Genomics, Diagnosis, Novel Targeted Therapies and Characterisation of the Drivers of Relapse in Philadelphia Chromosome-Like Acute Lymphoblastic Leukaemia
This thesis focuses on Philadelphia chromosome-like (BCR::ABL1-like) acute lymphoblastic leukaemia (Ph-like ALL), a subtype of B-cell ALL recently recognised as a distinct entity. The genomic drivers of Ph-like ALL are diverse. This thesis emphasises investigation of the JAK/STAT class of lesions. Ph-like ALL patients continue to have poor prognosis, in contrast to patients with other subtypes of B-ALL such as Philadelphia chromosome positive ALL, who have had significant improvements in outcomes with targeted therapies. A significant obstacle in Ph-like ALL has been imprecise case-by-case characterisation of the genomic landscape, which is especially relevant for lesions which have not yet been shown to be actionable by precision inhibitors. This thesis hypothesised that fluorescence in-situ hybridisation (FISH) would be an accurate, efficient and practical method for diagnosis of Ph-like ALL genomic lesions in the real-world. Based on current literature, it was postulated that a diagnostic algorithm could be developed by using FISH as a single initial investigation to identify relevant lesions. The dismal prognosis of JAK/STAT activated ALL demands new therapeutic approaches. In vitro models of JAK rearrangements have been limited by instability of relevant murine cell lines in culture, and an improved culture technique was developed using Ba/F3 cell lines to define a reliable model for testing relevant therapeutic agents against cell lines transfected with JAK fusions. The model was tested against standard responses previously published for the JAK2 inhibitor ruxolitinib, authenticating methods for determining lethal dose 50 (LD50). It was demonstrated that combination inhibitors would be more effective against JAK fusions known to confer particularly poor prognosis. In an in vitro model, proteosome inhibitors carfilzomib and bortezomib were combined with ruxolitinib and demonstrated potency and, for carfilzomib, synergy against the commonest JAK fusion, PAX5::JAK2. This synergy may be due to inhibition of STAT3/5 or oxidative phosphorylation, or both. Ongoing clinical trials of novel JAK/STAT inhibitors are at risk of compromise due to the emergence of resistance. The ETV6::JAK2 p.G993A in vitro model of JAK2 inhibitor resistant JAK/STAT activated ALL was used to investigate resistance to STAT3 and STAT5 inhibitors, pimozide and SH-4-54. Both were shown to overcome resistance. The investigation suggested the mechanism of action may be inhibition downstream of JAK2. Finally, this thesis predicted that the landscape of single nucleotide variants (SNVs) in Ph-like ALL at diagnosis and relapse may differ from that in non Ph-like Ph-negative B-ALL patients. SNVs at relapse in non Ph-like Ph-negative B-ALL patients demonstrated significant variance with the patterns at diagnosis, whereas no such findings were seen in the comparison for Phlike ALL. This finding has possible implications for the underlying mechanism of relapse or refractory status in Ph-like ALL. This thesis concludes with discussion of future prospects in precision approaches and therapeutics for Ph-like ALL associated genomic lesions.
acute lymphoblastic leukaemia, Ph-like, genomics
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