Background: Fusion of the FGFR1 kinase to various partner proteins facilitates constitutive activation of the kinase domain of FGFR1, and is associated bi-phenotypic leukaemias in paediatrics. We have identified the rare FGFR1 fusion, CNTRL-FGFR1, in two patients at the Royal Children's Hospital, using RNA Sequencing (RNA-Seq). CNTRL-FGFR1 arises from a t(8;9) translocation and has been reported to fuse exon 40 of CNTRL to exon 10 of FGFR1. This fusion is associated with poor clinical outcomes, and there are currently no targeted therapies to treat this disease. However, there have been previous reports of patients responding clinically to the ABL1 inhibitor, imatinib.
Methods: We cloned and expressed the full-length CNTRL-FGFR1 fusion in cytokine-dependent cell models, and established sensitivity to tyrosine kinase inhibitors (TKIs) and chemotherapy drugs, vincristine and dexamethasone. We used a cell dilution assay, whereby we diluted GFP positive cells (marker for CNTRL-FGFR1 expression) into parental cells, to test the lower limit of Droplet Digital PCR (ddPCR) to detect CNTRL-FGFR1 using breakpoint-specific primers.
Results: We have identified a novel CNTRL-FGFR1 fusion transcript, and shown that the CNTRL-FGFR1 fusion undergoes post-translational alternative splicing. We show that there are multiple alternative start sites for translation of the CNTRL-FGFR1 fusion, and that kinase domain expression is sufficient for transformation. CNTRL-FGFR1 Ba/F3 cells are sensitive to treatment with TKIs that reduce phosphorylation of FGFR1 and degrade MCL-1. In contrast, imatinib treatment has no effect on phosphorylation of FGFR1 or cell killing. Using CNTRL-FGFR1 transcript information from RNA-Seq, we were able to reliably detect CNTRL-FGFR1 expression to 1 cell in 100,000, using ddPCR.
Conclusions: In this study, we have further characterised the biology of the CNTRL-FGFR1 fusion, and have shown that RNA-Seq and ddPCR may be valuable tools for tracking the abundance of leukaemic cells in patient samples. Furthermore, we have highlighted the potential clinical efficacy of combining ponatinib treatment with chemotherapy drugs, dexamethasone and vincristine, to treat CNTRL-FGFR1 driven leukaemia.