2020 PhD projects and supervisory teams Doctoral Fellowships for Clinicians Influenza infection and the autophagy machinery. Supervisory team: Rupert Beale (primary supervisor, Crick) and Wendy Barclay (Imperial College London) Identification and validation of novel therapeutic targets for pancreatic cancer using human PDAC organoids. Supervisory team: Axel Behrens (primary supervisor, Crick) and Debashis Sarker (King’s College London) Resistance to infection and Parkinson’s disease: an exploration of LRRK2, PD risk alleles and macrophage function. Supervisory team: Maximiliano Gutierrez (primary supervisor, Crick) and Huw Morris (UCL) The molecular mechanism underlying Loeys-Dietz syndrome. Supervisory team: Caroline Hill (primary supervisor, Crick), David Abraham (UCL) and Nitha Naqvi (Royal Brompton Hospital) Molecular mechanisms for astrocyte misfunction in ALS. Supervisory team: Nicholas Luscombe (primary supervisor, Crick), Rickie Patani (Crick/UCL) and Jernej Ule (Crick/UCL) Linking neutrophils changes with tumour malignancy: investigating the potential of neutrophil-driven immunotherapy. Supervisory team: Ilaria Malanchi (primary supervisor, Crick), Victoria Sanz Moreno (Barts Cancer Institute/QMUL) and David Propper (Barts Cancer Institute/QMUL) Understanding intra-tumour heterogeneity in the response of ovarian cancer to PARP inhibitors. Supervisory team: Erik Sahai (primary supervisor, Crick) and Iain McNeish (Imperial College London) Profiling the evolutionary history of rare atypical cancer cells. Supervisory team: Peter Van Loo (primary supervisor, Crick) and Nischalan Pillay (UCL) Oncolytic Vaccinia virus therapy of ovarian cancer: finding novel targets for combination therapies. Supervisory team: Michael Way (primary supervisor, Crick) and Iain McNeish (Imperial College London) 2020 Doctoral fellowships for clinicians Influenza infection and the autophagy machinery A PhD project for the 2020 doctoral clinical fellows programme with Rupert Beale (primary supervisor, Crick) and Wendy Barclay (Imperial College London) We have discovered that influenza infection triggers an intracellular pathway that is related to autophagy but has a distinct molecular basis. Influenza M2 proton channel activity triggers a collapse in proton gradients, and hence intracellular pH gradients, within the cell. This causes lipidation of the key autophagy protein LC3, but this requires a domain of ATG16L1 (linked by GWAS studies to Crohn’s disease) that is dispensable for autophagy. Provocatively, M2 also encodes a highly conserved LIR motif which binds directly to LC3. M2 proton channel activity also causes inflammasome activation. There is at present no clear idea of how these mechanisms relate to one another or their biological purpose either for the host or the pathogen. This project aims to define the biological purpose of the influenza/autophagy machinery interaction – from the point of view of both host and pathogen. As well as generating M2 mutant influenza viruses and infecting model organisms, the student will explore the biological effects of mutations in genes previously defined in the lab to be important for this interaction. We anticipate there will be important effects on both innate and adaptive immune functions. This project would suit applicants from any medical or surgical speciality with an interest in infection and immunity. The partner institution for this project is Imperial College London. References: 1. Singanayagam A, Zambon M, Barclay W. Influenza virus with increased pH of HA activation has improved replication in cell culture but at the cost of infectivity in human airway epithelium., J Virol 2019 2. Fletcher K*, Ulferts R*, Jaquin E, Veith T, Gammoh N, Aresteh JM, Mayer U, Carding SR, Wileman T, Beale R†, Florey O†. The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes. EMBO J, 2018 3. Long JS, Giotis ES, Moncorge O, Frise R, Mistry B, James J, Morisson M, Iqbal M, Vignal A, Skinner MA, Barclay WS, Species difference in ANP32A underlies influenza A virus polymerase host restriction, Nature, 2016 4. Beale R*, Wise H*, Stuart A, Ravenhill BJ, Digard P, Randow F. A LC3-Interacting Motif in the Influenza A Virus M2 Protein Is Required to Subvert Autophagy and Maintain Virion Stability. Cell Host and Microbe 2014 2020 Doctoral fellowships for clinicians Identification and validation of novel therapeutic targets for pancreatic cancer using human PDAC organoids A PhD project for the 2020 doctoral clinical fellows programme with Axel Behrens (primary supervisor, Crick) and Debashis Sarker (King’s College London) Pancreatic ductal adenocarcinoma (PDAC) is one of the most challenging cancers to treat, with unchanged 5 year overall survival of <5% for the last 30 years. Identifying new and targetable pathways in human tumours is an important goal in order to develop more effective therapies. We have made fundamental contributions to the understanding of PDAC biology using mouse models [1-3]. Rspondin-based 3D tumour organoids derived from patient biopsies closely recapitulate several properties of the original tumour [4]. To extend our work towards patient benefit, in close collaboration with King's College Hospital, we have established a human PDAC (hPDAC) tumour organoid biobank. We have established a workflow that allows the isolation of PDAC organoids and wild-type organoids from the same patient (Figure 1 ). Figure 1 : Workflow to isolate human wild-type ductal and PDAC organoids. To date, we have established more than 20 matched normal ductal cells and PDAC cell pairs from PDAC patients, a number that is constantly increasing. The human PDAC organoid lines are routinely characterised by subcutaneous and orthotopic transplantation into immunodeficient mice. Exome sequencing and RNAseq is performed on both cell types isolated from PDAC patients. While all hPDAC patients enrolled in our biobank carried a mutation in the KRAS gene, the additional mutational landscape is diverse. Thus, we have established a human PDAC biobank that captures some of the genetic diversity of human PDAC. Here, we propose to use human pancreatic tumour organoids to develop and assess the efficacy of novel therapies. We have performed genetic and pharmacological screens and identified specific PDAC vulnerabilities. In one experimental approach, we investigated the role of deubiquitinases (DUBs) in PDAC. DUBs counteract the activity of E3 ubiquitin ligases. It has become clear that DUBs are druggable and several companies have DUB inhibitors in their portfolio. Since different DUBs are involved in multiple cancer-related signalling pathways [5], we hypothesized that specific DUBs may be involved in PDAC. As a first step to identify DUBs required for PDAC growth and maintenance, we used a custom-made lentiviral DUB shRNA library and compared the effect of DUB depletion in human wild-type ductal organoids with human PDAC organoids. Depletion of several DUBs, strongly inhibited the growth of PDAC organoids without having a measurable effect on wild-type pancreatic ductal cells. In this project, we want to further analyse the most interesting DUBs required for human PDAC growth, to validate them as potential therapeutic targets. Several complementary approaches, including biochemical characterisation, CRISPR/Cas-mediated genetic gene engineering of human PDAC organoids, usage of 2020 Doctoral fellowships for clinicians specific DUB inhibitors (where available) and transplantation studies will be used to elucidate DUB function in PDAC. The partner institution for this project is King’s College London. References: 1. Ferreira, R. M. M., Sancho, R., Messal, H. A., Nye, E., Spencer-Dene, B., Stone, R. K., . Behrens, A. (2017) Duct- and Acinar-Derived Pancreatic Ductal Adenocarcinomas Show Distinct Tumor Progression and Marker Expression. Cell Rep 21: 966-978. PubMed abstract 2. Messal, H. A., Alt, S., Ferreira, R. M. M., Gribben, C., Wang, V. M., Cotoi, C. G., . Behrens, A. (2019) Tissue curvature and apicobasal mechanical tension imbalance instruct cancer morphogenesis. Nature 566: 126-130. PubMed abstract 3. Gruber, R., Panayiotou, R., Nye, E., Spencer-Dene, B., Stamp, G. and Behrens, A. (2016) YAP1 and TAZ Control Pancreatic Cancer Initiation in Mice by Direct Upregulation of JAK-STAT3 Signaling. Gastroenterology 151: 526-539. PubMed abstract 4. Boj, S. F., Hwang, C. I., Baker, L. A., Chio, II, Engle, D. D., Corbo, V., . Tuveson, D. A. (2015) Organoid models of human and mouse ductal pancreatic cancer. Cell 160: 324-338. PubMed abstract 5. Ge, Z., Leighton, J. S., Wang, Y., Peng, X., Chen, Z., Chen, H., . Liang, H. (2018) Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep 23: 213-226 e213. PubMed abstract 2020 Doctoral fellowships for clinicians Resistance to infection and Parkinson’s disease: an exploration of LRRK2, PD risk alleles and macrophage function A PhD project for the 2020 doctoral clinical fellows programme with Maximiliano Gutierrez (primary supervisor, Crick) and Huw Morris (UCL) LRRK2 is the most important Mendelian gene causing Parkinson’s disease (PD) and the G2019S mutation is particularly common in Ashkenazi Jewish and North African populations, with the G2385R mutation common in Asian populations [1]. The LRRK2 gene has also been implicated in the risk of developing mycobacterial infections and inflammatory bowel disease, raising the possibility that PD risk alleles may be protective in early life and in populations with high risk of