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148415 - Transcriptomic-based quantification of the epithelial.pdf (3.73 MB)

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

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posted on 2023-05-21, 05:03 authored by Mandal, S, Tejaswi, T, Janivara, R, Srikrishnan, S, Thakur, P, Sahoo, S, Chakraborty, P, Sukhwinder SohalSukhwinder Sohal, Levine, H, George, JT, Jolly, MK
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 algorithms 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.

History

Publication title

Biomolecules

Volume

12

Article number

29

Number

29

Pagination

1-21

ISSN

2218-273X

Department/School

School of Health Sciences

Publisher

MDPIAG

Place of publication

Switzerland

Rights statement

Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/).

Repository Status

  • Open

Socio-economic Objectives

Diagnosis of human diseases and conditions; Prevention of human diseases and conditions; Treatment of human diseases and conditions

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    University Of Tasmania

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