Single-cell RNA sequencing reveals mucosal BPIFA1-high-expressing neutrophils aid immune defense in SARS-CoV-2 breakthrough infection.

BACKGROUND

With the viral variants and waning of vaccine-induced immunity over time, SARS-CoV-2 breakthrough infections have become the next challenge following the COVID-19 pandemic, highlighting the need for broader and sustained immune responses. As the first defense against viral invasion, mucosal immunity is inducible by SARS-CoV-2 infection. Previous studies focused on serum antibodies and cellular immunity in the acquired immune, but the specific role of mucosal immunity in breakthrough infection remains to be elucidated.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) on nasal swabs and peripheral blood mononuclear cells from a prospective cohort of breakthrough-infected individuals. Findings were validated with flow cytometry and ELISA in a separate multicenter cohort. In vitro experiments using recombinant protein were conducted on the human monocytic leukemia cell THP-1, as effector cells, to investigate underlying mechanisms.

RESULTS

Mucosal neutrophils showed the most significant dynamic changes in post-infection. A unique subpopulation of high-BPIFA1-expressing (BPI+) neutrophils was identified and found to be positively correlated with neutralizing antibody and IgG levels in break-through patients (Pt) group.By scRNA-seq, cell communication analysis revealed enhanced interactions between BPI+ neutrophils and macrophages. In vitro, BPIFA1 stimulation activated the NF-κB pathway in THP-1 cells.

CONCLUSIONS

BPI+ neutrophils in the respiratory mucosa are pivotal in driving immune responses during breakthrough infection by modulating macrophage activity via the NF-κB pathway. It may trigger the production of interleukin-6, the immunostimulatory phenotype necessary for B cell engagement, to complete the innate-to-adaptive immunity relay, which highlights their potential as a target for novel mucosal vaccine strategies.