ArticleNature methods2025
Highly multiplexed 3D profiling of cell states and immune niches in human tumors.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights.bioRxiv : the preprint server for biology · 2026Article
- STAT3D as a new image-tailored Xenium-based spatial transcriptomics tool for accurately dissecting the tumor microenvironment.Nucleic acids research · 2026Article
- 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
- Epithelial-mesenchymal transition in carcinoma: navigating phenotypic states to target resistance and metastasis.Cancer metastasis reviews · 2026Review
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- CellTune: an integrative software for accurate cell classification in spatial proteomics.Nature methods · 2026Article
- Illuminating the Interface: In Situ Optical Insights Into Two-Electron ORR Pathways for HAdvanced materials (Deerfield Beach, Fla.) · 2026Review
- Assessing the Effects of a 3-Dimensional (3D) Pathology Tissue-Processing Workflow on Downstream Molecular Analyses.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- The initial melanoma T cell infiltrate is defined by tissue-resident programs restrained by regulatory T cells.Research square · 2026Article
- Scalable 3D cell-interaction analysis via supercell graphs for prostate cancer risk stratification.bioRxiv : the preprint server for biology · 2026Article
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- 3D pathology-guided microdissection.Nature methods · 2026Article
- Fault-tolerant 3D reconstruction from 2D spatial proteomics sections.bioRxiv : the preprint server for biology · 2026Article
- Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis.bioRxiv : the preprint server for biology · 2026Article
- Review
- Review
- Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.bioRxiv : the preprint server for biology · 2026Article
- An epigenetic switch in vascular phenotype augments anti-tumor immunity.Angiogenesis · 2026Article
- A Hallmark-Integrated, Agent-Based Framework for Intratumor Heterogeneity in Melanoma Evolution.Bulletin of mathematical biology · 2026Article
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Authors and funding
14 authors.
Funding
Abstract
Diseases such as cancer involve alterations in cell proportions, states and interactions, as well as complex changes in tissue morphology and architecture. Histopathological diagnosis of disease and most multiplexed spatial profiling relies on inspecting thin (4-5 µm) specimens. Here we describe a high-plex cyclic immunofluorescence method for three-dimensional tissue imaging and use it to show that few, if any, cells are intact in conventional thin tissue sections, reducing the accuracy of cell phenotyping and interaction analysis. However, three-dimensional cyclic immunofluorescence of sections eightfold to tenfold thicker enables accurate morphological assessment of diverse protein markers in intact tumor, immune and stromal cells. Moreover, the high resolution of this confocal approach generates images of cells in a preserved tissue environment at a level of detail previously limited to cell culture. Precise imaging of cell membranes also makes it possible to detect and map cell-cell contacts and juxtracrine signaling complexes in immune cell niches.
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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.