Defining B cell gene signatures associated with higher affinity antibodies

Background

Vaccination is one of the most impactful public health interventions to date beyond the provison of clean water, highlighted by the recent success of Covid19 vaccines. However, some highly variable pathogens continue to pose a major challenge for vaccinologists. In part this is because there remain many unanswered fundamental questions about how antibodies are generated and how this process can be manipulated for improved vaccination outcomes and the development of therapeutic antibodies.  It is well-established that antibodies are produced when B cells encounter their cognate antigen and become activated. Following this, the B cell can progresses through distinct differentiation states (plasmablast, memory B cell, plasma cell) and produce antibody into the blood to protect from infection. Immunological dogma suggests these changes in cellular phenotype are linked to the affinity of the B cell receptor for antigen but the precise mechanisms and decision points remain unclear. Successful vaccination outcomes against antigenically variable pathogens rely on both high levels of affinity maturation and appropriate anatomical locations of B cells and antibodies. Thus, it is crucial to investigate the control mechanisms of the vaccination responses which determine how B cell fate and homing link to the quality of the antibodies produced. This project will address this challenge specifically by addressing the three questions above to test the following Hypothesis: The phenotype of antigen-specific B cells is distinct at a transcriptomic level and varies with the degree of affinity maturation.

This project will address this hypothesis using well-established wet lab techniques but require the development of bespoke scripts and computational analysis pipelines and would suit a student with prior experience or a clear aptitude for bioinformatics. Next generation sequencing technologies, particularly the 10X system enable high throughput analysis of both antibody sequence and B cell phenotype. Specifically, this project will leverage these techniques to address the following questions using a transgenic mouse model:

(1) Do greater serological responses relate to differential anatomic distribution of antigen-specific cells?

(2) Are B cell repertoires with greater affinity maturation associated with distinct antigen-specific B cell phenotypes?

(3) Do different antigens induce shared antigen-specific B cell phenotypes across B cell populations with increased affinity maturation?

Main objectives of the project: These are outlined below as milestones, while (i) and (ii) are envisioned to be complete within the first year, some of the remaining milestones will continue throughout the project from the second year onwards as an iterative process.

Year 1 (at UCL/GSK): (i) Development and verification of immunogens at UCL. (ii) Immunisations: groups of 10 mice will receive distinct complex model antigens (e.g. HIV envelope and SARS-CoV-2 spike) each group receiving multiple adjuvanted immunogen doses at GSK

Year 2 (at GSK): (iii) Serological evaluation of binding strength (SPR), breadth (ELISA) at GSK. (iv)Antigen-specific FACS to isolate immunogen-specific B cells for transcriptomic and B Cell Repertoire analysis using 10X technology and NGS at GSK

Year 3 & 4 (at UCL): (v) Repertoire analysis to evaluate affinity maturation and clonal diversity.

(vi) Transcriptomic analysis to identify phenotypic modules associated to higher affinity maturation and clonal diversity.

The PhD student will work at both UCL and GSK. The McCoy lab is based in the UCL Institute of Immunity and Transplantation (IIT) within the UCL Division of Infection and Immunity is based in the Pears Building at the Royal Free Hospital site https://www.ucl.ac.uk/immunity-transplantation/. The IIT hosts research groups with diverse interests that will provide a supportive and stimulating environment, and has a dedicated bioinformatics space. While at the GSK Stevenage site, the student will be part of the Molecular Discovery Department at GSK (BPMD) who have state of the art equipment across all parts of the mAb discovery process and a strong track record in supervision and have hosted multiple CASE students

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