High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Jamie L. Marshall, Teia Noel, Qingbo S. Wang, Haiqi Chen, Evan Murray, Ayshwarya Subramanian, Katherine A. Vernon, Silvana Bazúa‐Valenti, Katie Liguori, Keith Keller, Robert R. Stickels, Breanna McBean, Rowan M. Heneghan, Astrid Weins, Evan Z. Macosko, Fei Chen, Anna Greka
Abstract
macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially restricted kidney filter and blood-flow-regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially restricted subpopulation of epithelial cells, we discovered perturbations in 77 genes associated with the unfolded protein response. Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods.