Project ID CM-HD2026_15

ThemeCM-HD

Co Supervisor 1A Prof Katie Doores Faculty of Life Sciences & Medicine, School of Immunology & Microbial Sciences, Department of Infectious DiseasesEmail

Co Supervisor 1B Dr Rushad Pavri Faculty of Life Sciences & Medicine, School of Immunology & Microbial Sciences, Peter Gorer Department of ImmunobiologyEmail

Deciphering the mutational pathways to broadly neutralizing antibodies against HIV-1 and SARS-CoV-2

Elicitation of neutralizing antibodies is critical to the success of most vaccines. However, in the case of highly variable pathogens, notably HIV-1 and SARS-CoV-2, protective antibodies require broad neutralizing activity against viral variants. Such antibodies are called broadly neutralizing antibodies (bnAbs). This is acquired by the process of somatic hypermutation (SHM), which modulates antigen-antibody affinity via mutagenesis of antigen-binding variable regions of antibodies. Although bnAbs have been isolated from infected and/or convalescent individuals, such desirable antibodies have been difficult to elicit through vaccination. Understanding the mutational pathways and the molecular principles that govern SHM is crucial for improving our ability to design effective vaccines and therapies.

To address these knowledge gaps, this project aims to systematically study how SHM generates potent, anti-viral antibodies in a controlled setting using a specialized human B cell system that we have engineered. We will focus on identifying how antibodies are diversified via SHM to target two major viruses: HIV-1 and SARS CoV 2. Specifically, SHM will be induced in cell lines expressing germline, unmutated precursors of mature bnAbs (Years 1-2) and B cell clones expressing antibodies with specificity towards HIV-1 Env or SARS-CoV-2 Spike will be selected by flow cytometry and functionally characterized for neutralization activity (Years 2-4). By longitudinally tracking SHM in this manner, we aim to map and study the mutational trajectories that lead to the production of potent, neutralizing antibodies against these viruses. Identifying the most probable mutational pathways leading to neutralization breadth (Years 2-4) will guide the design of vaccines that could trigger these potent antibodies in vivo.

Skills/techniques: This project will combine techniques in molecular biology and immunology (generating and characterizing transgenic B cell lines, next-generation sequencing of antibody libraries, FACS sorting, ELISA), biochemistry (antibody cloning/expression) and virology (viral infections, neutralization assays), in addition to critical thinking, presentation and project management skills.

Rotation project: Generation of a new germline bnAb expressing cell line and characterisation of an existing cell line to gain experience in several of the techniques outlined above.

Representative Publications

1. Seow J, Shalim ZA, Graham C, Kimuda S, Pillai A, Lechmere T, Kurshan A, Khimji AM, Snell LB, Nebbia G, Mant C, Waters A, Fox J, Malim MH, Doores KJ. Broad and potent neutralizing antibodies are elicited in vaccinated individuals following Delta/BA.1 breakthrough infection, mBio, 2023, e0120623. doi: 10.1128/mbio.01206-23;
2. C Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Dupont L, Lista MJ, Jimenez-Guardeño JM, Laing AG, Wu Y, Joseph M, Muir L, van Gils MJ, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJD, Malim MH, Doores KJ., Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant, Immunity, 2021, 54(6):1276-1289.e6. https://doi.org/10.1016/j.immuni.2021.03.023;
3. Walker LM, Huber M, Doores KJ, Falkowska E, Pejchal R, Julien JP, Wang SK, Ramos A, Chan-Hui PY, Moyle M, Mitcham JL, Hammond PW, Olsen OA, Phung P, Fling S, Wong CH, Phogat S, Wrin T, Simek MD; Protocol G Principal Investigators; Koff WC, Wilson IA, Burton DR, Poignard P., Broad neutralization coverage of HIV by multiple highly potent antibodies, Nature, 2011, 477, 466-470. doi: 10.1038/nature10373.

1. Tambe, A., MacCarthy, T., Pavri. R. Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions. Frontiers in Immunology (2024) 15:1407470. DOI: 10.3389/fimmu.2024.1407470;
2. Costea, J., Schoeberl, U. E., Malzl, D., Von der Linde, M., Fitz, J., Makharova, M., Goloborodko, A. and Pavri, R. A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Molecular Cell (2023). DOI: 10.1016/j.molcel.2023.01.014. PMID: 36736317;
3. Peycheva, M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, U. and Pavri, R. DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science 377, 6612 (2022). DOI: 10.1126/science.abj5502