Pheno-seq - linking visual features and gene expression in 3D cell culture systems.

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ID: 53485
2019
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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.
Reference Key
tirier2019phenoseqscientific Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Tirier, Stephan M;Park, Jeongbin;Preußer, Friedrich;Amrhein, Lisa;Gu, Zuguang;Steiger, Simon;Mallm, Jan-Philipp;Krieger, Teresa;Waschow, Marcel;Eismann, Björn;Gut, Marta;Gut, Ivo G;Rippe, Karsten;Schlesner, Matthias;Theis, Fabian;Fuchs, Christiane;Ball, Claudia R;Glimm, Hanno;Eils, Roland;Conrad, Christian;
Journal Scientific reports
Year 2019
DOI
10.1038/s41598-019-48771-4
URL
Keywords
banking regulations dodd-frank act fdic insurance fiduciary activities financial reporting governmental oversight

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