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Reversal of enhancer dysregulation to combat cohesin-mutant leukemia

A postgraduate research opportunity at the University of Otago.


Academic background
Sciences, Health Sciences
Host campus
Honours, Master’s, PhD
Pathology (Dunedin)
Dr Jisha Antony, Professor Julia Horsfield


Acute myeloid leukaemia (AML) is an aggressive cancer of the bone marrow with an overall survival of ~30%. Outcomes for older patients are especially poor, with cure rates of only 10-15%. Treatment for AML has not changed substantially in more than 30 years and new therapies are urgently needed.

The cohesin complex plays key roles in the three-dimensional (3D) organisation of chromatin and is essential for cell division and gene expression. Mutations in cohesin are found in 12-15% of AMLs and promote leukaemia by blocking cell differentiation and promoting self-renewal. Cohesin brings regulatory elements, known as ‘enhancers’, to genes, to regulate their expression in response to signalling pathways. We previously found that cohesin mutations lead to dysregulated expression of the RUNX1 and ERG genes, which are crucial for haematopoiesis and are frequently altered in AML.

In exciting preliminary experiments, we found that the BRD4 inhibitor JQ1 (which blocks enhancer function) reduces the gene expression spikes in RUNX1 and ERG in cohesin-mutant cells. In chromosome capture assays, we found that the RUNX1 enhancer eR1 inappropriately contacts a RUNX1 promoter. Thus, in leukemias where 3D chromatin structure is disrupted by cohesin mutation (or potentially in other epigenetic regulators), enhancer-blocking drugs might be effective therapeutics. This project will use a CRISPR strategy to determine if dampening eR1 enhancer activity restores normal RUNX1 expression with potential to block leukaemia.

CRISPRi will be used to suppress RUNX1 enhancer eR1: We have shown that the eR1 RUNX1 enhancer is activated during megakaryocyte differentiation. CRISPRi to suppress eR1 will be delivered to parental and cohesin mutant cells using lentivirus. Enhancer activity will be stimulated by initiating megakaryocyte differentiation. Impact of CRISPRi-mediated enhancer suppression on expression of RUNX1 and ERG will be evaluated by quantitative PCR.

3C chromosome conformation capture assay will used to determine whether dampening of RUNX1 enhancer activity restores normal enhancer-promoter connections. Our chromosome capture assay shows that RUNX1 enhancer eR1 makes aberrant connections in cohesin mutant cells when stimulated to differentiate. A 3C chromosome capture assay will be used to determine whether dampening of RUNX1 enhancer activity restores normal levels of RUNX1 enhancer-promoter connections.

The results of this project would provide a rationale for using enhancer inhibition as a therapeutic strategy in leukaemias that have cohesin mutations and overexpression of RUNX1 and ERG.


Julia Horsfield