Precision Medicine DTP- Investigating proteolysis-controlled metabolism in Acute Myeloid Leukaemia at University of Edinburgh

Additional supervisors: Dr Mikael Bjorklund & Dr Karen Keeshan (University of Glasgow)

Background

Acute myeloid leukaemia (AML) is heterogenous disease characterized by clonal expansion of immature myeloid cells and bone marrow failure. Recent advances in identifying drug targets and understanding the underlying biology improved prognosis, however, the majority of patients eventually relapse and are dying of the disease. 

Metabolic rewiring and cellular reprogramming are hallmarks of AML oncogenesis. The metabolic alterations are often subtype specific, with associated changes in epigenetic and regulatory factors promoting oncogenic pathways. Targeting abnormal or diseases sustaining metabolic activities in AML provides promising opportunities for personalized therapeutic intervention with enhanced therapeutic windows and robust clinical efficacy. 

Some subtypes of AML cells strictly depend on NMNAT1, a key enzyme in nuclear NAD+ biosynthesis, to survive and proliferate (1). Nuclear NAD+ levels are tightly linked to the activity of NAD+-dependent enzymes known to function in epigenetic gene regulation, such as histone deacetylases, suggesting a correlation between NMNAT1 levels and changes in the epigenetic landscape of AML. How NMNAT1 levels are controlled and altered in different AML subtypes is not understood. We recently discovered that the CTLH E3 ubiquitin ligase targets NMNAT1 for proteasomal degradation thereby modulating NAD+-dependent metabolic pathways (2). We hypothesize that by controlling CTLH E3 activity we can selectively target NAD+-metabolic vulnerability of AML subtypes. To address this, we will investigate how CTLH E3-dependent NMNAT1 levels and rewiring of NAD+ metabolism effects chromatin organization and epigenetic regulation and how these impacts on AML cell fate.

Aims

1. Investigate CTLH E3 activity in modulating vulnerability of AML subtypes. Generation of CRISPR-based genome edited AML cell lines (initially 3 different AML subtypes with NMNAT1 dependency: MOLM13, OCI-AML2, THP1) with engineered inactive or constitutive active CTLH E3 - causing increased or decreased NMNAT1 levels, respectively - and assessing their viability and proliferation. Given the dependency of NAD+ biosynthesis in AML to evade apoptosis (1), the studies will further explore predicted changes in the efficacy of AML cancer drugs, such as apoptosis inducing Bcl2 inhibitors. Leukaemia development and progression of selected vulnerable CTLH E3-defective AML subtypes will be assayed using murine xenograft models.
2. Investigate regulation of NAD+-biosynthesis by CTLH E3 in AML subtypes. To correlate CTLH E3-modulated NMNAT1 levels with nuclear NAD+ levels we will apply focused metabolomics to assess changes in NAD+ biosynthesis in parental and CTLH E3-defective AML cells. Complementary, nuclear NAD+ levels will be assayed using fluorescent NAD+ probes (SoNar probes) for quantitative cell imaging (fluorescence microscopy, flow cytometry).
3. Investigate the effect of CTLH E3 activity on chromatin/epigenetic gene regulation in AML subtypes. To investigate chromatin/epigenetic gene regulation by deregulated NMNAT1 and nuclear NAD+ levels in AML cells, we will determine genome-wide histone acetylation pattern (ChIP-Seq) correlated with matching transcriptome analyses of parental and CTLH E3 deficient AML cells. Furthermore, we will apply ATAC-Seq to assess chromatin structure by CTLH E3-dependent alterations of nuclear NAD+ levels.

Key findings will be validated in AML patient samples (Glasgow Biobank). The outcomes of this project are directly relevant to current precision medicine treatments and clinical trials in AML. We envision that drug-targeting CTLH E3-medited NAD+ metabolism will open up new therapeutic avenues in personalized AML treatments. 

Training outcomes

• Cancer metabolism
• Somatic genetics using CRISPR-Cas9 and CRISPRi editing technologies
• Biochemistry and cell biology of ubiquitin-mediated signalling to study protein homeostasis
• State-of-the-art technologies (ChIP-Seq, ATAC-Seq) to study chromatin regulation/epigenetics in cancer cells
• Quantitative skills training: in silico analysis of proteomics, metabolomics, and genomics data, state-of-the-art imaging technology and analysis of metabolites in cells

Q&A Session

If you have any questions regarding this project, you are invited to attend a Q&A session hosted by the Supervisor(s) on Tuesday 2nd December at 10am GMT via Microsoft Teams. Click here to join the meeting.

About the Programme

This MRC programme is a joint programme delivered between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection and will be awarded upon successful completion of your PhD will be awarded by your lead institution.

All applications should be made via the University of Edinburgh, irrespective of project location. For those applying to a University of Glasgow project, your application along with any supporting documents will be shared with the University of Glasgow. Please note, you must apply to a specific project as advertised on the Precision Medicine webpages and FindAPhD. Additional information on the application process is available at the link below:

https://www.ed.ac.uk/usher/precision-medicine/app-process-eligibility-criteria

For more information about Precision Medicine visit:

http://www.ed.ac.uk/usher/precision-medicine