Elucidating the role of CHD4 as a chromatin and epigenetic modifier in acute myeloid leukaemia

Abstract

Acute Myeloid Leukaemia (AML) are an array of blood cell disorders arising from alterations within myeloid precursors. The NuRD complex controls nucleosome assembly and chromatin accessibility; CHD4 is a core subunit involved in a multitude of functions including epigenetic regulation, DNA replication and repair and cell cycle progression. However, little is known about the molecular function of CHD4-NuRD in AML. Publicly available TCGA AML transcriptomic data was analysed (N=161), which showed that patients (N=82) who express below median CHD4 levels have a poorer prognostic outcome (P=0.047). We then explored the function of CHD4-NuRD in AML using two CHD4 knockout (CHD4-/-) isogenic cell line models created using CRISPR/Cas9 to assess the mechanism of function of CHD4 within AML progression and evaluate if there is targetable therapeutic potential. Phenotype analysis of CHD4-/- models showed DNA damage marker 53BP1 increases significantly, highlighting the increased DNA damage response which was accompanied by reduced cellular proliferation in CHD4-/- cells. Cell cycle analysis showed a decrease in cells entering the S and G2/M phases alongside an increase in cells in G1 phase suggesting a potential cell cycle checkpoint deficiency causing stunted proliferation. We measured the response of CHD4-/- cells in response to chemotherapy drugs commonly used in AML. A drug screen (160 DNA damaging compounds) showed an increased sensitivity of CHD4-/- cells to compounds targeting DNA/RNA synthesis and the topoisomerase pathways, indicating that CHD4 is furthering the damage caused by improper cell cycle leading to cell death. Our data has identified a role of CHD4 in AML progression mediated through loss of cell cycle progression control and an elevated DNA damage response. Therefore, targeting cells with lower CHD4 expression with compounds affecting cellular differentiation/ proliferation may have an impact on patient outcome.

Thesis is embargoed until 31 July 2027.

Date of Award	Jul 2023
Original language	English
Awarding Institution	Queen's University Belfast
Sponsors	Leukaemia & Lymphoma NI
Supervisor	Ken Mills (Supervisor), Adone Tielenius Kruythoff-Mohd Sarip (Supervisor) & Yaser Atlasi (Supervisor)