@article{76e9a749162146d1a9b969a409759135,
title = "Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach",
abstract = "Epithelial–mesenchymal transition (EMT) is a dynamic and complex cellular process that is known to be hijacked by cancer cells to facilitate invasion, metastasis and therapeutic resistance. Several quantitative measures to assess the interplay between EMT and cancer progression are available, based on large scale genome and transcriptome data. However, these large scale multi-omics studies have repeatedly illustrated a lack of correlation in mRNA and protein abundances that may be influenced by diverse post-translational regulation. Hence, it is imperative to understand how changes in the EMT proteome are associated with the process of oncogenic transformation. To this effect, we developed a parallel reaction monitoring-based targeted proteomics method for quantifying abundances of EMT-associated proteins across cancer cell lines. Our study revealed that quantitative measurement of EMT proteome which enabled a more accurate assessment than transcriptomics data and revealed specific discrepancies against a backdrop of generally strong concordance between proteomic and transcriptomic data. We further demonstrated that changes in our EMT proteome panel might play a role in tumor transformation across cancer types. In future, this EMT panel assay has the potential to be used for clinical samples to guide treatment choices and to congregate functional information for the development and advancing novel therapeutics.",
keywords = "Epithelial-mesenchymal transition, Mass spectrometry, Pan-cancer targeted proteomics, Parallel reaction monitoring",
author = "Jain, {Ankit P.} and Janani Sambath and Gajanan Sathe and George, {Irene A.} and Akhilesh Pandey and Thompson, {Erik W.} and Prashant Kumar",
note = "Funding Information: This work was supported in part by grant funding from the Australia-India Council of the Department of Foreign Affairs and Trade, Australia (280-AIC 2017: A cross-cultural landscape to improve breast cancer outcomes; EWT, PK). The Translational Research Institute (EWT) receives support from the Australian Government. This research was funded in part by the Department of Science and Technology (DST), Ramanujan Fellowship, Government of India, grant number SB/S2/RJN-077/2015 awarded to PK. This work was also supported by the DBT/Wellcome Trust India Alliance Margdarshi Fellowship (Grant Number IA/M/15/1/502023) awarded to AP. IAG is a recipient of Junior Research Fellowship from Council of Scientific and Industrial Research (CSIR), Government of India. We thank the Department of Biotechnology (DBT), Government of India, for research support to the Institute of Bioinformatics (IOB), Bangalore. We thank the “Ma-nipal Academy of Higher Education”, Madhav Nagar, Manipal 576104, India, for research support to the Institute of Bio-informatics. Funding Information: Data used in this publication were generated by the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC) and Cancer Cell Line Encyclopedia (CCLE). We thank Jean Paul Thiery (Department of Biochemistry, National University of Singapore, Singapore) for providing bladder cancer cell lines. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = dec,
doi = "10.1186/s12967-021-03227-0",
language = "English (US)",
volume = "20",
journal = "Journal of Translational Medicine",
issn = "1479-5876",
publisher = "BioMed Central",
number = "1",
}