Dissecting the role of pathologically co-opted HIF-1 within aberrant RNA-splicing driving malignant haematopoiesis

Blood cancer is currently the third leading cause of cancer deaths in the UK. Myeloproliferative neoplasms (MPNs) are a group of incurable blood cancers with transformation into acute myeloid leukaemia underscoring high mortality rates: median survival for these patients is a mere 2.5 months. Current treatments for MPNs alleviate disease symptoms, however they fail to eradicate the root cause of these cancers: mutant haematopoietic stem cells (HSCs). A DNA mutation in the Janus Kinase 2 gene (JAK2V617F) in HSCs is found in over half of patients with MPNs. Our laboratory has recently discovered that this mutation alters gene expression via reprogramming of the transcription factor HIF-1 and the hypoxic response, an essential cellular mechanism that regulates oxygen levels within cells. Our early data also indicate that HIF-1 reprogramming changes how RNA, the key cellular messenger, is processed, substantially altering gene expression. This project will reveal how pathologically activated HIF-1 interacts with RNA and RNA-binding proteins to alter RNA-processing/splicing and gene expression in JAK2VF HSCs. We will apply single-input multi-output chromatin-interactome methodologies developed in our laboratory specifically for HSCs to identify the DNA, RNA and protein interactors of HIF-1, identifying therapeutic vulnerabilities that can be exploited to specifically target JAK2V617F mutant HSCs. We will evaluate these new targets in clinically relevant patient derived xenograft models, using verified lentiviral shRNA-vectors for human samples, thereby providing early validation of the translational capacity of target candidates. Our laboratory has recently developed the COVID19-vaccine biotechnology for application to HSCs, enabling functional delivery of RNA via lipid nanoparticles (LNPs) to alter gene expression. This project will leverage this technology to target the therapeutic vulnerabilities we identify, developing RNA cell therapies that can specifically target and undermine mutant JAK2VF HSCs, whilst leaving normal HSCs unaffected. Together, this project will deliver deep mechanistic insight into the dynamic co-option of the hypoxic cellular machinery to induce aberrant splicing in MPNs, applying state-of-the-art chromatin interactome technologies, and unlocking new avenues for targeted cell-therapies that exploit malignant reprogramming of HIF-1.