ArticleNature communications2017
Estimation of immune cell content in tumour tissue using single-cell RNA-seq data.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
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Who cites it
165 citing papers in PubMed.
- Tumour microenvironment characterisation to stratify patients for hyperthermic intraperitoneal chemotherapy in high-grade serous ovarian cancer (OVHIPEC-1).British journal of cancer · 2024Trial
- The Chromatin Accessibility Landscape of Peripheral Blood Mononuclear Cells in Patients With Systemic Lupus Erythematosus at Single-Cell Resolution.Frontiers in immunology · 2021Trial
- Single-cell RNA sequencing of terminal ileal biopsies identifies signatures of Crohn's disease pathogenesis.Nature genetics · 2026Article
- A Multiresolution Breast Cancer CIBERSORTx Resource Validated for Accuracy, Interpretive Limits, and Biological and Clinical Coherence in Tumor Microenvironment Deconvolution.Methods and protocols · 2026Article
- scPER: A Rigorous Computational Approach to Determine Cellular Subtypes in Tumors Aligned With Cancer Phenotypes From Total RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.Genome biology · 2026Article
- Multiomics reveals the mechanism of KNG1 in promoting tumor progression in adamantinomatous craniopharyngioma.Journal of neuro-oncology · 2026Article
- Article
- Clinical Insights on "Applying Metabolomics and Aptamer-Based Proteomics to Determine Pathophysiologic Differences in Decompensated Cirrhosis Patients Hospitalized with Acute Kidney Injury".Digestive diseases and sciences · 2026Article
- Single-cell RNA transcriptomics divulged altered gene expressions in monocytes and HLA variations in decompensated cirrhosis patients with sepsis.Scientific reports · 2025Article
- Spatial Profiling Identifies Tumor-Associated Stroma Enrichment and MIF as Potential Immunotherapy Targets in Primary Ewing Sarcomas.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Harnessing ovarian cancer ascites for translational science: models, biomarkers, and therapeutics.Molecular cancer · 2025Review
- BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration.Genome biology · 2025Article
- Metabolic Stress-Induced Choline Kinase α (CHKA) Activation in Endothelial Subpopulation Contributes to Diabetes-Associated Microvascular Dysfunction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Approaching the holistic transcriptome-convolution and deconvolution in transcriptomics.Briefings in bioinformatics · 2025Review
- A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor.Scientific data · 2025Article
- Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling.Nature communications · 2025Article
- DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle.Briefings in bioinformatics · 2025Article
- Morphometric analysis of neoplastic cell clusters in high-grade serous ovarian cancer ascites identifies a promising prognostic factor: a retrospective study.Journal of ovarian research · 2025Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As interactions between the immune system and tumour cells are governed by a complex network of cell-cell interactions, knowing the specific immune cell composition of a solid tumour may be essential to predict a patient's response to immunotherapy. Here, we analyse in depth how to derive the cellular composition of a solid tumour from bulk gene expression data by mathematical deconvolution, using indication-specific and cell type-specific reference gene expression profiles (RGEPs) from tumour-derived single-cell RNA sequencing data. We demonstrate that tumour-derived RGEPs are essential for the successful deconvolution and that RGEPs from peripheral blood are insufficient. We distinguish nine major cell types, as well as three T cell subtypes. Using the tumour-derived RGEPs, we can estimate the content of many tumours associated immune and stromal cell types, their therapeutically relevant ratios, as well as an improved gene expression profile of the malignant cells.
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