Induction of germinal centers in human Peyer’s patches shapes robust intestinal adaptive immunity in early life.

Introduction/Rationale: Early life is a critical period in which the immune system encounters a variety of new antigens including pathogens, food antigens, and vaccines. Many of these initial exposures occur in mucosal sites such as the gut, where Peyer’s patches (PP) house local B cell responses that establish protection or maintain homeostasis. However, the dynamics of intestinal adaptive immunity during development remains poorly defined in humans.

Methods: We profiled paired PP and mesenteric lymph nodes (MLN) from pediatric human organ donors aged 0-11 years using immunofluorescence microscopy and single-cell RNA-seq (scRNA-seq) to investigate germinal center (GC) dynamics across space and time.

Results: We found robust induction of GC reactions in PPs and MLNs, significantly greater in PPs, peaking at ~2 years and declining thereafter. Profiling by scRNA-seq revealed prominent GC, plasma, and memory B cell populations, with GC B cell proportions declining and memory B cells increasing across age. GC B cells consisted of 6 subsets corresponding to distinct light and dark zone B cells, which provides a unique window into human GC formation and somatic hypermutation (SHM). Paired BCR analysis showed large clonal expansion in GC B cells and age-associated higher SHM frequency, consistent with ongoing affinity maturation. Interestingly, clonal overlap was minimal between spatially separated PPs within the same donor, indicating GC responses in the gut are highly compartmentalized. Complementing these B cell dynamics, three transcriptionally distinct follicular helper T cell subsets showed discrete dynamics with age and GC magnitude, suggesting subset specific contributions to GC induction and waning.

Conclusion: Together, our data demonstrate that the first two years of life is a critical window to establish intestinal adaptive immunity, driven by expansive and spatially compartmentalized GC activity in PPs, with implications for the timing and design of vaccination and immunotherapy strategies in children.