ArticleScientific reports2019
Pheno-seq - linking visual features and gene expression in 3D cell culture systems.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Uncovering functional divergence and cellular clusters with specific gene signatures in HNSCC clonal spheroids.Cell communication and signaling : CCS · 2025Article
- Review
- Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging.Nature communications · 2022Article
- Article
- Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.Nature methods · 2022Article
- Organoids in image-based phenotypic chemical screens.Experimental & molecular medicine · 2021Review
- Volumetric growth tracking of patient-derived cancer organoids using optical coherence tomography.Biomedical optics express · 2021Article
- stochprofML: stochastic profiling using maximum likelihood estimation in R.BMC bioinformatics · 2021Article
- Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer.Cancers · 2021Article
- Patient-derived cancer organoid tracking with wide-field one-photon redox imaging to assess treatment response.Journal of biomedical optics · 2021Article
- cola: an R/Bioconductor package for consensus partitioning through a general framework.Nucleic acids research · 2021Article
- Engineered Tools to Study Intercellular Communication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Deterministic culturing of single cells in 3D.Scientific reports · 2020Article
- 'Omics Approaches to Explore the Breast Cancer Landscape.Frontiers in cell and developmental biology · 2019Review
- Review
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Patient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce "pheno-seq" to directly link visual features of 3D cell culture systems with profiling their transcriptome. As prototypic applications breast and colorectal cancer (CRC) spheroids were analyzed by pheno-seq. We identified characteristic gene expression signatures of epithelial-to-mesenchymal transition that are associated with invasive growth behavior of clonal breast cancer spheroids. Furthermore, we linked long-term proliferative capacity in a patient-derived model of CRC to a lowly abundant PROX1-positive cancer stem cell subtype. We anticipate that the ability to integrate transcriptome analysis and morphological patho-phenotypes of cancer cells will provide novel insight on the molecular origins of intratumor heterogeneity.
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