Neurobiology of multisensory decision making in humans

Studentship strategic priority area:Basic and Clinical Research
Keywords:DNA replication stress, ovarian, glioblastoma, therapy, biomarker

Background
Faithful duplication of the genome is essential to cell division and requires complex regulation and assembly of nucleotides and replication factors to be completed efficiently. Disruption of these processes causes DNA replication stress (RS) manifest as slowing/stalling of replication forks and generation of DNA double strand breaks (DSBs) associated with activation of the DNA damage response (DDR). RS is a primary driver of genomic instability in cancer and an appealing therapeutic target due to aberrant tumour cell DDR and the absence of RS in normal cells. Both glioblastoma (GBM) and high grade serous tubo-ovarian carcinoma (HGSC) demonstrate genomic instability and activation of DDR, with underlying RS implicated in this phenotype. Recent advances in DDR targeted therapy include approval of PARP inhibitors in platinum sensitive relapsed HGSC, ongoing phase I/II trials of olaparib with radiotherapy and/or temozolomide in GBM, and proposed trials of combined ATR and PARP inhibition (CAiPi) in GBM and HGSC. Robust biomarkers allowing patient selection through identification of tumours exhibiting elevated RS and aberrant RS responses will be key to the clinical success of these approaches. This project will identify predictive biomarkers for RS targeted therapy in GBM and HGSC for validation in forthcoming clinical trials.

Aims
1) To characterise RS levels/responses to Pi, Ai and CAiPi in panels of HGSC and primary GBM cell lines
Ai, Pi and CAiPi responses will be correlated with levels of RS using DNA fibre assays, DDR protein immunofluorescence, existing RNA sequencing data and mechanistic insights from identification of proteins on nascent DNA (iPOND).

2) To investigate genomic determinants of response to CAiPi
Existing whole genome sequencing data of GBM cell lines will be analysed to investigate genomic and structural abnormalities associated with differential responses (Collaboration; D McArt, Belfast UK). Breaks labelling in situ and sequencing (BLISS) will investigate the influence of genomic sites of CAiPi generated DSBs on response.

3) To validate candidate biomarkers in vivo and in existing clinical datasets
Candidate biomarkers will be validated utilising intracranial xenografts from GBM cell lines exhibiting differential sensitivities to Ai, Pi and CAiPi. Prevalence of candidate IHC biomarkers will be quantified in existing clinical datasets for HGSC (SCOTROC 1, 4) and GBM (OPARATIC, PARADIGM, PARADIGM-2) and recurrent GBM datasets.

Training Outcomes
This project provides excellent exposure to basic and complex techniques including primary cell culture, immunofluorescence, Western blotting, BLISS, iPOND and in vivo models. The student will become proficient in analysing data from whole genome/RNA sequencing and develop expertise in statistical analyses necessary for pre-clinical development of biomarkers for novel therapies.

The project has strong commitment from Astra Zeneca as an industry partner who will provide invaluable experience and insight in a non-academic setting and the opportunity to work with commercially minded scientists on applied research.The studentship meets several MRC DTP strategic priorities in quantitative skills and whole organism physiology. The student will gain skills in bioinformatics analysis of genomic and transcriptomic data, basic and translational laboratory research and in vivo studies.

Conclusion
This project will identify biomarkers of response to DNA replication stress targeted therapies in HGSC and GBM by utilising genomic and transcriptomic characterization of HGSC and GBM cell line panels, with validation in in vivo tumour models and clinical trial datasets with corresponding outcome data. This will provide a precision approach for optimal utilization of DDR targeting therapies in the clinic.