Abstract IA006: Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis

Abstract

Abstract Interactions between transcription factors (TF) and chromatin factors (CF) regulate gene expression programmes to determine cellular fate. However, unlike for TF, the exact role of CF in this process is poorly understood. Using haematopoiesis as a model system, we address this fundamental question in lineage choice of normal haematopoiesis and the maintenance of acute myeloid leukaemia (AML). To do this, we have functionally characterized the requirement ex vivo of 550 CFs in normal lineage differentiation and further dissected, with single-cell resolution, the roles of 40 CFs during in vivo lineage commitment (using Perturb-seq). Further, utilizing epigenetic profiling (ATAC-seq and ChIP-seq) we have probed TF-CF interactions that have lineage regulatory potential. Finally, we compare the functions of key CFs and their TF-associations between normal and malignant haematopoiesis. These studies demonstrate, both ex vivo and in vivo, that similar complexes, including three MLL-H3K4 COMPASS methyltransferases (KMTs) and non-canonical (nc-BAF) and canonical BAF (c-BAF) complexes, regulate disparate lineage decisions across haematopoiesis. However, somewhat paradoxically, we demonstrate that unrelated Repressive complexes function similarly, but non-redundantly, to restrain excessive myeloid differentiation and protect lineage diversity. We identify interactions between CF and TF that explain the regulatory function of CF and demonstrate that KO of the nc-BAF member Brd9 leads to a premalignant accumulation of myeloid progenitors, related to impaired recruitment of late myeloid TFs. Finally, utilizing similar experiments in a relevant murine AML model, we identify perturbations of MLL-, BAF- and Repressive CF that trigger partial differentiation and loss of leukaemia potential. Our data also highlight opposing functions for the same CF in normal and malignant haematopoiesis. CFs such as COMPASS members and cBAF remodelers are critical for the balanced differentiation of specific normal haematopoietic lineages, however the same CF are critical for the maintenance of leukaemia fitness, where they act predominantly to maintain differentiation blockade. Finally, we demonstrate that this altered effect occurs through the differential utilization of TF by CF complexes between normal and malignant haematopoiesis, such as corrupted Stat5a-CF interactions, potentially identifying specific CF-TF complexes as therapeutic targets in AML. Taken all together, our work greatly elucidates the role of CF and their TF partners across normal and malignant haematopoiesis. Citation Format: Brian Huntly. Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA006.