IgA clonal lineage analysis reveals class switch dynamics in human gut

IgA is the dominant antibody class in the gut, secreted by over 75,000 plasma cells daily. Human IgA subtypes show distinct anatomical expression patterns, with IgA1 dominating in serum and IgA2 is abundant at sites colonized by a large microbiota, including the distal intestine. IgA1 has a longer hinge region than IgA2, making it more vulnerable to degradation by bacterial proteases. Direct IgM to IgA2 switching, rather than sequential switching through IgA1, may allow B cells to acquire resistance to BCR degradation. We aimed to estimate the relative frequencies of these two pathways.

Ig RNA was obtained from cells sampled at the normal terminal ileum and the ascending colon of four patients undergoing right hemicolectomy and sequenced. Sequences were pre-processed using pRESTO, assigned for sub-isotype using a custom python script and annotated using IMGT/HighV-QUEST. Clones were assigned using Change-O and sampling depth was assessed using rarefaction plots. Lineage trees were constructed using IgTree© and analyzed using PopTree© and custom R scripts.

More clones were shared between IgA1 and IgA2 than between IgM and IgA2. Lineage tree analysis revealed that the most abundant class switching in the intestine is from IgA1 to IgA2. IgM cells equally switched to IgA1 or IgA2, but IgA1 to IgA2 switching was significantly much more abundant than IgM to IgA2. Finally, although both IgA1 and IgA2 sequences were highly mutated, especially in clones containing the other sub-isotype, most switches were associated with at most two mutations, suggesting that at least some switching occurs outside germinal centers.