Yes. The colors in the final row are unrelated. This shows Leiden Cluster and not cell types.

The first three rows of Fig 1d are colored as indicated in the legend. Row 4 highlights the antigen specific T cells and row 5 is coloured by leiden clustering. If you want to explore the cell types I recommend having a look at the anndata object: www.ncbi.nlm.nih.gov/geo/query/ac...

Thanks. Are you going to be in asilomar this weekend?

I cannot believe you still have that picture! That's when all the fun started almost two years ago....

🧵 10/10 This work establishes a framework for studying tissue immune networks and reveals how cellular positioning shapes immune cell identity and function. Full paper: www.nature.com/articles/s41...
Big thanks again to all the authors for their incredible work! ❤️

🧵 9/10 Technical innovation: We developed a strategy for pooled optically encoded gene perturbations compatible with spatial transcriptomics, enabling mechanistic studies in situ

🧵 8/10 Our spatial framework reveals that T cell location and functional state are fundamentally intertwined - establishing a new paradigm for understanding tissue immunity

🧵 7/10 Importantly, we validated these findings in human tissue. Analysis of healthy human terminal ileum revealed similar spatial organization of CD8 T cell states

🧵 6/10 TGFβ signaling proved essential for proper TRM positioning. TGFβRII KO cells showed impaired migration to the villus tip and reduced acquisition of tissue-residency programs

🧵 5/10 Using CRISPR-based perturbations with spatial readout, we demonstrated that CXCR3 signaling is crucial for early positioning of effector cells. Loss of CXCR3 altered cellular positioning and subsequent differentiation fate

🧵 4/10 This diversity is regulated by:
1. Distinct ligand-receptor activities
2. Spatial cytokine gradients
3. Specialized cellular contacts creating a complex molecular landscape that guides TRM differentiation

🧵 3/10 Key finding: We identified two distinct TRM states defined by their location:
• Differentiated TRM cells (Gzma+, Gzmb+, Itgae+) in upper villus
• Progenitor-like TRM cells (Tcf7+, Slamf6+) in lower villus/crypt

🧵 2/10 Using spatial transcriptomics (Xenium & MERSCOPE), we discovered that intestinal TRM cells occupy distinct niches that shape their phenotype and function. We developed computational approaches to map cells along three anatomical axes 📊