Probing HIV-1 Vaccination Through Deep B Cell Repertoire Sequencing and Functional Characterization

Abstract

Understanding why vaccine-engaged B cells fail to mature into functional lineages remains a challenge in Human Immunodeficiency Virus 1 (HIV-1) vaccine development. This dissertation examined antibody function and repertoire maturation in rhesus macaques (Macaca mulatta) immunized with HIV-1 10014.F8 (F8) Envelope glycoprotein (Env), derived from an individual with broad neutralizing activity. F8 Env was presented as a SOSIP trimer, ferritin-displayed Env, or liposome-displayed Env to test whether antigen format altered humoral function and B cell evolution. Serum activity was linked to lineage-level maturation using serology, bulk memory B cell immunoglobulin heavy chain sequencing, single-cell V(D)J sequencing, monoclonal antibody expression, and Hinge-Seq. F8 trimer immunization induced Env-binding antibodies and detectable Fc activity, but neutralization breadth remained limited. Functionally anchored repertoire analysis showed Env-specific lineages were recruited yet less mutated than non-Env-binding background lineages. Ferritin display increased binding titers and avidity but did not improve neutralization, Fc activity, or lineage maturation. This series of findings indicates that F8 Env vaccination achieved antigen engagement without coordinated functional maturation, and antigen valency alone was insufficient to overcome this bottleneck.