ArticleNature biomedical engineering2020
Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies.
Article in Nature biomedical engineering, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 36 citations in OpenAlex.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Deep molecular profiling in three dimensions.Nature methods · 2026Article
- Whole-organ spatial transcriptional analysis at cellular resolution using TRISCO.Nature protocols · 2026Review
- Three-dimensional quantitative tissue clearing reveals differences in osteovascular niche of aged and young human mesenchymal stromal cells.Nature biomedical engineering · 2026Article
- A Field-Friendly, Non-Toxic Fixative for Integrated Morphological and Molecular Research in Non-Model Invertebrates.Ecology and evolution · 2026Article
- In-situ dual-lighting system for HER2 nucleic acid and protein co-localization through simultaneous visual signal amplification in single pathological sections.Communications medicine · 2025Article
- A Simple and Fast Optical Clearing Method for Whole-Mount Fluorescence In Situ Hybridization (FISH) Imaging.Journal of biophotonics · 2025Article
- A novel protein-preserving passive tissue clearing approach using sodium cholate and urea for whole-organ imaging.Experimental & molecular medicine · 2025Article
- Clonal diversity shapes the tumour microenvironment leading to distinct immunotherapy responses in metastatic urothelial carcinoma.Nature communications · 2025Article
- Unlocking the potential of large-scale 3D imaging with tissue clearing techniques.Microscopy (Oxford, England) · 2025Review
- Three-dimensional imaging of upper tract urothelial carcinoma improves diagnostic yield and accuracy.JCI insight · 2024Article
- Volumetric imaging of the tumor microvasculature reflects outcomes and genomic states of clear cell renal cell carcinoma.The journal of pathology. Clinical research · 2024Article
- Blueprints from plane to space: outlook of next-generation three-dimensional histopathology.Cancer science · 2024Review
- Consultation on UTUC II Stockholm 2022: diagnostic and prognostic methods-what's around the corner?World journal of urology · 2023Review
- Directionality of developing skeletal muscles is set by mechanical forces.Nature communications · 2023Article
- Multidimensional Imaging of Breast Cancer.Cold Spring Harbor perspectives in medicine · 2023Review
- OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics.PLoS computational biology · 2022Article
- Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution.Science (New York, N.Y.) · 2022Article
- 3D imaging for driving cancer discovery.The EMBO journal · 2022Review
- Tissue clearing to examine tumour complexity in three dimensions.Nature reviews. Cancer · 2021Review
Corrections and comments
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Authors and funding
21 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microscopy analysis of tumour samples is commonly performed on fixed, thinly sectioned and protein-labelled tissues. However, these examinations do not reveal the intricate three-dimensional structures of tumours, nor enable the detection of aberrant transcripts. Here, we report a method, which we name DIIFCO (for diagnosing in situ immunofluorescence-labelled cleared oncosamples), for the multimodal volumetric imaging of RNAs and proteins in intact tumour volumes and organoids. We used DIIFCO to spatially profile the expression of diverse coding RNAs and non-coding RNAs at the single-cell resolution in a variety of cancer tissues. Quantitative single-cell analysis revealed spatial niches of cancer stem-like cells, and showed that the niches were present at a higher density in triple-negative breast cancer tissue. The improved molecular phenotyping and histopathological diagnosis of cancers may lead to new insights into the biology of tumours of patients.
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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 Socratic graph.