukemia
Allogeneic-hematopoietic stem cell transplantation
Copy number alterations
European Group for the Immunological Classification of Leukemias
Early T cell precursor acute lymphoblastic leukemia
Interphase fluorescence in situ hybridization
Minimal residual disease
Programa Español para el Tratamiento de Hemopatías Malignas
Quantitative polymerase chain reaction
Relative copy number
Single nucleotide polymorphism array
T cell acute lymphoblastic leukemia
White blood cell count
World Health Organization
At present, treatment response based on minimal residual disease (MRD), monitoring for early and accurate identification of high-risk patients in whom treatment might be intensified, represents a milestone in virtually all childhood and adult acute lymphoblastic leukemia (ALL) trials [1, 2]. Despite this, more extended molecular analyses performed at diagnosis in ALL have also proven to contribute to the identification of ALL subtypes that respond better to specific targeted therapies and to refine the classical risk-stratification schemes used at baseline . However, from all genomic markers identified so far , only a few are routinely used for the clinical management of ALL, particularly in T cell ALL (T-ALL). This is due to the still limited data available about their frequency and independent prognostic impact, in large cohorts of T-ALL patients homogeneously treated in the MRD era.
Here, we investigated the presence and frequency of copy-number-value alterations (CNA) at chromosome 9p21 which involved the CDKN2A/ARF and CDKN2B genes in a cohort of 64 adult T-ALL patients enrolled in two consecutive Spanish PETHEMA (Programa Español para el Tratamiento de Hemopatías Malignas) trials (details about the patient cohort are available in Additional file 1: Figure S2 and Table S4), using a genomic quantitative polymerase chain reaction (qPCR) technique [5, 6] (Additional file 1: Table S1). An overall frequency of CNA at chromosome 9p21 of 55% (35/64 cases) was observed, 20% of the cases (13/64) showing a discrepant CNA profile for the CDKN2A/ARF and CDKN2B genes. Of note, the CNA values identified by qPCR were fully concordant with those obtained by SNP-arrays and iFISH analyses, once qPCR CNA values had been corrected for the contamination by normal DNA-diploid cells in the sample (Additional file 1: Table S2).
Association between the CNA status for the CDKN2A/ARF/CDKN2B locus and early response to treatment as assessed by the MRD levels detected at the end of induction therapy
CDN2A/ARF/CDKN2B gene status
MRD ≤ 0.1%
MRD ≤ 0.01%
Bi or mono-allelic deletion (n = 30)
No deletion (n = 30)
Bi or mono-allelic deletion (n = 27)
No deletion (n = 28)
CDKN2A/ARF and/or CDKN2B
Bi or mono-allelic deletion (n = 32)
No deletion (n = 23)
As a consequence of their better response to induction treatment, most patients with an altered CDKN2A/ARF/CDKN2B CNV (32/34, 94%) did not require an allogeneic-hematopoietic stem cell transplantation (allo-HSCT) according to the treatment protocol, in contrast to 11/28 patients (40%) with a normal diploid CDKN2A/ARF/CDKN2B genotype (p = 0.001).
When we searched for independent prognosis factors for OS, we observed that despite deletions of the CDKN2B gene (particularly mono-allelic CDKN2B gene deletions), but not the CDKN2A/ARF gene deletions, conferred a better prognosis in terms of OS (3y OS probability of 63% [43–83%] vs.37% [18–55%], p = 0.045) (Additional file 1: Figure S1A-B) in the univariate analysis, MRD after induction therapy was the only variable with an independent predictive value for OS in the multivariate analysis (Additional file 1: Table S3). Our results are in line with the findings reported by Liu et al. , but need to be validated in a larger and independent cohort of adult T-ALL. Recently, it has been highlighted the importance of NOTCH I/FBXW7 and N/K RAS/ PTEN point mutations in the OS of adult T-ALL patients , therefore would be interesting to assess the impact of these point mutations in our cohort in combination, or not, with CDKN2B deletions.
In summary, here, we confirm the high frequency of (mono and bi-allelic) deletions of the CDKN2A/ARF/CDKN2B genes also in adult T-ALL, and highlight the specific association between the loss of the CDKN2A/ARF and CDKN2B genes and a better response to therapy and prolonged OS, respectively. More importantly, identification of CNA in the CDKN2A/ARF/CDKN2B gene locus, together with the MRD levels at the end of induction, contributed to the identification of a subgroup of T-ALL patients in whom intensification of therapy with an allo-HSCT might not be of great clinical benefit.
We would like to thank Ernest Terribes for his advice and help in qPCR design and analysis as well as Alba García and Jesús-María Hernández-Rivas for providing some DNA samples. We are grateful to Isabel Granada for her helpful advice regarding cytogenetic and FISH analyses. This project was supported by the Asociación Española Contra el Cáncer, AECC (project ref.: GC16173697BIGA), by CERCA Program/Generalitat de Catalunya, the Catalan Government: 2014-SGR225 (GRE), Obra Social “La Caixa” and by Celgene Spain. E. Genescà is the recipient of agrant from the Spanish Health Ministry (ISCIII, CA12/00468) and an unrestricted grant from Gilead.A. Gonzalez-Perez is supported by a Ramon y Cajal fellowship (RYC-2013-14554) of the Educational Ministry (Madrid, Spain). This work was also partially supported by FEDER funds from the ISCIII (PT13/0010/0026, CIBERONC (CB16/12/00284 and CB16/12/00400), Madrid, Spain).
Availability of data and materials
The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
EG designed the study, analyzed the data, and wrote the manuscript. AL and GB performed the experiments and analyzed the data. MM performed statistical analyses. NR-X and PG-M performed FISH analyses. JR and JJ contributed to data analysis. AG-P helped to the SNP array analysis. SM, RG, MTA, MJM, JM-L, LZ, PB, CG, MT, AC, AN, JE, MP, JN, JG-C, MA, JC, PM, MB, and SV provided samples and clinical data. EF and FS provided economical support to the project though the IJC. AO provided samples, and together with JMR contributed to manuscript writing. All authors have read and approved the manuscript.
Ethics approval and consent to participate
Samples were obtained in accordance with the principles of the Declaration of Helsinki and the Spanish legislation for protection of personal data and research on human samples, after patients provided their written informed consent. The study was approved by the Institutional Review Board of the Hospital Germans Trias i Pujol (Badalona, Spain).
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- 1.Borowitz MJ, et al. Clinical significance of minimal residual disease in childhood acute lymphoblastic leukemia and its relationship to other prognostic factors: a Children’s Oncology Group study. Blood. 2008;111:5477–85.Google Scholar
- 2.Toubai T, et al. Minimal residual disease (MRD) monitoring using rearrangement of T-cell receptor and immunoglobulin H gene in the treatment of adult acute lymphoblastic leukemia patients. Am J Hematol. 2005;80:181–7.Google Scholar
- 3.Beldjord K, et al. Oncogenetics and minimal residual disease are independent outcome predictors in adult patients with acute lymphoblastic leukemia. Blood. 2014;123:3739–49.Google Scholar
- 4.Iacobucci I, Mullighan CG. Genetic basis of acute lymphoblastic leukemia. J Clin Oncol. 2017;35:975–83.Google Scholar
- 5.Bertin R, et al. CDKN2A, CDKN2B, and MTAP gene dosage permits precise characterization of mono- and bi-allelic 9p21 deletions in childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer. 2003;37:44–57.Google Scholar
- 6.Terribas E, et al. Probe-based quantitative PCR assay for detecting constitutional and somatic deletions in the NF1 gene: application to genetic testing and tumor analysis. Clin Chem. 2013;59(6):928–37.Google Scholar
- 7.Bene MC, et al. Proposals for the immunological classification of acute leukemias. European Group for the Immunological Characterization of Leukemias (EGIL). Leukemia. 1995;9(10):1783–6.Google Scholar
- 8.Zuurbier L, et al. Immature MEF2C-dysregulated T-cell leukemia patients have an early T-cell precursor acute lymphoblastic leukemia gene signature and typically have non-rearranged T-cell receptors. Haematologica. 2014;99(1):94–102.Google Scholar
- 9.Theunissen P, et al. Standardized flow cytometry for highly sensitive MRD measurements in B-cell acute lymphoblastic leukemia. Blood. 2017;129(3):347–57.Google Scholar
- 10.Liu Y, et al. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet. 2017;49:1211–8.Google Scholar
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