A Multi-Omic and Functional Genomic Approach to Investigate the Mechanism of Action of Epigenetic Drugs in Myeloid Malignancies

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Self-renewal is a critical and essential property that allows stem cells to regenerate and maintain the homeostasis of functionally diverse cell populations. Its deregulation frequently results in various pathological conditions ranging from pre-mature aging to cancer (Soteriou and Fuchs, 2018). Loss of self-renewal in haematopoietic stem cell (HSC) directly links to a number of haematopoietic degenerative disorders including bone marrow failure, whereas its aberrant activation is a defining and indispensable feature of leukaemia stem cells (LSCs) that sustain the disease (Deininger et al., 2017). Myeloid malignancies including Acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) characterized by the uncontrolled growth of abnormal myeloid cells that build up in the bone marrow and interfere with normal blood cell functions, is the paradigm for LSC hypothesis (Kreso and Dick, 2014), in which a small fraction of leukaemia cells (i.e., LSCs) at the apex of the cancer differentiation hierarchy drive and sustain the disease (Zeisig et al., 2012). Cancer cell heterogeneity is a major cause for disease relapse and treatment failure. In spite of the effort in characterizing these cells over the past decades, their rarity has significantly limited the progress for their isolation and characterization. Recent advance in high throughout DNA sequencing technology and functional genomics have identified epigenetic deregulation as a common driver for both AML and MDS. Therefore a number of epigenetic inhibitors have been recently used in pre-clinical or even clinical settings for these diseases. One of the intriguing AML subtypes involve mutations affecting master epigenetic regulator Mixed Lineage Leukemia (MLL) on 11q23, which accounts for around 5-10% of AML cases (Zeisig et al., 2012). MLL, a histone H3K4 methyltransferase, can fuse to more than 80 different translocation partners, resulting in replacement of its H3K4 methyltransferase activity with different epigenetic activities almost invariably associated with transcriptional activation (Zeisig and So, 2016) and poor prognosis in patients (Zeisig et al., 2012), highlighting the important roles of transcriptional and epigenetic deregulation in AML (Cheung and So, 2011). Sharing the same challenging, the underlying mechanisms that mediate cellular and molecular heterogeneity of HSCs/LSCs remain largely unknown, which adversely impacts on our ability to monitor and design better therapeutics. The recent advance in single cell multiomics has provided an unprecedented opportunity to characterize the important cellular and molecular features of these cells. Intriguingly, we have recently demonstrated that stem cell heterogeneity and functions in AML can also be transcriptionally/epigenetically governed by their cells-of-origin (Zeisig et al., 2021). Therefore the PhD project aims to identify and further characterize the key molecular features/pathways that regulate stem cell functions and fate decision. The end-product of this endeavour not only will establish the molecular principles, but also facilitate the design of specific therapeutics in modulating self-renewal activities in normal and malignant stem cells, which can be potentially translated into patient benefits. The primary aim of the investigation is to characterise the cellular and molecular features of HSCs and LSCs, which are key to understand their functions in mediating normal and malignant haematopoiesis.