Graduate Studentships

Projects on the tissue macrophage in SARS-CoV-2 and Neuroinflammation using human pluripotent stem cell and aptamer technologies

1. Role of alveolar macrophages in Covid19 pathology

This project is offered as part of our department’s Graduate Studentship competition, and builds on the development by Dr Sally Cowley in our lab of a hiPSC-derived model of the alveolar epithelium, including both type 2 pneumocytes and alveolar macrophages. The aim is to sue this genetically tractable and pathophysiologically relevant tissue-in-a-dish to study the severe tissue inflammation in the lungs, and the role of macrophages, viral products and therapeutic agents in modulating it. Further details, including background reading, can be seen here.

2. Anti-S SOMAmers as functional probes and potential therapeutic agents for Covid19

This is an MRC Enterprise (iCASE) studentship, offered through the Oxford  MRC Doctoral Training Partnership competition in collaboration  SomaLogic, Inc, Boulder, CO,.USA. This builds on work we have recently done with with Dr Nebojsa Janjic, Chief Scientist at SomaLogic, who would be a co-supervisor, to isolate high-affinity nucleic acid ligands to the spike glycoprotein of SARS-CoV-2 and related viruses. You would be expected to spend at least 3 months of your studentship in Colorado at SomLogic’s headquarters.

Further details of the project, and how to apply are to be found here, and here.

3. SOMAmer technology to diagnose coronavirus infection: veterinary and zoonotic implications

This is  a BBSRC iCASE studentship, offered through the Oxford Interdisciplinary Bioscience DTP . The Principal supervisor is Dr Erica Bickerton of the Pirbright Institute, who is an expert on coronavirus pathogens of veterinary species. it is co-supervised by Atherton Mutombwera, founder of Hutano Diagnostics, and William James. Further details are available at FindaPhD.

4. Immunopathogenesis of Covid19 in the lung

This is a project related to #1, above, offered through the CSC-CAMS/PUMC Oxford High-level Innovative Talent Scholarships scheme. It is restricted to students of the “Chinese Academy of Medical Sciences & Peking Union Medical College” who are enrolled there on an MD level course.

In the great majority of cases, infection of the ACE2-rich epithelia of the upper airways by SARS-CoV-2 results in a self-limiting and mild disease that transmits epidemically by aerosol and droplets. In a small proportion of cases, and particularly in the elderly and those with metabolic and inflammatory diseases, the virus descends to the alveoli, where infection of type 2 pneumocytes and alveolar macrophages is followed by interstitial pneumonitis and mononuclear cell infiltration. Even in patients that recover from Covid19 pneumonia, sequelae involving microthrombi and inflammation at multiple extrapulmonary sites – probably in the absence of local virus replication – often result in long-term disability.

As part of the global effort to understand this pathological switch, we have established an experimentally tractable and physiologically authentic “alveolus-in-a-dish” model using human pluripotent stem-cell-derived Type2 pneumocytes and macrophages. The student will join a team of stem cell technologists and virologists with a track record in both hiPSC tissue models and SARS-CoV-2 to test key hypotheses concerning the molecular and cellular mechanism of the immunopathological “switch”. They will benefit from established collaborations between the host laboratory and the networks of immunologists and physiologists that have been established in relation both to Covid19 and neuroinflammatory disease.

By October 2021, many critical questions in the field will have been resolved, and others will have arisen, meaning that the project will need to remain flexible until shortly before it commences. Nevertheless, currently open questions provide a useful indication of the likely project:

  1. To what extent do antibodies possess the potential to case an enhancement (ADE) of viral infection and/or exacerbation of inflammatory responses to infection in the alveolus-in-a-dish? Antibodies would include non-neutralizing mAbs, neutralizing mAbs at sub-neutralizing concentration, polyclonal convalescent sera, and sera from vaccine trial participants. The effect of isotype, FcR-binding, complement activation, etc will be examined.
  2. To what extent do non-infectious RNP complexes derived from vRNA fragments and host proteins (“toxic flotsam™”) found in patient tissues provoke inflammatory responses in the model?
  3. To what extent can primary Th cells from convalescent subjects respond to virus-infected, of virus- antigen-pulsed can MHC Class II-matched alveolar macrophages? What potentially pathological reactions do such responses provoke in pneumocytes?
  4. To what extent do widely available drugs, such as Beclometasone, Budesonide, and so on, ameliorate the potentially pathological responses identified above?

Training opportunities

The student will:

  1. receive a comprehensive training in human pluripotent stem cell technology, including propagation, quality control, differentiation (macrophage, neuron, pneumocyte) and use (2Dand 3D models) in the James & Lillian Martin Centre for Stem Cell Research, directed by the supervisor;
  2. be trained in safe and effective working methods for both hazard group 2 viruses (such as lentivirus vectors and ZIKV) and hazard group 3 SARS-CoV-2 in the core virus facility directed by the supervisor. They would learn how to propagate, titrate and sequence virus, and how to evaluate the potency of antiviral agents;
  3. be trained in high content confocal image analysis (OperaPhenix), flow cytometry (including ImageStream), ELISA, ELIspot and other relevant immunoassays
  4. learn standard, research-level methodologies in molecular and cell biology
  5. receive advanced training in data analysis, including bioinformatics and digital image analysis
  6. be trained in strict adherence to data integrity practice.