Modifying the impact of Anthracyclines on Clonal Selection in Clonal Haematopoiesis

Primary supervisor: Miguel Ganuza, Queen Mary University of London

Secondary supervisor: Elspeth Payne, UCL

Project

Project description:
Clonal haematopoiesis of indeterminate potential (CHIP), defined by the presence of large blood clones harbouring leukaemia-driver mutations, rises the risk for leukaemia. Previous exposure to chemotherapy in cancer patients heavily increases the risk of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS)(1). It was assumed that this resulted from the mutagenic activity of the cancer-therapy. However, consistent with CHIP, recent insights show that leukaemia-funder clones predate chemotherapy, indicating that cancer-therapy selects clones harbouring mutations that confer chemotherapy-resistance. Anthracyclines are among the most effective cytotoxic treatments for many solid tumours and haematological malignancies. Unfortunately, following chemotherapy, 1% of patients will develop fatal therapy-related leukaemia [1]. There is tremendous interest on predicting the effect of cancer-therapies on clonal selection and on developing preventive therapies to block clonal evolution into fatal therapy-related leukaemia.

The full scope of cellular and molecular mechanisms driving clonal selection under anthracyclines remains unclear. This is largely due to the lack of appropriate animal systems that accurately recapitulate CHIP capturing the plethora of mutations found in humans.

To generate a murine preclinical inducible CHIP model encompassing mutations in ten of the most frequently mutated genes in human CH and to combine these mutations in hundreds of random combinations into the same mouse, we recently developed the Hydra mouse model. Based on a multi-lox modular allele and CRISPR/Cas9 technology, Hydra mice allow in vivo the generation of thousands of mutant CHIP blood clones harbouring random combinations of mutations in ten CHIP genes. This mouse model enables to study CHIP development under different insults and to evaluate protocols to prevent/block CHIP.

The Hydra model has been fully generated. Our data show that the system works as intended allowing to induce CHIP clones mimicking human CHIP. Based on the acquired mutations, CHIP clones will accumulate or vanish depending on cell-autonomous and environmental conditions (e.g. anthracyclines). We will monitor clonal selection, evolution and competition in Hydra mice by tracking and targeted-sequencing GFP⁺CHIP-mutant clones over time.

For the mutation combinations enriched under chemotherapy we will evaluate commercially available mutant-specific targeted therapies on blocking clonal accumulation in vivo. Moreover, we will genetically introduce these mutation combinations in vivo in zebrafish (Payne Lab). This will allow us to perform highthroughput drug screens for pharmacological therapies synthetically lethal for these mutations in haematopoietic cells [2].

Finally, we will determine the mechanisms driving clonal selection under anthracyclines in vitro by introducing the identified mutations into murine and human haematopoietic stem and progenitor cells, as we have successfully done [3,4].

Preventive therapies cannot be assessed directly in patients or easily inferred from retrospective human studies. Hence, this proposal is key and will inform novel strategies to block clonal selection and therapy-related leukaemia.

Candidate background

The ideal candidate will have a biomedical sciences degree and a strong desire to answer fundamental research questions. Previous laboratory experience (e.g. MSc) and on murine models will be advantageous. The candidate will acquire several transferrable skills and develop independent thinking. They will be expected to work flexible hours and as a part of a team.

Potential Research Placements

1. Elspeth Payne, UCL Cancer Institute
2. Kevin Rouault-Pierre, Barts Cancer Institute, Queen Mary University of London
3. Javier Herrero, UCL Cancer Institute

References

1. McNerney, M.E., Godley, L.A., and Le Beau, M.M. (2017). Therapy-related myeloid neoplasms: when genetics and environment collide. Nat Rev Cancer 17, 513-527. 10.1038/nrc.2017.60.
2. Lubin, A., Otterstrom, J., Hoade, Y., Bjedov, I., Stead, E., Whelan, M., Gestri, G., Paran, Y., Payne, E. (2021). A versatile, automated and high-throughput drug screening platform for zebrafish embryos. Biol Open 10 (9): bio058513.
3. Holmfeldt, P.*, Ganuza, M.*, Marathe, H., He, B., Hall, T., Kang, G., Moen, J., Pardieck, J., Saulsberry, A.C., Cico, A., et al. (2016). Functional screen identifies regulators of murine hematopoietic stem cell repopulation. J Exp Med 213, 433-449. 10.1084/jem.20150806. (*equal contribution).
4. Ganuza, M., Hall, T., Finkelstein, D., Wang, Y.D., Chabot, A., Kang, G., Bi, W., Wu, G., and McKinney- Freeman, S. (2019). The global clonal complexity of the murine blood system declines throughout life and after serial transplantation. Blood 133, 1927-1942. 10.1182/blood-2018-09-873059.