ArticleNature communications2023
Pan-cancer classification of single cells in the tumour microenvironment.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
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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.
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.
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Who cites it
66 citing papers in PubMed, 73 citations in OpenAlex.
- 4-1BBCell reports. Medicine · 2025Trial
- Molecular signals associated with intraperitoneal chemotherapy resistance in gastric cancer with peritoneal metastasis through PIPS GC trial integrated translational research.Scientific reports · 2025Trial
- ROCK2 regulates a stress-responsive transcriptional state and calcium signaling in renal cell carcinoma.Molecular and cellular biochemistry · 2026Article
- Interleukin-1 receptor-associated kinase 1 controls chemoresistance and immuno-killing in non-small cell lung cancer.Signal transduction and targeted therapy · 2026Article
- scTransMIL bridges patient-level disease states and single-cell transcriptomics for cancer screening and heterogeneity inference.Nature communications · 2026Article
- Immune-Responsive Bioinks Enable Vision-GuidedAdvanced functional materials · 2026Article
- Migration of immune cells in tumors and inflammation: molecular mechanisms and therapeutic targets.Signal transduction and targeted therapy · 2026Review
- A cDC1-NK/T-Malignant Cell Circuit Drives Immunogenic Remodeling Under PD-1 Blockade in Gastric Cancer.Cancer science · 2026Article
- A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well SNature protocols · 2026Review
- Single-cell transcriptomic analysis reveals tumor-immune determinants of lymph node colonization and progression in thyroid cancer.Science advances · 2026Article
- Integrative single-cell and spatial transcriptomic analysis reveals that ATG13 enriched in cancer-associated fibroblasts is associated with the suppression of ferroptosis in colorectal cancer.Discover oncology · 2026Article
- Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression.Nature genetics · 2026Article
- Deep interpretable radiogenomic workflow deciphers tumor microenvironment from breast MRI and identifies clinician-interpretable biomarkers.NPJ precision oncology · 2026Article
- Tumor glycosylation engages CD301b-mediated myeloid regulation in breast cancer.Research square · 2026Article
- Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner's Guide.bioRxiv : the preprint server for biology · 2026Article
- Chromatin unwinding state for in situ identification and lineage tracing of circulating tumor cells.iMeta · 2026Article
- Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.iScience · 2026Article
- Pyroptosis Modulates Multiple Immune Cell Populations in Targeted Therapy-Treated Melanoma.Cancer immunology research · 2026Article
- SCANBIT facilitates identification of tumor cell populations in scRNAseq data using pseudobulked SNV calls.bioRxiv : the preprint server for biology · 2026Article
- CAR-T cells in solid tumors: engineering, biomarkers, translational pathways and the road ahead.Frontiers in immunology · 2026Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing can reveal valuable insights into cellular heterogeneity within tumour microenvironments (TMEs), paving the way for a deep understanding of cellular mechanisms contributing to cancer. However, high heterogeneity among the same cancer types and low transcriptomic variation in immune cell subsets present challenges for accurate, high-resolution confirmation of cells' identities. Here we present scATOMIC; a modular annotation tool for malignant and non-malignant cells. We trained scATOMIC on >300,000 cancer, immune, and stromal cells defining a pan-cancer reference across 19 common cancers and employ a hierarchical approach, outperforming current classification methods. We extensively confirm scATOMIC's accuracy on 225 tumour biopsies encompassing >350,000 cancer and a variety of TME cells. Lastly, we demonstrate scATOMIC's practical significance to accurately subset breast cancers into clinically relevant subtypes and predict tumours' primary origin across metastatic cancers. Our approach represents a broadly applicable strategy to analyse multicellular cancer TMEs.
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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.