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Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts

Mandal, S and Tejaswi, T and Janivara, R and Srikrishnan, S and Thakur, P and Sahoo, S and Chakraborty, P and Sohal, SS and Levine, H and George, JT and Jolly, MK (2022) Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts. In: Biomolecules, 12 (1).

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Official URL: https://doi.org/10.3390/biom12010029

Abstract

Epithelial-mesenchymal plasticity (EMP) underlies embryonic development, wound healing, and cancer metastasis and fibrosis. Cancer cells exhibiting EMP often have more aggressive behavior, characterized by drug resistance, and tumor-initiating and immuno-evasive traits. Thus, the EMP status of cancer cells can be a critical indicator of patient prognosis. Here, we compare three distinct transcriptomic-based metrics�each derived using a different gene list and algorithm�that quantify the EMP spectrum. Our results for over 80 cancer-related RNA-seq datasets reveal a high degree of concordance among these metrics in quantifying the extent of EMP. Moreover, each metric, despite being trained on cancer expression profiles, recapitulates the expected changes in EMP scores for non-cancer contexts such as lung fibrosis and cellular reprogramming into induced pluripotent stem cells. Thus, we offer a scoring platform to quantify the extent of EMP in vitro and in vivo for diverse biological applications including cancer. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Item Type: Journal Article
Publication: Biomolecules
Publisher: MDPI
Additional Information: The copyright for this article belongs to the Author.
Keywords: messenger RNA; transcription factor Sox2; uvomorulin, Article; cystic fibrosis; human; tissue microarray; upregulation
Department/Centre: Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
UG Programme
Date Deposited: 12 Jan 2022 05:45
Last Modified: 12 Jan 2022 05:45
URI: http://eprints.iisc.ac.in/id/eprint/70921

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