Longitudinal profiling of antigen receptor gene repertoire dynamics in kidney transplant recipients after multiple SARS-CoV-2 vaccinations

Kidney transplant recipients (KTRs) exhibit impaired immune responses to vaccination against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, remaining vulnerable to severe coronavirus disease 2019 (COVID-19) even after multiple vaccine doses. We hypothesized that repeated SARS-CoV-2 vaccinations in KTRs might promote remodeling of the adaptive immune repertoire. In order to address this hypothesis and gain insight into adaptive immune dynamics in this population, we employed next-generation sequencing (NGS) to determine longitudinal alterations in immunoglobulin (IG) and T cell receptor (TR) gene repertoires following multiple mRNA vaccinations and functional experiments to assess lymphocyte signaling capacity. TR gene repertoire analysis revealed increased diversity and reduced clonality after booster immunizations, indicative of substantial repertoire renewal. Although the relative frequency of SARS-CoV-2-specific TR clonotypes remained stable over time, significant shifts in TRBV gene usage reflected dynamic reshaping of the TR clonal architecture. Parallel IG gene repertoire profiling demonstrated increased diversity and limited oligoclonal expansions after booster mRNA vaccination. These changes were accompanied by elevated levels of somatic hypermutation in IG clonotypes similar to published SARS-CoV-2-specific clonotypes, suggestive of more efficient humoral responses following repeated antigenic exposure. Phospho-specific flow cytometry analysis revealed initially diminished B cell receptor signaling, which was restored following multiple immunizations, consistent with reversal of B cell anergy status. Altogether, our findings support the notion that repeated SARS-CoV-2 vaccinations drive the remodeling of cellular and humoral immune landscapes in KTRs. These results underscore the importance of tailored vaccination strategies to optimize immune protection in immunocompromised individuals.