Identification and characterisation of Pu.1-driven gene regulatory complexes and networks in Acute Myeloid Leukaemia.

Abstract

PU.1, an ETS-family transcription factor, is a master haematopoietic regulator required for the development and differentiation of both mature lymphoid and myeloid cells. The dysregulation of key haematopoietic transcription factors, including PU.1, is a cardinal feature of acute myeloid leukaemia (AML) and PU.1 is either deleted or mutated at low frequency in AML, suggesting it as a tumour suppressor. However, we have demonstrated that loss of Pu.1 in human and murine AML cell lines leads to a lack of proliferation and maintenance of leukaemic cells, a finding corroborated by the DepMap consortium across genome-wide CRISPR screen. This suggests a fundamental role for Pu.1 in leukaemia maintenance and our study aims to provide mechanistic detail to this observation. Throughout this study, we utilise proteomic, transcriptomic, genomic and functional approaches within both mouse and human cell-lines and within the Npm1c/Flt3-ITD primary mouse model, making comparisons between leukaemia and appropriate normal control populations at every layer. Specifically, we have compared and contrasted; Multiomic data (sc + snRNAseq & snATACseq), integrative Bioinformatic analysis (SCENIC+), qPLEX-RIME mass spectrometry analysis, proximity ligation analysis (PLA) to verify leukaemia-specific/selective interactors, co-binding by CUT&RUN analysis and functional perturbation of gene regulatory complex (GRC) members. These studies provide insights into the specific molecular mechanisms of Pu.1 corruption within malignant stem and progenitor cells and allow us the ability to map potential Pu.1-specific regulatory networks associated with AML.