Abstract 309: Whole-transcriptome sequencing in chronic myeloid leukemia reveals novel gene mutations that may be associated with disease pathogenesis and progression

Abstract

Abstract Chronic myeloid leukemia (CML) has always been regarded as a genetically homogeneous disease. However, a proportion of patients (pts), especially in the high Sokal risk group, fail tyrosine kinase inhibitor therapy and progress to blast crisis (BC) – thus a certain degree of heterogeneity exists. It can be hypothesized that genetic factors additional to the Ph+ chromosome may be present in these pts. To address this issue, we are currently using massively parallel sequencing to perform a qualitative and quantitative survey of the whole transcriptome of Ph+ CML cells at diagnosis and at progression to BC. Results are being integrated with genome-wide search for copy number alterations by Affymetrix SNP 6.0 arrays. We used a Solexa Illumina Genome Analyzer to scan the transcriptome of a CML patient at the time of diagnosis, at the time of remission (major molecular response) and at the time of progression from chronic phase (CP) to lymphoid blast crisis (BC). Comparison of the SNVs identified in the diagnosis and relapse samples with the SNVs detected in the remission sample allowed the identification of eight missense mutations at diagnosis affecting the coding sequence of AMPD3, SUCNR1, FANCD2, INCENP, BSPRY, HEXDC, KIAA2018 and NUDT9 genes. Six of these mutations (FANCD2, INCENP, BSPRY, HEXDC, NUDT9) were also detected in the Ph+ clone re-emerged at the time of disease progression, together with seven additional missense mutations affecting the coding sequence of IDH2, DECR1, C4Orf14, MRM1, PRKD2, TCHP and ABL1 genes. IDH2, MRM1, AMPD3, and KIAA2018 mutations were found in additional pts. The IDH2 R140Q mutation was detected in 3/75 (4%) myeloid BC, 1/31 (3.2%) lymphoid BC, 0/34 Ph+ ALL and 0/23 Philadelphia-negative (Ph-) ALL pts. The MRM1 (mitochondrial rRNA methyltransferase 1) C120S mutation was found in 6/70 (9%) additional BC pts (2 lymphoid and 4 myeloid). AMPD3 (encoding adenosine monophosphate deaminase 3) and KIAA2018 (encoding a protein with predicted DNA binding and transcriptional regulation activity) genes were found to harbour the same point mutations (N334S and S1818G, respectively) in 1 out of 20 additional CP patients analyzed. Point mutations in untraslated regions where miRNAs are known to bind were also detected and are currently under validation. Digital gene expression profiling comparing progression to diagnosis showed significant upregulation of the B-cell developmental factor PAX5, its interactor Lef-1 and its targets IRF4, BLNK, Bik, EBF1, CD79A, CD79B, CD19, VpreB1, VpreB3, BOB1, RAG1 and RAG2; upregulation of PAX9; upregulation of WNT3A, WNT9A, GLI3 and downregulation of SFRP1 in the Wnt signalling pathway; downregulation of ITGA2B and ITGB3 integrin chains. In summary, our data highlighted putative key genes whose deregulation may be recurrent in a subset of CML patients and may favor disease progression. 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 309. doi:10.1158/1538-7445.AM2011-309