B cell receptor diversity and evolution through vaccination

<p dir="ltr">Antibodies are the primary correlate of protection for the majority of vaccine-preventable diseases, and the B cell receptor (BCR) repertoire encodes the full clonal diversity of the humoral immune response. Despite this, tools and frameworks to accurately characterize BCR repertoire data in the context of vaccination remain incomplete, and fundamental questions regarding how different vaccine platforms, antigen targets, and host immune status shape antibody quality and breadth are still unresolved. The overarching aim of this thesis was to advance the understanding of BCR repertoire dynamics in response to vaccination, through the development of dedicated analytical tools and their application across preclinical and clinical vaccine studies.</p><p dir="ltr">BCR repertoire data was generated using Sanger sequencing and high-throughput bulk sequencing in non-human primates and humans, integrated with antigen-specific single-cell sorting, functional antibody assays, and structural characterization by cryo-EM and negative-stain electron microscopy. A dedicated R/Bioconductor package, scifer, was developed to perform QC of BCR Sanger sequencing data directly from raw trace files and was shown to reduce spurious somatic hypermutation (SHM) calls that would otherwise confound downstream repertoire analyses. An unmodified mRNA-LNP rabies vaccine elicited higher and more durable neutralizing antibody titers than an approved inactivated vaccine in macaques, with broader cross-neutralization across lyssaviruses, without inducing a qualitatively distinct antigen-specific BCR repertoire in terms of gene usage, diversity, or SHM. Characterization of Human Respiratory Syncytial Virus (HRSV) nanoparticle vaccine-elicited antibodies in macaques identified LOR24 as a new class of site-III antibody capable of cross-neutralizing both HRSV and Human metapneumovirus (HMPV), with as few as three somatic mutations sufficient to confer this capacity. Structural analysis revealed that LOR24 and the HRSV-specific LOR69 antibodies, despite sharing a conserved germline-encoded binding motif with MPE8-like cross-neutralizing antibodies, adopt distinct angles of approach at site-III and drive different mechanisms of F-protein destabilization. In allogeneic hematopoietic stem cell transplant (HSCT) recipients, individuals who responded to mRNA SARS-CoV-2 vaccination mounted antibody and BCR repertoire responses comparable to those of healthy controls, and transitional B cell proportions at the time of vaccination were identified as a candidate predictor of vaccine responsiveness.</p><p dir="ltr">Taken together, these findings demonstrate that detailed characterization of the BCR repertoire at the clonal level yields directly actionable insights for vaccine design, therapeutic antibody development, and the clinical management of immunocompromised individuals.</p><h3 dir="ltr">List of scientific papers</h3><p dir="ltr">I. <b>Arcoverde </b><b>Cerveira R,</b> Lenart K*, Martin M*, Hinchcliff MJ, Hellgren F, Ye K, Assis Geraldo J, Kreslavsky T, Ols S, Loré K. Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells. ImmunoInformatics 16, 100046 (2024). <a href="https://doi.org/10.1016/j.immuno.2024.100046" rel="noreferrer" target="_blank">https://doi.org/10.1016/j.immuno.2024.100046</a></p><p dir="ltr">II. Hellgren F*, Cagigi A*, <b>Arcoverde </b><b>Cerveira R*</b>, Ols S, Kern T, Lin A, Eriksson B, Dodds MG, Jasny E, Schwendt K, Freuling C, Müller T, Corcoran M, Karlsson Hedestam GB, Petsch B, Loré K. Unmodified rabies mRNA vaccine elicits high cross-neutralizing antibody titers and diverse B cell memory responses. Nature Communications. 14, 3713 (2023). <a href="https://doi.org/10.1038/s41467-023-39421-5" rel="noreferrer" target="_blank">https://doi.org/10.1038/s41467-023-39421-5</a></p><p dir="ltr">III. Ols S*, Borst AJ*, <b>Arcoverde </b><b>Cerveira R*</b>, Bermúdez Méndez E, Gegenfurtner F, Eray E, Weidle C, Miranda M, Peng Z, Carr K, Skotheim R, Kochmann J, Brunette N, Lenart K, Perez L, Karlsson Hedestam GB, Antanasijevic A, Neil King P** , Loré K**. Distinct mechanisms of antibody neutralization from binding a conserved pneumovirus epitope. [Manuscript]</p><p dir="ltr">IV. Hellgren F, <b>Arcoverde </b><b>Cerveira R,</b> Lindgren G, Chen P, Lenart K, Ols S, Cagigi A, Valentini D, Rocavert Barranco M, Shaloom Vitus E, Corcoran M, Gwon YD, Forsell MNE, Evander M, COVAXID Study Group, Bergman P, Buggert M, Ljunggren HG, Aleman S, Karlsson Hedestam GB, Björklund A, Nordlander A, Ljungman P, Mielke S** , Loré K**. The impact of B cell reconstitution on mRNA vaccine responses in allogeneic stem cell transplant recipients. Clinical Translational Immunology. 15, e70077 (2026). <a href="https://doi.org/10.1002/cti2.70077" rel="noreferrer" target="_blank">https://doi.org/10.1002/cti2.70077</a></p><p dir="ltr">*/ ** These authors contributed equally.</p>