Evidence map›Paper›PMID 39529126›Full record

ArticleGenome biology2024

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

Eloise Withnell, Maria Secrier

Abstract read
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In one paragraph

Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Eloise WithnellDepartment of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
Maria SecrierDepartment of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK. m.secrier@ucl.ac.uk.ORCID 0000-0003-2758-1741

Funding

Biotechnology and Biological Sciences Research Council BB/R01356X/1Wellcome Trust 204841/Z/16/ZWellcome Trust 218529/Z/19/Z
6 · The paper itself

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.

Indexed as

Breast NeoplasmsEpithelial-Mesenchymal TransitionTranscriptomeTumor MicroenvironmentFemaleHumansSoftwareCell plasticityEpithelial-to-mesenchymal transitionHotspot analysisSpatial transcriptomicsTumor microenvironment

Identifiers

PMID39529126
PMCPMC11552145

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.