A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations

Abstract The small intestine houses an array of immune cells that receive diverse inputs from food intake, microbiota, and other cues that vary by time of day. However, how diurnal variation influences intestinal immune cell proportions and functions is unclear. Here, we use flow cytometry and single cell RNA sequencing to establish an atlas of 815,073 mouse small intestine immune cells at four times across the day-night cycle. These data suggest possible temporal coordination of dendritic cell antigen processing and subsequent T cell antigen recognition. Most cells express circadian clock genes and have intrinsic oscillatory transcriptomes. However, differentiated antibody-producing plasma cells have minimal circadian gene expression and instead may receive extrinsic oscillatory cues from other cell types. Finally, certain populations of B cells are extremely dynamic, with broad transcriptional changes within a six hour time span. This dataset provides insight into the circadian dynamics of intestinal immunity. Summary An atlas of 815,073 small intestine immune cells across four time-points reveals a large proportion of naïve B and T cells. Gene expression profiles suggest coordination of antigen processing in dendritic cells prior to antigen recognition by T cells. Th17 and innate lymphoid cells have high expression of circadian clock genes and most immune cells have rhythmic gene expression. Populations of certain B cell subtypes, including transitional B cells and centrocytes, are extremely dynamic with large shifts over a six hour time frame. Terminally differentiated antibody-producing plasma cells have minimal circadian gene expression and few oscillatory genes.