New preprint: SpatialTRACE
SpatialTRACE predicts anatomical axes and regions in spatial transcriptomics and microscopy — even from DAPI alone.
Read the preprintResearch Focus
How tissues shape immune responses
How does a tissue tell its immune cells what to do? Immune cells constantly read signals from their surroundings: tissue damage, the microbiome, nerves, stromal cells, metabolites. We study how these cues are integrated to drive immune responses, and how we can manipulate them to treat disease.
Much of our work so far is on tissue-resident memory T cells. We found that where a T cell sits decides which signals it receives, and those signals decide what it becomes. Now we want to know which signals matter most, and whether we can turn them up or down to improve immunity against infection and cancer, or to calm autoimmunity.
Xenium experiment of a mouse small intestine. Immunofluorescence and cell outlines are shown.
To study this, we map where cells sit in a tissue and which genes they switch on. Then we perturb genes in mouse models to test which signals matter.
A few current projects are below. The projects page has the rest, including older work.
Current
Spatial Orchestration of small intestinal tissue-resident T cells
Using spatial transcriptomics, we try to overcome limitations of single-cell sequencing and study T cells in intact tissues to understand which cell-cell interactions, gradients and cellular niches promote memory formation in barrier tissues.
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Current
Transcriptional regulation of tissue-resident memory cells
How do tissue-resident memory cells adapt to unique tissue microenvironments? How do they sense environmental signals? How are they incorporated? Using mouse models of acute viral infection, combined with genetic perturbations and single-cell sequencing, we explore the transcriptional networks that govern the acclimatization of T cells to various barrier tissues.
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