A novel BCR-ABL1 fusion gene with genetic heterogeneity indicates a good prognosis in a chronic myeloid leukemia case

Abstract

Background: Chronic myelogenous leukemia (CML) is a pluripotent hematopoietic stem cell disorder caused by the fusion of the BCR and ABL1 genes. Quantitative RT-PCR (qRT-PCR) is a routinely performed screening technique to identify BCR-ABL1 fusion genes, but a limitation of this method is its inability to recognize novel fusions that have not been previously characterized. Next-generation sequencing (NGS) is an effective and sensitive detection method for the determination of novel BCR-ABL1 fusion genes as well as previously characterized ones. The oncoprotein tyrosine kinase BCR-ABL1 is a constitutively active kinase involved in the activation of a number of signaling pathways, and it has been the therapeutic target for tyrosine kinase inhibitors (TKIs) such as imatinib. Reports have presented opposing viewpoints about the effect of the disrupted Src homology 3 (SH3) domain on TKI efficacy.

Findings: We here report that using NGS we identified a novel BCR-ABL1 fusion gene with breakpoints in the BCR intron 14 and the ABL1 intron 2, leading to partial deletion of its SH3 domain. In the present case, the patient received targeted therapy with the TKI imatinib at 400 mg/day and no adverse reaction was reported. The patient eventually entered remission with decreased proliferation of karyocytes and granulocytes. We also identified mutations in genes, including TP53, FLT3, ASXL1, SETBP1, CEBPA and CBL, that seemed to have an influence on the outcome of TKI therapy targeting the BCR-ABL1 protein.

Conclusions: Together with previously reported results, it is clear that the genetic heterogeneity of CML patients significantly affects the presentation of the disease and its progression and therefore should inform the design of the therapeutic strategy.

Keywords: BCR-ABL1; CML; Genetic heterogeneity; NGS; SH3 domain.

Fig. 1

Summary of FISH and molecular studies. a Image of bone marrow aspiration (400x) showing hypercellularity with elevated level of myeloblasts, eosinophils, and basophils. b FISH analysis. Separated green and red signals indicate probe-targeted sequences located on different chromosomes in a normal nucleus. Yellowish signal formed from the colocalization of green and red fluorescent signals indicates the fusion of BCR and ABL1 genes. c The breaking point (or fusion junction) and flanking sequences from BCR Intron 14 and ABL1 intron 2. d BCR-ABL1 cDNA sequence around the fusion junction and related chromatogram are shown. The junctions are indicated with arrows. e Image of bone marrow aspiration after imatinib targeted therapy. f FISH analysis after imatinib targeted therapy