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Supervisors names
Laura Donovan
Background: One of the most significant unmet clinical challenges in paediatric oncology is the development of therapeutic strategies for recurrent medulloblastoma (R-MB). Following upfront conventional treatments, MB disease relapse occurs in 30% of cases and is near universally fatal, accounting for 10% of all childhood cancer deaths. Routine biopsies of R-MBs have only begun in the last 5-years, as surgery at time of recurrence is associated with significant morbidity; consequently, biological material for interrogation has historically been very rare. Paediatric oncology therapies have commonly been designed using treatment-naïve biopsies but tested in phase I/II trials on children with recurrent disease(1); unsurprisingly, no successful therapies exist for the treatment of R-MB.
Until recently, assumptions were made that R-MB is identical to the primary tumour and response to therapy will be the same; however, recent evidence suggests that >40% added genetic defects emerge at relapse, with mutations in epigenetic regulators accounting for the majority of genetic pertubations(2,3). Epigenetic modifications alter DNA accessibility and chromatin structure, thereby regulating patterns of gene expression, without altering the genome sequence itself. This interchangeable nature represents a therapeutically relevant target for primary and R-MB.
The lead supervisor demonstrated immune priming with epigenetic agents plus immunotherapy as powerful cerebellar tumour therapeutics(4). We propose to build upon this using epigenetic CRISPR libraries to identify therapeutic vulnerabilities in primary and R-MB models, for validation in immune-competent mouse models for rapid clinical translation.
Aims/Objectives/timeframe: We hypothesise that functional genomic screens utilizing CRISPR-Cas9 in clinically relevant models of recurrent MB can identify genes regulated by epigenetic driver mutations, leading to the definition of targetable therapeutic vulnerabilities.
- Aim-1: To conduct loss-of-function epigenetic CRISPR-Cas9 screens in primary versus radiotherapy-induced R-MB. (Year 1)
- Aim-2: To Identify of candidate epigenetic driver mutations depleted in medulloblastoma recurrence for development of a refined epigenetic loss-of-function CRISPR screen. (Year 1-2)
- Aim-3: Validation of candidate driver mutations depleted in the tumour recurrence. (Year 3)
Methods: We will employ 3-independent patient-derived xenograft MB models, and a MYC-driven immune-competent MB model, each proven to faithfully replicate human primary, metastatic, and radiotherapy-induced recurrent disease in vivo, establishing their clinical relevance. Utilizing two epigenetic CRISPR libraries, a mouse library (948 genes, 4-gRNAs/gene, totalling 3794-gRNAs) and a human library (2508 genes, 5/6-gRNAs/gene, totalling 20,051-gRNAs). These libraries specifically target essential epigenetic driver genes that hold therapeutic potential and have been fully optimized for in vitro applications.
We expect to develop a target list of filtered gene targets depleted in the tumour recurrence, for development into a refined a loss-of-function CRISPR library with single-cell transcriptome resolution(5), for downstream in vivo analysis in clinically relevant immune-competent mouse models of R-MB.
The feasibility and robustness of the project are supported by preliminary data. All aims/objectives/techniques fall within the expertise of the supervisory team and collaborators.
References
1. Morrissy, A.S. et al. Nature 529, 351–357(2016).
2. Jones, D.T.W. et al. Nature 488, 100-5(2012).
3. Pugh, T.J. et al. Nature 488, 106-110(2012).
4. Donovan, L.K. et al. Nature Medicine 26, 720-731(2020).
5. Donovan, L.K. et al. Nature 572, 67-73(2019).
Contact
Laura Donovan