SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-11-11 DOI:10.1186/s13059-024-03428-y

Eloise Withnell, Maria Secrier

引用次数: 0

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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SpottedPy 量化空间转录组热点之间的关系，揭示乳腺癌上皮-间质可塑性的环境线索

空间转录组学正在彻底改变对癌症组织内异质性的探索，然而捕捉细胞龛位及其空间关系仍然具有挑战性。我们介绍了 SpottedPy，这是一个 Python 软件包，旨在识别肿瘤热点并绘制癌症生态系统内的空间相互作用图。利用 SpottedPy，我们研究了乳腺癌的上皮-间质可塑性，并突出了与血管生成和缺氧区域相关的稳定壁龛，这些壁龛受到 CAFs 和巨噬细胞的保护。混合和间质热点的分布遵循转化梯度，反映了渐进的免疫抑制。我们的方法可灵活探索不同尺度的空间关系，从近邻到更广泛的组织模块，为肿瘤微环境动力学提供了新的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.