# B cell clonal selection in gut-associated germinal centers

> **NIH NIH R01** · ROCKEFELLER UNIVERSITY · 2022 · $824,340

## Abstract

In addition to playing a crucial role in physiological processes such as digestion of food, gut 
microbes also provide a low-grade stimulation of the intestinal immune system, which contains the 
majority of the lymphocytes and antibodies in the body. Colonization by gut microbiota 
influences adaptive immunity, in large part via gut- associated secondary lymphoid 
structures including gut-draining mesenteric lymph nodes (mLN) and Peyer patches (PPs). In 
turn, the gut-associated adaptive immune system provides crucial resistance mechanisms against 
enteric infections, but also represents a major regulator of the microbiota composition itself, in 
part via secretion of antibodies. However, how antibody formation and secretion in the intestine is 
regulated by, and regulate the microbiome is incompletely understood. Particularly, it remains 
unclear how naturally-occurring gut- associated germinal centers (gaGCs), essential structures 
 for B cell receptor affinity maturation and class switching, deal with the plethora of 
luminal antigens or in turn, develop in their absence. In our previous work and preliminary 
presented here, we demonstrate lines of evidence supporting the relevance and feasibility of the 
proposed studies. First, we developed a multicolor fate-mapping using "Brainbow" alleles 
as a system to measure the extent of positive GC selection (and thus of affinity maturation) in 
single GCs with high throughput. Second, we present data with supportive evidence of strong 
selection towards monoclonality, as well as affinity- based selection in gaGCs in the steady state. 
Third, by re-deriving our Brainbow mice into our existing GF facility, and by analyzing clonal 
dynamics and winner clones under absence of gut microbiota, we found that gaGCs are still 
abundantly observed in GF conditions, surprisingly consisting of highly public clonotypes 
 that undergo extraordinarily fast positive selection. We thus hypothesize that, despite the 
enormous antigenic diversity of the gut, affinity maturation towards commensals does take place in 
the physiology. In Aims 1&2, we propose to leverage the ability to readily identify "winner" B 
cell clones afforded by the Brainbow system (Aim 1) to isolate B cell clones with strong affinity 
maturation to steady state commensals, as a tool to gain insight into the basic biology underlying 
the clonal dynamics of gaGCs and the mucosal antibody response in general (Aim 2). In Aim 3, we 
propose to investigate the biology of the unusual GCs observed in GF mice to determine 
the origin, specificity, and function of public B cell clones that dominate the intestinal 
response in the absence of microbiota. By combining our complementary expertise in gut (Mucida lab) 
and B cell biology (Victora lab), with gnotobiotic and state-of-the-art imaging, single-cell 
sequencing, biochemical and microbiology approaches, we seek to determine the influence of 
the microbiome on B cell selection, antibody affinity matur...

## Key facts

- **NIH application ID:** 10466919
- **Project number:** 5R01AI157137-03
- **Recipient organization:** ROCKEFELLER UNIVERSITY
- **Principal Investigator:** Daniel S Mucida
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $824,340
- **Award type:** 5
- **Project period:** 2020-09-17 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10466919

## Citation

> US National Institutes of Health, RePORTER application 10466919, B cell clonal selection in gut-associated germinal centers (5R01AI157137-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10466919. Licensed CC0.

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