Biology subjects

Abbad, A.

Publications and source records attributed to Abbad, A..

3 recordsLinked to original sources

bioRxiv2026

Clonotype specificity distinguishes epitope-tailored and permissive somatic hypermutation

Identifying antibody features that reliably encode epitope specificity poses a major barrier towards modeling antigen-antibody interactions. Affinity maturation offers a unique opportunity to probe the molecular basis of antigen-antibody interactions by revealing how individual somatic hypermutations (SHM) refine antibody binding. Using SARS-CoV-2 spike-specific germinal center B-cell repertoires, we show that antibodies harboring multiple SHMs that are restricted to their respective clonotypes (clonotype-restricted SHMs) preferentially recognize cryptic epitopes. We structurally characterized three such antibodies: two recognized a cryptic epitope on the receptor-binding domain whereas a third bound an N-terminal domain epitope that is almost entirely occluded in prefusion spike. In contrast, SHMs shared across multiple clonotypes using the same V gene recur across antibodies targeting diverse antigens but generally fail to enhance affinity when introduced into diverse antibody backgrounds. Together, these findings define a spectrum of SHM behavior, distinguishing epitope-tailored mutations from broadly recurrent but largely permissive substitutions.

immunology↗

bioRxiv2026

The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response

The continued mutational pressure on the SARS-CoV-2 S1 subunit underscores the need to target the conserved S2 region for pan-coronavirus vaccine development. A detailed molecular understanding of S2-directed immune responses is therefore essential. In this study, we identified the S2 apex as the most immunodominant epitope within the S2 subunit, eliciting robust antibody responses despite occlusion by S1, using electron-microscopy-based polyclonal epitope mapping (EMPEM) of plasma from infected and vaccinated individuals. Structure-guided sequence analysis with antibody databases revealed that antibodies targeting a poorly characterized S2 Apex-B site form a convergent public clonotype, which is predominantly derived from the IGHV3-30 germline with a 14-residue CDRH3 containing a G/S-G-S/N-Y motif. This clonotype is extensively expanded, accounting for up to 40% of total spike-reactive antibody sequence counts in individual vaccinated donors. This study elucidates the molecular basis the high-frequency elicitation of this non-neutralizing clonotype emphasizing that its immunodominance acts as a primary hurdle for universal coronavirus vaccines and underscore the need for precision antigen design to redirect immunity toward more potent neutralizing targets.

immunology↗

bioRxiv2022

Receptor binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2

Neutralization assays are experimental surrogates for the effectiveness of infection- or vaccine-elicited polyclonal antibodies and therapeutic monoclonal antibodies targeting SARS-CoV-2. However, the measured neutralization can depend on details of the experimental assay. Here we systematically assess how ACE2 expression in target cells affects neutralization by antibodies to different spike epitopes in lentivirus pseudovirus neutralization assays. For high ACE2-expressing target cells, receptor binding domain (RBD) antibodies account for nearly all neutralizing activity in polyclonal human sera. But for lower ACE2-expressing target cells, antibodies targeting regions outside the RBD make a larger (although still modest) contribution to serum neutralization. These serum-level results are mirrored for monoclonal antibodies: N-terminal domain (NTD) antibodies and RBD antibodies that do not compete for ACE2 binding incompletely neutralize on high ACE2-expressing target cells, but completely neutralize on cells with lower ACE2 expression. Our results show that ACE2 expression level in the target cells is an important experimental variable, and that high ACE2 expression emphasizes the role of a subset of RBD-directed antibodies.

immunology↗