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Updated: Jun 7, 2025
Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
Published on: July 6, 2022
SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of
Eloise Withnell1, Maria Secrier2
1Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
Abstract:
Spatial transcriptomics is revolutionizing the exploration of intratissue heterogeneity in cancer, yet capturing cellular niches and their spatial relationships remains challenging. We introduce SpottedPy, a Python package designed to identify tumor hotspots and map spatial interactions within the cancer ecosystem. Using SpottedPy, we examine epithelial-mesenchymal plasticity in breast cancer and highlight stable niches associated with angiogenic and hypoxic regions, shielded by CAFs and macrophages. Hybrid and mesenchymal hotspot distribution follows transformation gradients reflecting progressive immunosuppression. Our method offers flexibility to explore spatial relationships at different scales, from immediate neighbors to broader tissue modules, providing new insights into tumor microenvironment dynamics.
