How about combining single-cell and spatial transcriptomics to study tissue and cellular spatiotemporal dynamics in colon aging? .Aidan Daly, @f_cambuli, @RichBonneauNYC, Aviv Regev, and I are happy to share our latest pre-print (1/16):.

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This is an awesome course!.

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Thanks to the many collaborators @broadinstitute, @nygenome, @scilifelab, @MIT, @BrighamWomens, @nyuniversity, @FlatironCCB, @UU_University and last but not least; @NYGCtech and @ColumbiaBME @Cancer_dynamics.

We believe that this model framework has utility in a wide range of tissue systems, and hope that it may help to bridge the gap between single-cell and spatial transcriptomic studies!.

In conclusion, we demonstrate how contextual spatial and temporal information can help decipher large-scale molecular datasets, and how statistical models like cSplotch can be used to connect tissue architecture with the tissue alterations leading to aging and disease (15/16).

Aging was associated with a pervasive loss of goblet cells and a diffuse inflammatory state, spanning expression programs in multiple cells across the colon, and with distinct consequences at different levels of the crypt axis and in distinct regions of the colon (14/16)

To do so, we combined cSplotch with Dialogue to map multicellular programs

Finally, we looked at the cellular spatiotemporal dynamics across the entire mouse life span (12/16)

We report cell-type specific positional patterns from the base to the apex and a correlated gene expression switch between biosynthetic and cytoarchitectural regulators. Most genes displayed pan-colonic variation, but a few were region specific (11/16)

We next shift our focus to the vertical crypt axis (10/16)

And notable instances of cellular gene expression variance in multiple cell types, including goblets and ISCs, correlating with distinct digestive functions (9/16)