Elucidating the mutational trajectories of mature anti-HIV1 and anti-SARS-CoV-2 antibodies through in vitro longitudinal screening

Background and importance: The essential role of the adaptive immune system is to provide long-term protection against pathogens via the production of antibodies. To combat the complexity of pathogens in the environment, our immune system has evolved the capacity to produce a vast diversity of antibodies from a relatively small set of genes. This diversity is primarily achieved through somatic hypermutation (SHM), during which mutations are introduced into the antibody-encoding genes in B lymphocytes, a specialized type of white blood cell. These mutations subtly alter the "shape" of antibodies, affecting their binding strength, or affinity, towards the pathogen or vaccine. However, in the case of some pathogens, notably HIV-1, protective antibodies are difficult to elicit, highlighting the need for a deeper understanding of the mutational pathways and the molecular principles that govern the mutation reaction to design more effective vaccination regimens. Aims and objectives: Despite the importance of SHM, we still lack a thorough understanding of how it works, particularly the exact mutagenic pathways and mechanisms that lead to the evolution of the desired protective antibodies. Understanding these pathways is crucial for improving our ability to design effective vaccines and therapies. To address these gaps in our knowledge, our research 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 and optimized for this purpose. Specifically, we will focus on identifying how antibodies are diversified via SHM to target two major viruses, human immunodeficiency virus-1 (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agents for AIDS and COVID-19, respectively. By tracking the mutations that occur across multiple timepoints (referred to as a longitudinal analysis), we aim to map and study the mutational trajectories that lead to the production of potent, neutralizing antibodies against these viruses. Additionally, we will investigate how neighbouring DNA sequences influence, either positively or negatively, the occurrence of higher affinity-conferring mutations in the antibody genes and thereby gain mechanistic insights into the rules and principles guiding the evolution of the mature antibodies. Potential benefits and relevance: Understanding the development of HIV-1 and SARS-CoV-2 broadly neutralizing antibodies (i.e. antibodies that can neutralize the majority of viral variants) can guide the design of vaccines that could trigger these potent antibodies. By identifying the most probable mutational pathways that can generate the desired protective antibodies, we can pinpoint the best targets for vaccine development. This is especially important for current strategies where vaccines are crafted to gradually activate and mature specific B cells in a systematic, stepwise manner that enables them to produce the desired protective antibodies over time. Additionally, since SHM can also contribute to cancer (due to undesired mutation of cancer-causing oncogenes), deciphering the rules governing the mutation process will be of direct relevance towards understanding the genesis of B cell cancers. Another potential benefit of our research is the discovery of new neutralizing antibodies against HIV-1 and SARS-CoV-2. Finally, and more generally, our experimental system could we used as a template for studying antibody maturation against a range of pathogens.