Modelling and functional characterisation of tumour heterogeneity in human AML arisen from different cells-of-origin with single cell multi-omics approaches

Primary Supervisor: Prof Eric So, School of Cancer and Pharmaceutical Sciences, King’s College London

Secondary Supervisor: Prof Adrian Thrasher, Infection, Immunity, Inflammation Programme, University College London

Acute myeloid leukaemia (AML) together with acute lymphoid leukaemia (ALL) account for about 1/3 of all paediatric cancers. In contrast to childhood ALL which has a relatively favourable prognosis, AML has a much poorer projection and is one of the deadliest cancers. AML maintained by a small fraction of cancer stem cells is frequently initiated and driven by mutations affecting transcriptional and epigenetic machinery[1]. While hematopoietic stem cells (HSCs) have been traditionally viewed as the origins of human leukaemia, we and others have previously shown that mutated transcription factors can also confer self-renewal properties to otherwise short-lived myeloid progenitors to initiate AML in mouse models[2]. Importantly, these genetically and immunophenotypically identical AML exhibit different biology and responses to treatments, revealing an additional level of tumour heterogeneity originating from their cells-of-origin[3]. In this PhD project, we seek to provide new insights into this issue by using adeno-associated viral (AAVs) vectors in combination with CRISPRCAS9 genome editing approach to recreate some of the most commonly AML mutations in human HSCs and early progenitors. Establishing these models will enable us to prospectively identify the potential origins of the AML stem cells and characterize the transcriptional and epigenetic landscapes of the transformed cells leading to the observed cellular heterogeneity. In addition to single cell RNAseq and FACS/CyTOF for assessment of molecular and cellular heterogeneity of the resultant cancer, we will also simultaneously determine mRNA and protein expression in single cells using BD Rhapsody, a nanowell-based cartridge technology, which will allow us for the first time to study and integrate the transcriptomic and proteomic data at a truly single cell level to comprehensively characterize AML heterogeneity. The endeavour will lead to discovery of novel molecular markers and methods in monitoring and targeting rare population of leukaemic stem cells.

This cross-disciplinary project will take the full advantage of the expertise and support of complementing research groups within the newly formed CRUK City of London Centre. The team includes Prof. So’s group at KCL who pioneered modelling human AML and characterizing their aberrant epigenetic networks[1-3]; Prof. Thrasher’s group at UCL who has a long standing interest and track record in applying genome editing technologies in human haematopoietic stem and progenitor cells[4]; Dr Liswoski’s group at Children Medical Research Institute (CMRI) Sydney/UCL who specializes in developing novel AAV vectors for effective gene transfer and genome editing in HSCs[5]; and Prof. Ciccarelli’s group at the Crick/KCL who is an expert in cancer genomics and bioinformatics. The student is expected to be exposed and receive training in all these areas during the PhD. In addition, the student may also have an opportunity to receive training on novel vector development at the CMRI.

The candidate should have a minimum upper second class BSc, but preferably a MSc in Biomedical/Biological Sciences; Biochemistry; or related subjects. Prior work experiences in a research lab or industry will be considered favourably.

Potential research placements

1. Leukaemia and Stem Cell Biology in KCL led by Prof. So will provide training on cancer biology, epigenetics, and single cell multiomics.

2. Molecular and Cellular Immunology in UCL led by Prof. Thrasher will provide training on gene transfer/genome editing technology in HSPCs and molecular immunology.

3. Caner Bioinformatics in the Crick led by Prof. Ciccarelli will provide bio-informatic and computational training on cancer genetics and epigenetics in particularly on big data analysis.

The funding for this studentship covers students with home tuition fee status only. For more information on home tuition fee status please visit the UKCISA website. Please note that we will only be able to offer studentships to candidates that have home tuition fee status or provide evidence that they can fund the international portion of the tuition fee from external sources (i.e. not self-funded).

References

1. Zeisig, B.B., et al., SnapShot: Acute myeloid leukemia. Cancer Cell, 22(5): p. 698-698 e1. doi: 10.1016/j.ccr.2012.10.017. (2012)

2. So, C.W., et al., MLL-GAS7 transforms multipotent hematopoietic progenitors and induces mixed lineage leukemias in mice. Cancer Cell, 3(2): p. 161-71. doi: 10.1016/s1535-6108(03)00019-9. (2003)

3. Siriboonpiputtana, T., et al., Transcriptional memory of cells of origin overrides beta-catenin requirement of MLL cancer stem cells. EMBO J, 2017. 36(21): p. 3139-3155.

4. Booth, C., H.B. Gaspar, and A.J. Thrasher, Treating Immunodeficiency through HSC Gene Therapy. Trends Mol Med, 22(4): p. 317-327. doi: 10.15252/embj.201797994.(2016)

5. Lisowski, L., S.S. Tay, and I.E. Alexander, Adeno-associated virus serotypes for gene therapeutics. Curr Opin Pharmacol. 24: p. 59-67. doi: 10.1016/j.coph.2015.07.006. (2015)

For any informal enquiries on the project please contact Prof Eric So: eric.so@kcl.ac.uk

For any enquiries on the CRUK CoL Centre programme please contact Annabelle Scott: annabelle.scott@ucl.ac.uk