SpottedPy Quantifies Relationships Between Spatial Transcriptomic Hotspots and Uncovers Environmental Cues of Epithelial-mesenchymal Plasticity in Breast Cancer

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2024 Nov 11

PMID 39529126

Authors

Eloise Withnell

Maria Secrier

Affiliations

Soon will be listed here.

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.

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