Investigating antibody affinity maturation during B cell exhaustion in viral infection

Lead Research Organisation: University College London
Department Name: Infection


During long-term infection the human immune system continually tries to get rid of the infectious agent without success. For example, during HIV infection which is life-long. One of the ways the immune system tries to overcome HIV is by producing antibodies that block the virus from entering new cells. However, HIV then rapidly mutates within the person and becomes resistant to their antibodies. Our immune system tries to keep up, and mutates the antibodies so that they can block the new version of HIV. This mutational arms race between antibodies and virus continues over many years. In some HIV+ individuals the result is highly-mutated antibodies but these are still unable to halt the virus. This is partly because the virus can mutate faster than the antibodies, but given the antibodies catch up repeatedly during infection it's likely the virus uses other tactics counteract human antibodies as a safeguard. I hypothesise that one of these tactics is to interfere with normal behaviour of the cells, called B cells, that make antibodies so that less antibody is present in the body to act against the virus.

It is already known that during long-term infections some B cells become exhausted and can't complete the role they need to play in the body's defense. This exhaustion can be tested for in the laboratory by measuring the amount of particular proteins on the surface of individual B cells. Previously it was thought that these cells had no role in the ongoing immune response and were just casualties of the relentless infection. However, studies in malaria infection have shown that the exhausted B cells have the genetic blueprints for very highly-mutated antibodies against the parasite, suggesting they have participated in the same kind of mutational arms race between pathogen and antibodies seen in HIV infection. Therefore, I want to test whether highly-mutated antibodies that target HIV during long-term infection come from exhausted B cells. I also want to know if numbers of exhausted B cells increase at times in the mutational arms race when the virus gains the upper-hand. If this is true, then it would suggest a way to make antibodies more effective against HIV would be to re-invigorate the exhausted B cells and bring them back to a normal level of activity.

Technical Summary

The humoural immune system continuously attempts to clear chronic infections where antigen persists. An example of this is HIV infection where anti-viral antibodies continue to be produced until the immune system eventually collapses. Longitudinal sampling shows that the virus mutates to become resistant to antibody neutralisation over time. However, antibodies then develop to neutralise the mutated virus pressuring the virus to mutate again. Recent studies of the co-evolution of antibodies and virus highlight the great selection pressure the antibodies exert on the virus. Thus, it would be advantageous for the virus to employ additional mechanisms to evade humoural responses. I hypothesise that one mechanism is to drive antigen-specific B cells to an exhausted phenotype. This undermines the effectiveness of the immune response by side-tracking HIV-specific B cells away from differentiation into antibody secreting long-lived plasma cells.

Chronic infections, including HIV, result in increased frequencies of exhausted B cells (CD21low/CD27low cells). In this study, HIV-specific B cells will be separated by FACS using autologous envelope protein probes. Exhaustion markers will be quantified allowing correlation of antibody affinity for HIV with B cell exhaustion at a single cell level. In addition, transcriptional profiling of each B cell will allow greater definition of their exhaustion phenotype. This will allow evaluation of whether the exhausted subset acts as an alternative cell fate for the B cells that are most highly affinity-matured. To establish whether B cell exhaustion aids virus escape from neutralising antibodies, I will use flow cytometric analysis of longitudinal samples to link the frequency of exhausted B cells with the ability of virus to escape contemporaneous serum neutralisation. From this work I will define whether virus-induced B cell exhaustion limits the appearance of neutralising anti-HIV antibodies and thus contributes to immune evasion.

Planned Impact

The principal impact of my research will be greater understanding of how individual B cell function is linked to affinity maturation of the antibody that each B cell produces, and in turn the antibody's ability to inhibit HIV infection. This will be of great interest to scientists who study infectious diseases and also to researchers engaged in trying to develop new vaccines or to improve efficacy of existing vaccines. My work will generate large amounts of B cell transcriptomic data alongside linked functional and sequence data for multiple antibodies and also extensive datasets of HIV envelope gene sequences. These data will inform the field and also provide frameworks for the evaluation of their research.

HIV infection is known to result in B cell dysfunction but the mechanisms of how this occurs and the functional impact on the contribution of antibodies to the control of viral infection in vivo is unclear. My work will elucidate details of how this dysfunction affects the affinity of antibodies produced and whether B cell exhaustion is limiting the ability of antibodies to block virus. This work will primarily inform understanding of how HIV-specific antibody responses can be altered in a vaccine development setting or via immunotherapy in HIV+ individuals. More widely, my research will establish the groundwork for understanding the role of exhausted B cells during viral infection that can then be investigated in other chronic conditions.

During my proposed programme of work I will acquire new skills in generating and analysing transcriptomic data sets through my collaborations at UCL and further afield. These skills will enable me complete the aims of this research project and to progress in my transition to an independent research scientist. This work will open up new avenues for scientific investigations of B cells in other infectious diseases and place me in an optimal position to gain project grants and investigator level funding in the future. Furthermore, during the project I will train a post-doctoral researcher in single B cell cloning, recombinant antibody production and a wide range of virological assays. They will also benefit from interaction with collaborating groups of scientists studying different cells involved in immune dysfunction in HIV.
Description HIV infection cohort study 
Organisation Central and North West London NHS Foundation Trust
Department Mortimer Market Centre
Country United Kingdom 
Sector Public 
PI Contribution We have cloned HIV viral envelope proteins from HIV-infected individuals, characterised their entry into human cells. We have also tested plasma and monoclonal antibodies for anti-HIV activity
Collaborator Contribution Prof. Gupta has previously recruited a cohort of individuals who are HIV-infected and not receiving therapy because they spontaneously control virus. His team have processed blood and stored plasma and PBMC samples since 2011.
Impact Manuscript published in Nature, march 2019 HIV-1 remission following CCR5?32/?32 haematopoietic stem-cell transplantation Ravindra K Gupta, Sultan Abdul-jawad, Laura E McCoy, Hoi Ping Mok, Dimitra Peppa, Maria Salgado, Javier Martinez-Picado, Monique Nijhuis, Annemarie M. J. Wensing, Helen Lee, Paul Grant, Eleni Nastouli, Jonathan Lambert, Matthew Pace, Fanny Salasc, Christopher Monit, Andrew Innes, Luke Muir, Laura Waters, John Frater, Andrew M. L. Lever, S. G. Edwards, Ian H. Gabriel & Eduardo Olavarria
Start Year 2016
Description Interview with BBC World News TV 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was interviewed by the Impact program on the 5th of March 2019 about the HIV-1 remission case known as the "London Patient" as I participated in this study
Year(s) Of Engagement Activity 2019
Description Microbio Soc HIV Vaccine Video 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The Microbiology Society came to my laboratory to make a short video highlighting ongoing work to understand HIV infection. They interviewed me and my former mentor Prof. Weiss and filmed members of my team working in the laboratory. This was distributed on their website to Society member and promoted actively on social media.
Year(s) Of Engagement Activity 2018
Description Science podcast 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact I spoke to scientists at the University Glasgow CVR as part of their contagious thinking podcast series. We discussed my career path into running an academic lab as well as the work I do now. This podcast is primarily aimed at junior scientists to give insight into how careers in academia can progress and the challenges they involve.
Year(s) Of Engagement Activity 2019