Game of clones within immunological niches

Coordinated communication among different types of immune cells within specialized niches is essential for mounting a protective immune response against harmful microorganisms. Within these niches immune cells exchange signals that are essential for activation of cells bearing various antigen-specific receptors that mediate pathogen clearance. Our studies focus on the humoral immune response and how different adaptive immune cells, primarily B and T lymphocytes cooperate for the generation of pathogen-specific high-affinity antibodies and establishment of long-lasting immunity. For this, we use intravital two-photon laser scanning microscopy that allows visualization of immune cell dynamics deep within tissues of living mice. In addition, we examine the distribution of various immune cells within multiple niches and compartments using whole organ imaging by light sheet fluorescence microscopy. This imaging approach allows us to visualize all the immune cells as they recognize the pathogen and generate a complete picture of the immune response. These techniques allow us to visualize immune cell niches in various organs including the intestinal tract.

Gut-derived antigens trigger immunoglobulin A (IgA) immune responses that are initiated by cognate B cells in the Peyer’s patch (PP) within specialized niches. These cells colonize the subepithelial domes (SEDs) of the PP and subsequently infiltrate into special type of niches known as germinal centers (GCs). We defined the pre-GC events and the nices at which affinity-based B cell selection occurred in PPs. Using whole-organ imaging, we showed that the affinity of the B cell antigen receptor (BCR) regulated infiltration of antigen-specific B cells into GCs, but not clonal competition in the SED. Follicular helper-like T cells resided in the SED and promoted its B cell colonization, independently of the magnitude of BCR affinity. Imaging and immunoglobulin sequencing indicated that selective clonal-expansion ensued during infiltration into GCs. Thus, in PPs, in contrast to draining lymph nodes and spleen, T cells predominantly promoted the expansion of B cells without clonal selection during pre-GC events. Understanding immune cell communications within specialized niches can lead to the design of improved vaccines against infectious pathogens. Our studies may also lead to the discovery of novel checkpoints that can be targeted in autoimmune diseases and prevent the formation of pathogenic anti-self antibodies.