ArticleCell2023
Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer.
Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers.
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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.
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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.
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Who cites it
203 citing papers in PubMed.
- Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Trial
- Spatial Transcriptomics Analysis of Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Article
- From cell counts to cellular interactions: Cu-Cyto and the co-localization index as a spatial framework for the tumor immune microenvironment of rectal cancer.International journal of clinical oncology · 2026Review
- Tertiary lymphoid structures in cancer: their development, composition, clinical prognosis, and the drivers of the anti-tumor responses.Molecular biomedicine · 2026Review
- Spatial Integration of Protein and Chromosomal States Reveals Early Copy-Number Changes and Genotype-Associated Immune Neighborhoods in Serous Ovarian Cancer Evolution.Cancer discovery · 2026Article
- Article
- Current Advances in Spatial Pathology of Nasal Polyps: Challenges, Opportunities for Artificial Intelligence, and Future Directions.World journal of otorhinolaryngology - head and neck surgery · 2026Review
- Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT).Nature communications · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Development of a universal imaging "phenome" using shape, appearance and motion (SAM) features and the SAM Phenotype Observation Tool (SPOT).Nature communications · 2026Article
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Deep-learning triage of three-dimensional pathology datasets for comprehensive and efficient pathologist assessments.Nature biomedical engineering · 2026Article
- Senescence and Hypoxia Regulate Colon Cancer Cell Transcriptome and Secretome: Insights into Cancer Cell Senescence Pathophysiology.Biomolecules · 2026Article
- Prediction of single cell expression from low-plex immunofluorescence images for guiding precision oncology.NPJ precision oncology · 2026Article
- The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit.bioRxiv : the preprint server for biology · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Dihydroartemisinin inhibits mutant KRAS to potentiate regorafenib plus anti-PD-1 in KRAS-mutant colorectal cancer liver metastases.Cell death & disease · 2026Article
- ISPAT-3D: Spatially Varying Conditional Volumetric Network Estimation for 3D Tumor Imaging.Research square · 2026Article
143 more citing papers are in PubMed but not listed here.
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11 authors.
Funding
Abstract
Advanced solid cancers are complex assemblies of tumor, immune, and stromal cells characterized by high intratumoral variation. We use highly multiplexed tissue imaging, 3D reconstruction, spatial statistics, and machine learning to identify cell types and states underlying morphological features of known diagnostic and prognostic significance in colorectal cancer. Quantitation of these features in high-plex marker space reveals recurrent transitions from one tumor morphology to the next, some of which are coincident with long-range gradients in the expression of oncogenes and epigenetic regulators. At the tumor invasive margin, where tumor, normal, and immune cells compete, T cell suppression involves multiple cell types and 3D imaging shows that seemingly localized 2D features such as tertiary lymphoid structures are commonly interconnected and have graded molecular properties. Thus, while cancer genetics emphasizes the importance of discrete changes in tumor state, whole-specimen imaging reveals large-scale morphological and molecular gradients analogous to those in developing tissues.
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Registered trials
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.