Expression of BCR–ABL1 oncogene relative to ABL1 gene changes overtime in chronic myeloid leukemia Manu Gupta a,1 , Lili Milani a , Monica Hermansson b , Bengt Simonsson c , Berit Markeva ¨rn d , Ann Christine Syva ¨nen a , Gisela Barbany e, * a Molecular Medicine, Department of Medical Sciences, Uppsala University, Sweden b Department of Genetics and Pathology, Uppsala University Hospital, Sweden c Hematology Section, Department of Medical Sciences, Uppsala University Hospital, Sweden d Department of Medicine, Hematology Section, Umea ˚ University Hospital, Sweden e Department of Molecular Medicine and Surgery, Clinical Genetics Unit, Karolinska Institute, 171 76 Stockholm, Sweden Received 5 December 2007 Available online 17 December 2007 Abstract Using a quantitative single nucleotide polymorphism (SNP) assay we have investigated the changes in the expression of the BCR– ABL1 oncogene relative to the wild-type ABL1 and BCR alleles in cells from chronic myeloid leukemia (CML) patients not responding to therapy. The results show a progressive increase in the BCR–ABL1 oncogene expression at the expense of decreased expression of the ABL1 allele, not involved in the fusion. No relative changes in the expression of the two BCR alleles were found. These results demon- strate that allele-specific changes in gene expression, with selective, progressive silencing of the wild-type ABL1 allele in favor of the onco- genic BCR–ABL1 allele occur in CML patients with therapy-resistant disease. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Imbalanced allelic expression; Quantitative SNP assay; Oncogene; BCR–ABL1 expression; Disease progression The natural history of chronic myeloid leukemia (CML) is to progress from a relative benign chronic phase to a more aggressive blast crisis often through an intermediate accelerated phase. CML was the first form of cancer to be consistently associated with a chromosomal abnormal- ity i.e. the Philadelphia chromosome that results from a translocation between the long arms of chromosomes 9 and 22. The translocation juxtaposes exons 1 to 13/14 of the BCR gene on to exon 2 of the ABL1 gene on the deriv- ative chromosome 22 (reviewed in [1]). The resulting fusion protein acts as an oncogene with deregulated tyrosine kinase activity. The presence of the bcr–abl fusion protein is the only known genetic abnormality associated with chronic phase CML, and it has been shown to recapitulate chronic myeloid leukemia in mice transplanted with bone marrow cells that are stably transfected with the fusion gene [2]. As disease progresses to accelerated phase, cellular pro- cesses that control differentiation and genomic stability are deranged, however, the underlying mechanisms are still poorly understood (reviewed in [1]). Experimental studies in cell lines have suggested that increased expression of BCR–ABL1 is likely to contribute to the phenotype of advanced disease [3]. Disease progression in CML patients has also been associated with increased BCR–ABL1 RNA expression [4]. ABL1 expression in CML is the sum of the expression levels of the wild-type ABL1 and the translo- cated ABL1, driven by the proximal promoter (Pa) embed- ded in the translocation. Progressive methylation of the nested Pa ABL1 promoter, with subsequent silencing of 0006-291X/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2007.12.029 * Corresponding author. Fax: +46 8 327734. E-mail address: gisela.barbany-bustinza@karolinska.se (G. Barbany). 1 Present address: Medical Oncology Unit, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK. www.elsevier.com/locate/ybbrc Available online at www.sciencedirect.com Biochemical and Biophysical Research Communications 366 (2008) 848–851