The relationship of mRNA with protein expression in CD8⁺T cells associates with gene class and gene characteristics

Abstract

T cell differentiation and activation induces substantial alterations in gene expression. While RNA sequencing and single cell RNA sequencing analysis provided important insights in the gene expression dynamics of T cells, it is not well understood how the mRNA expression translates into the protein landscape. By combining paired RNA-sequencing and mass spectrometry data of primary human CD8 + T cells, we found that mRNA expression is a poor proxy for the overall protein output. Irrespective of the differentiation or activation status, the correlation coefficient of human CD8 + T cells reached a mere 0.41-0.43. Only gene classes that mediate conserved cellular processes such as protein translation or cellular metabolism showed a strong correlation of mRNA with protein expression. In contrast, the mRNA expression and protein output of transcription factors, cell surface molecules, and secreted proteins -including cytokines -only mildly correlated. Conversely, highly conserved genes correlated well with the protein output. This was also true for the presence of AU-rich elements in the 3'untranslated region, in particular for mRNAs that encode secreted proteins.In conclusion, the in-depth characterization of the transcriptome and proteome in human CD8 + T cells emphasizes the need of combined mRNA and protein analysis for our understanding of T cell biology and function.

Toll‐like receptor‐2/7‐mediated T cell activation: An innate potential to augment CD8+ T cell cytokine production

“…By functioning as binding sites for RBPs, microRNAs and long non‐coding RNAs, these cis ‐regulatory elements together determine the protein output by influencing mRNA stability, decay, localization and translational rate 72 . Therefore, cytokine mRNA and protein levels do not always correlate and are dependent on T cell activation status 88‐90 …”

T cells at work: How post‐transcriptional mechanisms control T cell homeostasis and activation

“…A remarkable feature of T cell priming and activation is the substantial increase of proteins per cell [ 1 , 2 , 3 , 24 , 25 , 26 , 27 ]. Murine naïve CD8 + T cells that were activated for 24 h through the TCR tripled their protein amount [ 2 , 28 ].…”

“…This translated into an increase in copy numbers for over 6,000 proteins and an increase in cellular concentration for over 3,000 proteins [ 2 ]. Likewise, human effector and memory CD8 + T cells double their protein content per cell after 4 h of activation [ 1 , 25 ]. Thus, T cell activation substantially alters the proteome landscape of T cells.…”

Post‐transcriptional control of T‐cell cytokine production: Implications for cancer therapy

“…Lastly, cis ‐elements present in the 5’ and 3’UTRs of mRNA transcripts, functioning as binding hubs for miRNAs and RNA binding proteins (RBPs), can also alter mRNA localization, stability and translation. As such, the amount of effector molecule mRNA and the amount of effector molecules produced by T cells do not always correlate at a 1:1 ratio [66‐69] and depend on cellular activation status. Here, the current knowledge regarding the contribution of (alternative) splicing, RNA cis ‐elements and RBP binding on T‐cell cytokine production is discussed.…”

“…T cells express many other RBPs that can also influence T‐cell cytokine production [38,43,48,49,69]. Another AREbp that has been shown to be important in regulating T‐cell effector function is human antigen R (HuR) or ELAVL1 [93,119].…”