Investigating antibody affinity maturation during B cell exhaustion in viral infection
Lead Research Organisation:
University College London
Department Name: Infection
Abstract
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.
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.
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.
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.
Organisations
- University College London (Fellow, Lead Research Organisation)
- Francis Crick Institute (Collaboration)
- University College London Hospitals NHS Foundation Trust (Collaboration)
- Central and North West London NHS Foundation Trust (Collaboration)
- London School of Hygiene and Tropical Medicine (LSHTM) (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
Publications
Aitken J
(2020)
Scalable and robust SARS-CoV-2 testing in an academic center
in Nature Biotechnology
Alrubayyi A
(2021)
Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV.
in Nature communications
Alrubayyi A
(2023)
Natural killer cell responses during SARS-CoV-2 infection and vaccination in people living with HIV-1
in Scientific Reports
Alrubayyi A
(2021)
Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV.
in bioRxiv : the preprint server for biology
Arulkumaran N
(2021)
Sex differences in immunological responses to COVID-19: a cross-sectional analysis of a single-centre cohort.
in British journal of anaesthesia
Arulkumaran N
(2021)
Defining Potential Therapeutic Targets in Coronavirus Disease 2019: A Cross-Sectional Analysis of a Single-Center Cohort.
in Critical care explorations
Arulkumaran N
(2021)
Influence of IL-6 levels on patient survival in COVID-19.
in Journal of critical care
Burton AR
(2018)
Circulating and intrahepatic antiviral B cells are defective in hepatitis B.
in The Journal of clinical investigation
Cantoni D
(2022)
Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike.
in EMBO reports
Collier DA
(2021)
Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2.
in Nature
Collier DA
(2021)
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies.
in medRxiv : the preprint server for health sciences
Collier DA
(2021)
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
in Nature
Fox TA
(2021)
Low seropositivity and suboptimal neutralisation rates in patients fully vaccinated against COVID-19 with B-cell malignancies.
in British journal of haematology
Graham C
(2021)
Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike.
in bioRxiv : the preprint server for biology
Griffith SA
(2021)
To bnAb or Not to bnAb: Defining Broadly Neutralising Antibodies Against HIV-1.
in Frontiers in immunology
Gupta RK
(2019)
HIV-1 remission following CCR5?32/?32 haematopoietic stem-cell transplantation.
in Nature
Houlihan CF
(2020)
Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers.
in Lancet (London, England)
Jeffery-Smith A
(2022)
SARS-CoV-2-specific memory B cells can persist in the elderly who have lost detectable neutralizing antibodies.
in The Journal of clinical investigation
Kemp SA
(2021)
SARS-CoV-2 evolution during treatment of chronic infection.
in Nature
McCoy LE
(2018)
The expanding array of HIV broadly neutralizing antibodies.
in Retrovirology
Muir L
(2021)
Neutralizing Antibody Responses After SARS-CoV-2 Infection in End-Stage Kidney Disease and Protection Against Reinfection.
in Kidney international reports
Ng KW
(2020)
Preexisting and de novo humoral immunity to SARS-CoV-2 in humans.
in Science (New York, N.Y.)
O'Nions J
(2021)
SARS-CoV-2 antibody responses in patients with acute leukaemia.
in Leukemia
Rees-Spear C
(2021)
The impact of Spike mutations on SARS-CoV-2 neutralization
Rees-Spear C
(2021)
Vaccine responses in ageing and chronic viral infection.
in Oxford open immunology
Rees-Spear C
(2021)
The effect of spike mutations on SARS-CoV-2 neutralization.
in Cell reports
Rosa A
(2021)
SARS-CoV-2 recruits a haem metabolite to evade antibody immunity.
in medRxiv : the preprint server for health sciences
Rosa A
(2021)
SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.
in Science advances
Snow TAC
(2021)
Convalescent plasma for COVID-19: a meta-analysis, trial sequential analysis, and meta-regression.
in British journal of anaesthesia
Swadling L
(2022)
Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2.
in Nature
Touizer E
(2021)
Failure to seroconvert after two doses of BNT162b2 SARS-CoV-2 vaccine in a patient with uncontrolled HIV.
in The lancet. HIV
Voss JE
(2019)
Reprogramming the antigen specificity of B cells using genome-editing technologies.
in eLife
| Description | Determining the immunological basis for weakened SARS-CoV-2 vaccination outcomes |
| Amount | £425,104 (GBP) |
| Funding ID | MR/W020556/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 08/2022 |
| Description | Modulating affinity maturation during in vivo immunisation |
| Amount | £32,000 (GBP) |
| Funding ID | 2243420 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2023 |
| Description | The impact of B cell phenotypes in HIV infection on antibody responses. |
| Amount | £15,000 (GBP) |
| Funding ID | 2249900 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2023 |
| Description | UCL CV19 Rapid Response Call: Defining neutralising antibody responses to SARS-CoV-2 infection. |
| Amount | £45,868 (GBP) |
| Organisation | University College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 06/2020 |
| End | 05/2021 |
| Description | UCL Division of Infection and Immunity Postdoctoral Award to Luke Muir (post doc in my lab): Association between Ig isotype of SARS-CoV-2 serum neutralising antibodies and disease severity |
| Amount | £2,703 (GBP) |
| Organisation | University College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 12/2021 |
| 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. We have evaluated the response of HIV-infected individuals to SARS-CoV-2 infection |
| 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. Dr Peppa has recruited a cohort of individuals who are living with HIV and have been infected or exposed to SARS-CoV-2. |
| 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 https://doi.org/10.1038/s41586-019-1027-4 Manuscript published in Lancet HIV: Evidence for HIV-1 cure after CCR5?32/?32 allogeneic haemopoietic stem-cell transplantation 30 months post analytical treatment interruption: a case report. Gupta RK, Peppa D, Hill AL, Gálvez C, Salgado M, Pace M, McCoy LE, Griffith SA, Thornhill J, Alrubayyi A, Huyveneers LEP, Nastouli E, Grant P, Edwards SG, Innes AJ, Frater J, Nijhuis M, Wensing AMJ, Martinez-Picado J, Olavarria E. Lancet HIV. 2020 May;7(5):e340-e347. doi: 10.1016/S2352-3018(20)30069-2. Epub 2020 Mar 10. Preprint 2021 Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV. Alrubayyi A, Gea-Mallorquí E, Touizer E, Hameiri-Bowen D, Kopycinski J, Charlton B, Fisher-Pearson N, Muir L, Rosa A, Roustan C, Earl C, Cherepanov P, Pellegrino P, Waters L, Burns F, Kinloch S, Dong T, Dorrell L, Rowland-Jones S, McCoy LE, Peppa D. bioRxiv. 2021 Feb 16:2021.02.15.431215. doi: 10.1101/2021.02.15.431215. |
| Start Year | 2016 |
| Description | The Crick COVID19 Consortium |
| Organisation | Francis Crick Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I designed and developed the ELISA binding serology assays (published in Ng et al. Science 2020). I then worked with the pipeline team to train them in performing this assay and translate this research assay into a accredited diagnostic assay for ongoing use. |
| Collaborator Contribution | The CRICK COVID19 Consortium commenced on 19 March 2020 in response to the emerging COVID19 pandemic in a collaboration between University College London Hospitals, Health Services Laboratory (HSL), the Institute of Cancer Research and the Francis Crick Institute. The consortium has set up a high throughput RTPCR COVID19, binding serology diagnostics assays and neutralisation testing in an academic environment. |
| Impact | This collaboration involves both clinical hospital-based virologists and fundamental laboratory-based virologist/immunologists such as myself. There are two main published outputs: Ng et al. 2020 and Aitken et al. 2020. |
| Start Year | 2020 |
| Description | The Crick COVID19 Consortium |
| Organisation | University College London Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I designed and developed the ELISA binding serology assays (published in Ng et al. Science 2020). I then worked with the pipeline team to train them in performing this assay and translate this research assay into a accredited diagnostic assay for ongoing use. |
| Collaborator Contribution | The CRICK COVID19 Consortium commenced on 19 March 2020 in response to the emerging COVID19 pandemic in a collaboration between University College London Hospitals, Health Services Laboratory (HSL), the Institute of Cancer Research and the Francis Crick Institute. The consortium has set up a high throughput RTPCR COVID19, binding serology diagnostics assays and neutralisation testing in an academic environment. |
| Impact | This collaboration involves both clinical hospital-based virologists and fundamental laboratory-based virologist/immunologists such as myself. There are two main published outputs: Ng et al. 2020 and Aitken et al. 2020. |
| Start Year | 2020 |
| Description | UCLH SAFER study |
| Organisation | Francis Crick Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This study aims to monitor the infection of UCLH healthcare workers with SARS-CoV-2 via routine PCR testing and serological analysis. My laboratory established one of the serology assays and used it to determine seroprevalence in the cohort over the first 4 months of the pandemic as published (Houlihan et al. Lancet 2020) |
| Collaborator Contribution | The Safer investigators are drawn from multiple disciplines. Firstly the clinical team at UCLH who designed and led the study and managed clinical recruitment. They also performed PCR testing and sequencing along with investigators at The Francis Crick Institute. The Safer investigators also include behavioural and ethical scientists who are monitoring the response of the healthcare workers during the study. |
| Impact | Publication of results of first 4 months of the study in The Lancet. The study team includes behavioural scientists, medical ethicists, clinical virologists and fundamental viral immunology. |
| Start Year | 2020 |
| Description | UCLH SAFER study |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This study aims to monitor the infection of UCLH healthcare workers with SARS-CoV-2 via routine PCR testing and serological analysis. My laboratory established one of the serology assays and used it to determine seroprevalence in the cohort over the first 4 months of the pandemic as published (Houlihan et al. Lancet 2020) |
| Collaborator Contribution | The Safer investigators are drawn from multiple disciplines. Firstly the clinical team at UCLH who designed and led the study and managed clinical recruitment. They also performed PCR testing and sequencing along with investigators at The Francis Crick Institute. The Safer investigators also include behavioural and ethical scientists who are monitoring the response of the healthcare workers during the study. |
| Impact | Publication of results of first 4 months of the study in The Lancet. The study team includes behavioural scientists, medical ethicists, clinical virologists and fundamental viral immunology. |
| Start Year | 2020 |
| Description | UCLH SAFER study |
| Organisation | University College London Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This study aims to monitor the infection of UCLH healthcare workers with SARS-CoV-2 via routine PCR testing and serological analysis. My laboratory established one of the serology assays and used it to determine seroprevalence in the cohort over the first 4 months of the pandemic as published (Houlihan et al. Lancet 2020) |
| Collaborator Contribution | The Safer investigators are drawn from multiple disciplines. Firstly the clinical team at UCLH who designed and led the study and managed clinical recruitment. They also performed PCR testing and sequencing along with investigators at The Francis Crick Institute. The Safer investigators also include behavioural and ethical scientists who are monitoring the response of the healthcare workers during the study. |
| Impact | Publication of results of first 4 months of the study in The Lancet. The study team includes behavioural scientists, medical ethicists, clinical virologists and fundamental viral immunology. |
| Start Year | 2020 |
| Description | UCLH SAFER study |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This study aims to monitor the infection of UCLH healthcare workers with SARS-CoV-2 via routine PCR testing and serological analysis. My laboratory established one of the serology assays and used it to determine seroprevalence in the cohort over the first 4 months of the pandemic as published (Houlihan et al. Lancet 2020) |
| Collaborator Contribution | The Safer investigators are drawn from multiple disciplines. Firstly the clinical team at UCLH who designed and led the study and managed clinical recruitment. They also performed PCR testing and sequencing along with investigators at The Francis Crick Institute. The Safer investigators also include behavioural and ethical scientists who are monitoring the response of the healthcare workers during the study. |
| Impact | Publication of results of first 4 months of the study in The Lancet. The study team includes behavioural scientists, medical ethicists, clinical virologists and fundamental viral immunology. |
| Start Year | 2020 |
| 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 |
| URL | https://youtu.be/WraimR49uAA |
| 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 |
| URL | https://youtu.be/kv28x3AaN7Y |
| 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 |
| URL | https://cvrblog.myportfolio.com/podcast-s3-ep10-laura-mccoy |