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Modulating affinity maturation during in vivo immunisation


Project Description

During the 20th century, the ability to induce antibody responses via vaccination had a huge impact on livestock husbandry and human life expectancy. However, there remain many unanswered basic biological questions about how antibodies are generated and how this process can be manipulated. For example, (1) Can we increase in vivo affinity maturation of antibodies against complex antigens by co-delivery of antigen-specific antibody? (2) Can we increase diversity of the antibody response against complex antigens by modulating B cell signalling? Antibodies are produced when antigen-specific B cells undergo multiple rounds of mutation and selection for progressively improved antigen binding (affinity maturation)[1]. This process is self-limiting following immunisation and there is postulated to be an affinity “ceiling”[2] above which there is no selective advantage for additional antibody mutations. However, higher levels of antibody mutation (up to 45%) are possible and have been observed during chronic infection[3]. Therefore, this project aims to establish mechanisms to manipulate the response to produce a more diverse population of highly mutated antibodies. Specifically, by addressing the two questions above to test the following hypothesis: the antibody response to complex antigens can be improved by co-administration of antigen-specific antibodies[4] and modulation of B cell signalling[5]. This will be achieved by a combination of biochemistry/molecular biology laboratory work and the development of computational methods to analyse the data generated. Therefore, this project would ideally suit a candidate with a keen interest computational biology who wants to integrate wet-lab methods with bioinformatic approaches.

It is widely acknowledged that the constraints on antibody maturation in vivo differ depending on whether the antigen is a live pathogen, subcellular particle, a complex protein or a hapten such as NP [2]. Therefore, this project will establish whether altering the conditions above can increase the level of antibody affinity maturation and repertoire diversity induced by complex proteins, which represent the majority of targets for mAb biologic development. To achieve this, mice will be immunised with a viral antigen (the HIV envelope protein) instead of a simple model antigen. These immunisations will take place under different conditions to see what impact these conditions have on affinity maturation. Specifically, the project will investigate the effect of co-delivery of antigen-specific antibody[4] during immunisation and also the effects of molecules which alter B cell signalling[5].

The PhD project will have 3 phases. The first will be approximately 6 months at UCL preparing the reagents for the immunisation study. The second stage will take place within GSK’s Stevenage based campus for approximately 8 months. While at GSK the student will process spleen, lymph and blood samples and generate B cell receptor repertoire libraries by PCR for Next Generation Sequencing (NGS)[3] to assess changes at the population level. Please note the PhD student will not directly perform the immunisations or handle any live animals. The remainder of the project will be based at UCL and will involve a relatively minor wet lab component, namely, antigen-specific single cell cloning of antibodies via single cell fluorescence activated sorting (FACS)[6,7]. During the final phase the majority of the PhD student’s time will be devoted to the optimisation of computational methods to evaluate the BCR repertoire sequencing data and integrate this population level data with the insights gained by studying individual antibodies generated by single cell cloning.

Application Deadline

Applications must be complete, including both references, by 11th January 2019 at 5pm

Funding Notes

BBSRC CASE Studentship with GSK.
Fully funded place including home (UK) tuition fees and a tax-free stipend in the region of £16,553. Students from the EU are welcome to submit an application for funding, any offers will be subject to BBSRC approval and criteria.

References

1. Mesin L et al. Immunity. 2016 Sep 20;45(3):471-482.
2. Batista FD and Neuberger MS. Immunity. 1998 Jun;8(6):751-9.
3. Georgiou G et al. Nat Biotechnol. 2014 Feb;32(2):158-68.
4. Zhang Y et al. J Exp Med. 2013 Mar 11;210(3):457-64.
5. Keating R eta l. Nat Immunol. 2013 Dec;14(12):1266-76. doi: 10.1038/ni.2741.
6. McCoy LE and Burton DR. Immunol Rev. 2017 Jan;275(1):11-20.
7. McCoy LE et al. Cell Rep. 2016 Aug 30;16(9):2327-38.

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