Using a high-throughput approach that combines enteroid monolayers and quantitative imaging, scientists identified conditions that enrich for specific cell types as well as interactions between pathways.
Sanman, L. E., Chen, I. W., Bieber, J. M., Steri, V., Trentesaux, C., Hann, B., Klein, O. D., Wu, L. F., & Altschuler, S. J. (2021). Transit-Amplifying Cells Coordinate Changes in Intestinal Epithelial Cell-Type Composition. Developmental Cell, 0(0). https://doi.org/10.1016/j.devcel.2020.12.020Cite
Scientists employed RNA-sequencing to asses transcriptomic response to ethanol exposure in 3D organoid lines derived from healthy colon. Paired regression analysis identified 2,162 differentially expressed genes in response to ethanol.
Devall, M., Plummer, S. J., Bryant, J., Jennelle, L. T., Eaton, S., Dampier, C. H., Huyghe, J. R., Peters, U., Powell, S. M., & Casey, G. (2021). Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model. Scientific Reports, 11(1), 432. https://doi.org/10.1038/s41598-020-80240-1Cite
The authors used single cell RNA-sequencing of patient tumors to identify three prognostic surface markers (LYPD3, TACSTD2, and LY6D) which correlated with myocardin-related transcription factor (nMRTF) and resistance to Smoothened inhibitors. The nMRTF cell state resembled transit-amplifying cells of the hair follicle matrix, with AP-1 and TGFß cooperativity driving nMRTF activation.
Yao, C. D., Haensel, D., Gaddam, S., Patel, T., Atwood, S. X., Sarin, K. Y., Whitson, R. J., McKellar, S., Shankar, G., Aasi, S., Rieger, K., & Oro, A. E. (2020). AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma. Nature Communications, 11(1), 5079. https://doi.org/10.1038/s41467-020-18762-5Cite