Abstract 311: Loss of the tumor suppressor genes CDKN2A/ARF impairs prognosis in adult BCR-ABL1 positive acute lymphoblastic leukemia (ALL)
Authors: Iacobucci Ilaria , Ferrari Anna , Papayannidis Cristina , Paoloni Francesca , Abbenante Mariachiara , Guadagnuolo Viviana , Ottaviani Emanuela , Cattina Federica , Vitale Antonella , Paolini Stefania , Soverini Simona , Parisi Sarah , Vignetti Marco , Baccarani Michele , Martinelli Giovanni 
Published: June 2012

Abstract
Rational: The tumor suppressor genes p16 INK4a /CDKN2A, p14/ARF and p15 INK4b /CDKN2B on 9p21 locus encode critical factors for the regulation of cell cycle and/or apoptosis and are often inactivated in many tumors.
Aims: To explore the frequency and size of deletions affecting the 9p21 locus in adult BCR-ABL1-positive ALL, to determine the main mechanism of inactivation and to investigate their prognostic role.
Patients and methods: 112 patients were analyzed: 82 (73%) de novo cases, 11 (10%) unpaired relapse cases, 19 (17%) diagnosis-relapse matched samples. The median age was 53 years (range: 18-76) and the median blast percentage was 90% (range, 18-99). Affymetrix single nucleotide polymorphism (SNP) arrays (GeneChip® Human Mapping 250K NspI and Genome-Wide Human SNP 6.0) were used to identify at a high resolution copy number changes on 9p21; PCR amplification and subsequent sequencing were performed in search of mutations; gene-expression profiling (Affymetrix Human Exon 1ST Array) was performed to draw a specific signature associated with deletions.
Results: At diagnosis, CDKN2A/ARF and CDKN2B genomic alterations were identified in 29% and 24% of patients, respectively. Deletions were monoallelic in the majority of cases (72%) with a median of 1,012 kb in size (range, 2.8-31,319 kb). In some of them, 43%, the minimal overlapping region of the lost area spanned only the CDKN2A/ARF/CDKN2B gene locus, but more often (57%) the loss was considerable larger and extended sometimes over the entire short arm. Analysis of the genomic status at the relapse showed an almost significant increase in the detection rate of CDKN2A/ARF loss (47%) compared to diagnosis (p = 0.06). The mutation screening performed on each exon of ARF, CDKN2A and CDKN2B genes showed that the 9p21 locus is rarely affected by missense point mutations with only the identification of D146N in the CDKN2A exon 2. Furthermore, 2 mutations were found in the 5’UTR of CDKN2A [UTR A 21965011 (33%), UTR G/A 21965011 (47%), UTR C/T 21964875 (3%)]. Since the prognostic relevance of CDKN2A/ARF deletions is still controversial in literature, we addressed this issue in our study cohort (81 patients evaluable), finding out that deletions in this locus are significantly associated with poor outcome both in terms of disease free-survival (p=0.001) and cumulative incidence of relapse (p=0.001).
Conclusions: The inactivation of CDKN2A/ARF is a frequent event in Ph+ ALL. Deletions are frequently acquired at the leukemia progression and work as a poor prognostic marker, impairing disease free-survival and cumulative incidence of relapse. Novel treatment strategies targeting the ARF-MDM2-p53 pathway may be effective in this subset of patients and in vitro studies are ongoing to confirm this hypothesis.
Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Programma di Ricerca Regione – Università 2007 – 2009.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 311. doi:10.1158/1538-7445.AM2011-311