Elsevier

Leukemia Research

Volume 35, Issue 8, August 2011, Pages 1052-1059
Leukemia Research

A polymorphism in the chromosome 9p21 ANRIL locus is associated to Philadelphia positive acute lymphoblastic leukemia

https://doi.org/10.1016/j.leukres.2011.02.020Get rights and content

Abstract

Little is known about alterations of cyclin dependent kinase inhibitors p15INK4B, p16INK4A and of MDM2 inhibitor p14ARF due to single nucleotide polymorphisms (SNPs) located within the CDKN2A/B genes and/or neighbouring loci. In order to investigate the potential involvement of such common DNA sequence variants in leukemia susceptibility, an association study was performed by genotyping 23 SNPs spanning the MTAP, CDKN2A/B and CDKN2BAS loci, as well as relative intergenic regions, in a case-control cohort made up of 149 leukemia patients, including Philadelphia positive (Ph+) acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) samples, and 183 healthy controls. rs564398, mapping to the CDKN2BAS locus that encodes for ANRIL antisense non-coding RNA, showed a statistically significant correlation with the ALL phenotype, with a risk pattern that was compatible with an overdominant model of disease susceptibility and a OR of 2 (95% CI, 1.20–3.33; p = 7.1 × 10−3). We hypothesized that this association reflects the capability of some ANRIL polymorphisms to contribute to its transcription changes responsible for alterations of CDKN2A/B expression profiles, thus leading to abnormal proliferative boosts and consequent increased ALL susceptibility.

Introduction

Among genes that are supposed to be involved in altered molecular pathways leading to leukemogenesis, the CDKN2A/B locus is particularly noteworthy since it encodes for the INK4-class cyclin dependent kinase (CDK) inhibitors p15INK4B, p16INK4A and for p14ARF, which inhibits MDM2's E3 ligase activity stabilizing p53 [1], [2]. p15INK4B, p16INK4A act as tumour suppressors by inhibiting the proliferative kinases CDK4 and CDK6 thus blocking the cell-cycle division during the G1/S phase, whereas p14ARF acts as a tumour suppressor by inhibiting MDM2. Alterations of such proteins have been long implicated in many cancer types [3] and their inactivation is frequently observed also in several haeamatologic malignancies [4]. It has been argued that mechanisms which enable the continuous self-renewal of haematopoietic stem cells (HSCs) must prevent the execution of senescence programs regulated by the retinoblastoma (RB) protein and p53 tumour suppressors and that p16INK4A and p15INK4B may contribute to the maintenance of the RB protein in its growth-suppressive mode. Also in mice, disruption of the Rb and p53 signalling networks through CDKN2A/B alterations results in abnormal self-renewing capabilities typical of cancer cells. In particular, although both CDKN2A and CDKN2B are individually regulated and can independently act as tumour suppressors, mice lacking the entire CDKN2A/B cluster are found to be the most prone to develop tumours, mimicking the phenotype of acute lymphoblastic leukemia (ALL) [5].

That being so, the CDKN2A/B locus clearly appears to be a plausible candidate leukemia susceptibility locus, although to date it has been found to be inactivated in several haeamatologic malignancies mainly due to deletion, aberrant repression or epigenetic silencing [6] and little is known about the potential influence of its single nucleotide polymorphisms (SNPs) on leukemia risk. A candidate-gene study has identified some CDKN2A/B promoter SNPs that may predispose to childhood pre-B ALL [7], but no susceptibility alleles were found on this cell-cycle checkpoint locus by genome-wide association (GWA) studies [8], [9], with a single recent exception [10]. Moreover, the genomic region immediately upstream of the CDKN2A/B locus has also turned out to be extremely intriguing since it contains several SNPs associated with risk of coronary artery disease (CAD) [11], [12], ischemic stroke [13], abdominal aortic aneurysm [14], type 2 diabetes mellitus (T2DM) [15], [16] and gestational diabetes mellitus (GDM) [17]. In particular, SNPs showing the strongest association with CAD and T2DM did not map within annotated genes, suggesting that neighbouring loci may mediate disease associations by acting as regulatory elements of CDKN2A/B expression [18], [19].

To comprehensively investigate whether polymorphisms within this broad genomic region may correlate also with increased susceptibility to haeamatologic malignancies in adult ALL patients, an association study was performed by genotyping 23 SNPs spanning the MTAP, CDKN2A/B and CDKN2BAS loci, as well as relative intergenic regions, in a case-control cohort made up of 149 leukemia patients, including 92 Philadelphia positive (Ph+) ALL and 57 acute myeloid leukemia (AML) samples, and 183 healthy controls.

Section snippets

Leukemia patients and healthy controls

Association analysis between SNPs and disease phenotypes was performed on a case-control cohort made up of 92 Italian subjects affected by Ph+ ALL, 57 Italian subjects affected by AML and 183 unrelated healthy Italian individuals.

Since DNAs of ALL and AML patients were extracted from peripheral blood samples with high percentages of blast cells, the evidence that regions in the 9p are recurrently deleted in ALL was taken into account to check the reliability of the obtained genotypes. For our

Results

A total of 17 SNPs, spanning the 9p genomic interval that encompasses the MTAP, CDKN2A/B and CDKN2BAS loci (Fig. 1), were successfully genotyped and used for investigating their potential associations with the ALL/AML phenotypes. Five SNPs (rs1012713, rs10965179, rs34011899, rs3731232, rs3218010) with MAF <0.05 in cases and controls, as well as one SNP (rs3931609) showing >20% missing call rates, were instead excluded from the association analysis.

Genotypes of the 17 informative polymorphisms

Discussion

Potential correlations between Ph+ ALL and AML susceptibilities and SNPs located on a wide 9p interval spanning the MTAP, CDKN2A/B and CDKN2BAS loci were investigated by means of a “candidate genomic region” association study. For this purpose, 23 SNPs belonging to such region were carefully selected and genotyped on a case-control cohort made up of 149 leukemia patients, including Ph+ ALL and AML positive-cases, and 183 healthy controls.

The present study was thus focused on genes encoding for

Conflict of interest

The authors have no conflicts of interest to disclose.

Acknowledgements

We thank European LeukemiaNet, AIL, AIRC, Fondazione Del Monte di Bologna e Ravenna, FIRB 2006, Ateneo RFO grants, Project of integreted program (PIO), Programma di Ricerca Regione – Università 2007–2009, Fondazione Cassa di Risparmio in Bologna for supporting the CRBA. Contributions. I.I. and M.S. contributed equally to this work; I.I., G.M, P.G. and V.M. provided conception and design; I.I., A.L. A.F., C.P. E.O., S.S., M.V., V.M. and G.M. responsible for collection of samples and clinical

References (39)

  • H.G. Drexler

    Review of alterations of the cyclin-dependent kinase inhibitor INK4 family genes p15, p16, p18 and p19 in human leukemia-lymphoma cells

    Leukemia

    (1998)
  • E. Papaemmanuil et al.

    Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia

    Nat Genet

    (2009)
  • L.R. Trevino et al.

    Germline genomic variants associated with childhood acute lymphoblastic leukemia

    Nat Genet

    (2009)
  • A.L. Sherborne et al.

    Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk

    Nat Genet

    (2010)
  • N.J. Samani et al.

    Genomewide association analysis of coronary artery disease

    N Engl J Med

    (2007)
  • H.M. Broadbent et al.

    Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p

    Hum Mol Genet

    (2008)
  • M. Matarin et al.

    Whole genome analyses suggest ischemic stroke and heart disease share an association with polymorphisms on chromosome 9p21

    Stroke

    (2008)
  • A. Helgadottir et al.

    The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm

    Nat Genet

    (2008)
  • L.J. Scott et al.

    A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants

    Science

    (2007)
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