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

自我更新是干细胞再生和维持功能多样化细胞群稳态的关键和基本特性。它的放松经常导致各种病理状况，从早衰到癌症（Soteriou和Fuchs， 2018）。造血干细胞（HSC）自我更新的丧失与包括骨髓衰竭在内的许多造血退行性疾病直接相关，而其异常激活是维持疾病的白血病干细胞（LSCs）的决定性和不可或缺的特征（Deininger et al., 2017）。髓系恶性肿瘤包括急性髓系白血病（AML）和骨髓增生异常综合征（MDS），其特征是骨髓中积聚的异常髓系细胞不受控制地生长并干扰正常的血细胞功能，这是LSC假说的范例（Kreso和Dick， 2014），其中处于癌症分化层次顶端的一小部分白血病细胞（即LSCs）驱动并维持疾病（Zeisig et al., 2012）。肿瘤细胞异质性是疾病复发和治疗失败的主要原因。尽管在过去的几十年里对这些细胞进行了表征，但它们的稀缺性极大地限制了它们的分离和表征的进展。高通量DNA测序技术和功能基因组学的最新进展已经确定表观遗传失调是AML和MDS的共同驱动因素。因此，一些表观遗传抑制剂最近被用于这些疾病的临床前甚至临床设置。有趣的AML亚型之一涉及影响主表观遗传调控因子混合谱系白血病（MLL） 11q23的突变，约占AML病例的5-10% （Zeisig et al., 2012）。MLL是一种组蛋白H3K4甲基转移酶，可以融合到80多种不同的易位伴侣，导致其H3K4甲基转移酶活性被不同的表观遗传活性所取代，几乎总是与转录激活相关（Zeisig等，2016），患者预后不良（Zeisig等，2012），突出了转录和表观遗传失调在AML中的重要作用（张等，2011）。同样具有挑战性的是，介导hsc /LSCs细胞和分子异质性的潜在机制在很大程度上仍然未知，这对我们监测和设计更好的治疗方法的能力产生了不利影响。单细胞多组学的最新进展为描述这些细胞的重要细胞和分子特征提供了前所未有的机会。有趣的是，我们最近证明，AML中的干细胞异质性和功能也可以由它们的起源细胞在转录/表观遗传学上控制（Zeisig等人，2021）。因此，博士项目旨在确定和进一步表征调节干细胞功能和命运决定的关键分子特征/途径。这一努力的最终成果不仅将建立分子原理，而且还将有助于设计调节正常和恶性干细胞自我更新活动的特定治疗方法，这可能会转化为患者的利益。该研究的主要目的是表征造血干细胞和LSCs的细胞和分子特征，这是了解它们在介导正常和恶性造血中的功能的关键。

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.