ArticleeLife2025
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Reference-guided pseudotime inference across species and biological contexts.bioRxiv : the preprint server for biology · 2026Article
- Prognostic RNA-splicing archetypes in breast cancer identified by extended pre-training of histopathology foundation models.Nature communications · 2026Article
- Intestinal stearoyl-CoA desaturase-2 is highly expressed and nutritionally regulated but dispensable for energy balance.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2026Article
- SpatialFusion: A lightweight multimodal foundation model for pathway-informed spatial niche mapping.bioRxiv : the preprint server for biology · 2026Article
- Impact and correction of segmentation errors in spatial transcriptomics.Nature genetics · 2026Article
- Spatial immune archetypes in gastric and colorectal cancer: a proposed conceptual framework for immunotherapy resistance and therapeutic remodeling.Frontiers in immunology · 2026Review
- MEX3A Modulates PPARγ Pathway Activity and Colorectal Cancer Growth.Cellular and molecular gastroenterology and hepatology · 2026Article
- Developmental regulation of intestinalbioRxiv : the preprint server for biology · 2025Article
- Article
- Rehydration rescues Il22Nature communications · 2025Article
- FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data.bioRxiv : the preprint server for biology · 2025Article
- EGFR controls transcriptional and metabolic rewiring in KRASEMBO molecular medicine · 2025Article
- High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer.Nature genetics · 2025Article
- Multi-Omics Meets Premalignancy: Paving the Way for Early Prevention of Cancer.Research (Washington, D.C.) · 2025Review
- Spatial Transcriptomic Technologies.Cells · 2023Review
- Article
- Emergence of division of labor in tissues through cell interactions and spatial cues.Cell reports · 2023Article
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27 authors.
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Abstract
While advances in single-cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single-cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled inducible genetic CRC mouse models that recapitulate key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Comparing to scRNA-seq and bulk RNA-seq data from human CRC, we find that both cell composition and layout features were conserved between the species, with mouse neighborhoods correlating with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease. Our work offers a comprehensive framework that is applicable across various tissues, tumors, and disease conditions, with tools for the extrapolation of findings from experimental mouse models to human diseases.
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