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Tirier, S.M.* ; Park, J.* ; Preußer, F.* ; Amrhein, L. ; Gu, Z.* ; Steiger, S.* ; Mallm, J.P.* ; Krieger, T.* ; Waschow, M.* ; Eismann, B.* ; Gut, M.* ; Gut, I.G.* ; Rippe, K.* ; Schlesner, M.* ; Theis, F.J. ; Fuchs, C. ; Ball, C.R.* ; Glimm, H.* ; Conrad, C.*

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

Sci. Rep. 9:12367 (2019)

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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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