Abstract 1138: First Application of Whole-Transcriptome Sequencing to a High-Risk Chronic Myeloid Leukemia (CML) Patient at Diagnosis and at the Time of Disease Progression to Blast Crisis (BC)

Abstract

Abstract Philadelphia-positive (Ph+) CML is generally regarded as a genetically heterogeneous disease and therapy with Bcr-Abl inhibitors results in high response rates. Nevertheless, resistance may develop, especially in high Sokal risk patients, and progression to BC still represents a major concern. The biological bases underlying high risk as well as the determinants of disease progression remain largely unknown. High-throughput technologies are nowadays available that allow to perform genome-wide studies with unprecedented informativity and resolution. We have integrated three such technologies - massively-parallel sequencing, gene expression profiling (GEP) by microarrays and high-resolution karyotyping by SNP-arrays - for a deeper characterization of a high-risk tyrosine kinase inhibitor-resistant patient at presentation and at the time of progression to BC. After having obtained written informed consent from her next of kin the samples collected at diagnosis, at the time of remission and at the time of progression were used for RNA and DNA extraction. Paired-end RNAseq was performed on an Illumina/Solexa Genome Analyzer. The number of 75bp-long sequence reads obtained was 40,193,384 (corresponding to 3.01 billion bases), 35,592,588 (2.7 billion bases), and 32,867,700 (2.5 billion bases) for diagnosis, remission and progression samples, respectively. Both custom scripts and published algorithms were used for read alignment and mapping against the human reference genome (NCBI build 36.1) and for subsequent single nucleotide variant (SNV) calling. Comparison of the SNVs identified in the diagnosis and relapse samples with the SNVs present in the remission sample was crucial to rule out all the inherited sequence variants besides known SNPs that were nonspecific of Ph+ leukemia cells. Twenty-nine mutations in the coding sequence of 28 genes were found at diagnosis (17 missense, 12 silent). Eighteen mutations (11 missense, 7 silent) in 18 additional genes were found to have emerged at the time of disease progression. In parallel, high-resolution (<1kb) genome wide copy number alteration (CNA) and loss of heterozigosity (LOH) analyses were performed on DNA using the Genome-Wide SNP Arrays 6.0 (Affymetrix) and GEP was performed on RNA using the GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix). Detailed results of all analyses will be presented onsite. Our data provide a comprehensive overview of the complexity of the Ph+ cell genome and transcriptome of a high-risk patient both at the time of diagnosis and at the time of resistance and progression to BC. Genome-wide integrated approaches like this might provide novel insights and fill the gaps in our knowledge of the pathogenesis of CML and of the mechanisms of disease progression. Supported by European LeukemiaNet, 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 1138.