Enhancer RNAs Modulate Three-dimensional Enhancer Function and Regulate Leukemia-specific Gene Expression in Acute Myeloid Leukemia

• Applicant: Dr. Haiyang Yun
• Subject Area: Hematology, Oncology ; General Genetics and Functional Genome Biology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 506619416

Acute myeloid leukemia (AML) is the most common acute leukemias in adults and it has a very dismal treatment outcome, with only less than 30% patients being curable. AML is not considered as a single disease entity, due to its heterogeneity in clinical features and disease progression driven by various genetic aberrations among patients. Investigation into the underling molecular mechanisms is in high demand, in order to identify novel targets as predictive biomarker and for therapeutics. In a recent study, we demonstrated the dynamic remodelling of chromatin landscape at three-dimensional (3D) level upon leukemia induction. This involves significant modifications and structure changes at enhancers, which are DNA elements with cis-regulatory potential on target gene transcription. Along with other preliminary work, we detected transcriptional activity and enhancer RNA (eRNAs) transcripts at leukemia-specific enhancers. Therefore, we hypothesize that dysregulated eRNAs may modulate chromatin and re-organize enhancer 3D structure in AML. And we speculate that leukemia-specific eRNAs and their origin enhancers are essential to maintain leukemia propagation, and might be suitable therapy targets and of prognostic impact. We thereby prepare this project proposal, aiming to identify eRNAs that are aberrantly expressed in leukemia and to characterize their functional importance in the maintenance of AML. Furthermore, we aim to gain further insight into the molecular mechanisms underscoring the contribution of eRNAs to leukemogenesis through modulating enhancer states at 3D genome level. To this end, using combined genomic approaches including ChIP-seq, ATAC-seq und Bru-Seq, we will first profile transcriptionally active enhancers and expression of eRNAs at these enhancers which are specific in mouse leukemia. By performing CRISPR inactivation (CRISPRi) screen on enhancers, we will then identify leukmemia-specific enhancers and eRNAs that maintain leukemia cell growth. This will be followed by further in-depth characterization of enhancers and the respective eRNAs using loss-of-function assays. We will study how eRNAs modulate enhancer priming, activation, and 3D remodeling to control leukemia-specific gene expression programme. Subsequently, we will cross-validate the mouse candidate enhancers and eRNAs in relevant human AML cells. We will verify the functional importance of candidate human enhancers homologous to their mouse counterparts and the respective eRNAs in human primary AML cells in vitro and in xenograft mouse models. To further translate these finding, we will evaluate the clinical relevance of candidate enhancer activity or eRNA expression levels in AML patients. In all, the proposed work will lead a better understanding of the role of eRNAs in the pathogenesis of AML and will help us to identify specific eRNAs as prognostic markers and potential therapeutic targets in human AML.

• DFG Programme: Research Grants