ArticleiScience2024
Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer.
Article in iScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Characterization of SPP1 + macrophages and their correlation with resistance to neoadjuvant chemotherapy in colorectal cancer liver metastasis.Molecular biomedicine · 2026Article
- DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage.Briefings in bioinformatics · 2026Article
- Single-cell and spatial transcriptomics identify CAPG as a key driver of cisplatin resistance in bladder cancer.Functional & integrative genomics · 2026Article
- Mutation-specific dynamics of dedifferentiation trajectories and tumor-stromal interactions in thyroid cancer.Molecular cancer · 2026Article
- A machine learning-guided epithelial plasticity score refines prognostication and immune-context stratification in muscle-invasive bladder cancer.Discover oncology · 2026Article
- A Tumor-Promoting Inflammatory SPP1+ Macrophage-IL6-CRP Axis Drives Immune Dysfunction in Bladder Cancer.Cancer discovery · 2026Article
- Article
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- Article
- Structure-based virtual screening identifies ethyl rosmarinate as a SLC1A6-targeted therapeutic candidate for bladder cancer.Frontiers in pharmacology · 2026Article
- Transcriptional regulatory network analysis identifies GRN as a key regulator bridging chemotherapy and immunotherapy response in small cell lung cancer.Journal of hematology & oncology · 2025Article
- β2-integrins as biomarkers in urothelial cancer.PloS one · 2025Article
- Therapeutic implications of cancer-associated fibroblast heterogeneity: insights from single-cell and multi-omics analysis.Frontiers in immunology · 2025Article
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Authors and funding
13 authors.
Funding
Abstract
Interactions within the tumor microenvironment (TME) significantly influence tumor progression and treatment responses. While single-cell RNA sequencing (scRNA-seq) and spatial genomics facilitate TME exploration, many clinical cohorts are assessed at the bulk tissue level. Integrating scRNA-seq and bulk tissue RNA-seq data through computational deconvolution is essential for obtaining clinically relevant insights. Our method, ProM, enables the examination of major and minor cell types. Through evaluation against existing methods using paired single-cell and bulk RNA sequencing of human urothelial cancer (UC) samples, ProM demonstrates superiority. Application to UC cohorts treated with immune checkpoint inhibitors reveals pre-treatment cellular features associated with poor outcomes, such as elevated SPP1 expression in macrophage/monocytes (MM). Our deconvolution method and paired single-cell and bulk tissue RNA-seq dataset contribute novel insights into TME heterogeneity and resistance to immune checkpoint blockade.
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Registered trials
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