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bioRxiv · 10.64898/2026.01.24.701519

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

Maples, R. W.·Quinn, G.·Srinivasan, T.·Dende, C.·Hooper, L. V.·Pfeiffer, J. K.
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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. SummaryO_LIAn atlas of 815,073 small intestine immune cells across four time-points reveals a large proportion of naive B and T cells. C_LIO_LIGene expression profiles suggest coordination of antigen processing in dendritic cells prior to antigen recognition by T cells. C_LIO_LITh17 and innate lymphoid cells have high expression of circadian clock genes and most immune cells have rhythmic gene expression. C_LIO_LIPopulations of certain B cell subtypes, including transitional B cells and centrocytes, are extremely dynamic with large shifts over a six hour time frame. C_LIO_LITerminally differentiated antibody-producing plasma cells have minimal circadian gene expression and few oscillatory genes. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/701519v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@162f451org.highwire.dtl.DTLVardef@1960711org.highwire.dtl.DTLVardef@a9fd4aorg.highwire.dtl.DTLVardef@341f42_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Maples, R. W., Quinn, G., Srinivasan, T., Dende, C., Hooper, L. V., Pfeiffer, J. K.. 2026-01-26. A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations. https://doi.org/10.64898/2026.01.24.701519

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