ArticleOncotarget2017
Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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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.
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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
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
- What are the applications of single-cell RNA sequencing in cancer research: a systematic review.Journal of experimental & clinical cancer research : CR · 2021Pooled it
- Gene expression signatures predict response to therapy with growth hormone.The pharmacogenomics journal · 2021Trial
- Mutation-informed gene pairs to predict melanoma metastasis.Cell communication and signaling : CCS · 2026Article
- Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.Fundamental research · 2026Article
- Consensus spectral clustering with weighted similarity functions for single-cell RNA sequencing data.Communications in statistics: Simulation and computation · 2025Article
- Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication.Computational and structural biotechnology journal · 2024Article
- A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections.Current issues in molecular biology · 2024Article
- Heterogeneity and molecular landscape of melanoma: implications for targeted therapy.Molecular biomedicine · 2024Review
- Review
- Single-cell RNA sequencing in melanoma: what have we learned so far?EBioMedicine · 2024Review
- Mechanisms of Melanoma Progression and Treatment Resistance: Role of Cancer Stem-like Cells.Cancers · 2024Review
- Article
- Fate mapping melanoma persister cells through regression and into recurrent disease in adult zebrafish.Disease models & mechanisms · 2022Article
- Heterogeneity in Melanoma.Cancers · 2022Review
- Characterization of gene cluster heterogeneity in single-cell transcriptomic data within and across cancer types.Biology open · 2022Article
- Persister state-directed transitioning and vulnerability in melanoma.Nature communications · 2022Article
- Transcriptional states of CAR-T infusion relate to neurotoxicity - lessons from high-resolution single-cell SOM expression portraying.Frontiers in immunology · 2022Article
- Cell type identification from single-cell transcriptomes in melanoma.BMC medical genomics · 2021Article
- Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma.iScience · 2021Article
- Cancer cell metabolic plasticity in migration and metastasis.Clinical & experimental metastasis · 2021Review
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy.
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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.