Abstract 2143: High-Resolution Molecular Karyotyping of Chronic Myeloid Leukemia Patients in Blast Crisis by 6.0 SNP-Arrays Identifies Focal Copy Number Alterations Affecting the Whole Sequence or Specific Exons of Oncogenes and Tumor Suppressor Genes
Authors: Gnani Alessandra , Soverini Simona , Colarossi Sabrina , Castagnetti Fausto , Astolfi Annalisa , Formica Serena , Palandri Francesca , Iacobucci Ilaria , Gugliotta Gabriele , Poerio Angela , Amabile Marilina , Marzocchi Giulia , Testoni Nicoletta , Abruzzese Elisabetta , Rosti Gianantonio , Capranico Giovanni , Baccarani Michele , Martinelli Giovanni 
Published: February 2011

Abstract
Despite the striking efficacy of targeted therapy for chronic myeloid leukemia (CML), a proportion of patients (pts) still experience progression from the initial chronic phase to an acute phase (blast crisis; BC) characterized by high disease aggressiveness and poor prognosis. BC is known to be associated with accumulation of additional genetic alterations, but these alterations have so far been only partially characterized. We used Human 6.0 SNP Arrays (Affymetrix) to perform high-resolution molecular karyotyping of 29 DNA samples from BC (myeloid, n=17 lymphoid, n=11) CML pts. The 6.0 SNP Array technology relies on 1.8 million markers evenly spaced across the genome, with a median inter-marker distance &lt;700 bp. We decided to exploit this unprecedented resolution aiming our analysis to the identification of very small CNAs that may have been missed by previous studies using less sensitive assays. Gains/losses mapping to known regions of copy number variation (CNV) were excluded. Our approach revealed a number of focal gains or losses ranging from 4 to 47Kb, affecting a single gene or, more frequently, only part of a gene. Amplifications were as frequent as monoallelic deletions and involved the promoter region and/or one or more exons. In some cases, a complex pattern of amplification of some exons and monoallelic deletion of others was recognized within the same gene. Alterations involved the following genes: AKT3; CDC73; RB1; JAK2; JAK1;K ERG; ETS1; SMAD; PIK3CA; EPHA3; RUNX1T1; ETV1; AKT2; MDM4; KALRN; FHIT; K-RAS; PTEN; FAF1; SKAP2; PTCH1; GAS2; FGFR2; SOS1; NRG1; MET; PBX4; ETV5; N-RAS, HGF, TEC; PAK2; H-RAS. The precise anatomy of alterations involving each gene will be presented. Deeper characterization of these alterations at the DNA and RNA levels by polymerase chain reaction and sequencing is now ongoing; results will be presented. All the genes identified in our screening were transcription factors, adaptor proteins, receptor and non-receptor kinases involved in cell proliferation and apoptosis - with a known role as oncogenes or tumor suppressors or oncogene/tumor suppressor interactors. Although these results confirm a high degree of heterogeneity in the alterations detectable in BC CML pts, members of the RAS pathway were the most frequently altered genes. Deeper characterization by polymerase chain reaction and sequencing is ongoing and will be presented. In conclusion, the power of 6.0 SNP Array technology allowed us to detect previously unidentified alterations targeting whole or part of key oncogenes or tumor suppressors whose deregulation may play a role in determining the aggressive phenotype of BC CML and which may represent potential therapeutic targets. Supported by European LeukemiaNet, AIL, AIRC, PRIN, Fondazione del Monte di Bologna e Ravenna.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2143.