TY - JOUR
T1 - The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics
AU - Nicolet, Benoît P.
AU - Wolkers, Monika C.
N1 - Funding Information: Our study was supported by the Oncode Institute (grant to M. Wolkers), and the European research council (ERC-Printers 817533). These funding bodies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to thank Branka Popovic and Nordin Zandhuis for critical reading of this manuscript. Publisher Copyright: © 2022 Nicolet, Wolkers. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2022/10/1
Y1 - 2022/10/1
N2 - T cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and mass spectrometry data of primary human CD8+ T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3’UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.
AB - T cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and mass spectrometry data of primary human CD8+ T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3’UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.
UR - http://www.scopus.com/inward/record.url?scp=85140415612&partnerID=8YFLogxK
U2 - https://doi.org/10.1371/journal.pone.0276294
DO - https://doi.org/10.1371/journal.pone.0276294
M3 - Article
C2 - 36260607
SN - 1932-6203
VL - 17
JO - PLOS ONE
JF - PLOS ONE
IS - 10 October
M1 - e0276294
ER -