Macrophages direct location-dependent recall of B cell memory to vaccination [scRNA-seq and scVDJ-seq]

Vaccines generate long-lived plasma cells and memory B cells (Bmems) that may re-enter secondary germinal centers (GCs) to further mutate their B cell receptor upon boosting and re-exposure to antigen. We show that lymph nodes draining the primary vaccination site harbour a subset of Bmems that reside in the subcapsular niche, generate larger recall responses, and are more likely to re-enter GCs compared to circulating Bmems in non-draining lymph nodes. Depletion of CD169+ subcapsular sinus macrophages impairs Bmem proliferative expansion, secondary GC formation and secretion of affinity-matured antibodies upon boosting of the draining lymph node. This site-specific, niche-dependent control is associated with more rapid secretion of broadly neutralizing antibodies, GC participation and clonal expansion of SARS-CoV-2-specific B cells in healthy volunteers boosted with the BNT162b2 vaccine in the same versus opposite arm. These data reveal an unappreciated role for primed draining lymph node SSMs in Bmem cell fate determination. To test the impact of boosting location in human subjects, we recruited 30 healthy volunteers who were SARS-CoV-2-naïve and performed a prospective, controlled clinical study of boosting the homologous BNT162b2 mRNA vaccine, which encodes the Ancestral SARS-CoV-2 Spike protein, either in the same (boosted dLN, n=20) or opposite arm (boosted ndLN, n=10) 3 weeks after the priming dose (Figure 7A; Table S3). Fine needle biopsy (FNB) of both axillary lymph nodes were performed in a subset of 18 participants (n=9, boosted dLN; n=9, boosted ndLN) on day 5-7 after the second (booster) vaccine dose. We performed single-cell transcriptomic analysis (5' Gene Expression, VDJ-B) on fine needle biopsy samples of both axillary lymph nodes from six participants. Files with 007L (dLN), 007R (ndLN), 010L (dLN), 010R (ndLN), 012L (dLN), 012R (ndLN) are Same arm (Ipsilateral) vaccine group files. Files with 008L (ndLN), 008R (dLN), 011L (ndLN), 011R (dLN), 015L (ndLN), 015R (dLN) are Opposite arm (Contralateral) vaccine group files.