Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells

Abstract

The transcriptional network and protein regulators that govern T helper 17 (Th17) cell differentiation have been studied extensively using advanced genomic approaches. For a better understanding of these biological processes, we have moved a step forward, from gene- to protein-level characterization of Th17 cells. Mass spectrometry–based label-free quantitative (LFQ) proteomics analysis were made of in vitro differentiated murine Th17 and induced regulatory T (iTreg) cells. More than 4,000 proteins, covering almost all subcellular compartments, were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level. Our dataset provides a valuable resource, with new insights into the proteomic characteristics of Th17 and iTreg cells, which may prove useful in developing treatment of autoimmune diseases and developing tumor immunotherapy.

Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization

“…The expression of SATB1 in distinct Th and Treg cells is shown to be conserved between human and mouse (Ribeiro de Almeida et al., 2009, Ahlfors et al., 2010, Beyer et al., 2011). SATB1 expression has been previously reported to be upregulated in mouse Th17 cells (Ciofani et al., 2012, Mohammad et al., 2018). However, we found SATB1 transcription to be downregulated during human Th17 cell differentiation (Tuomela et al., 2012, Tuomela et al., 2016).…”

“…Our recent study identified conserved and diversified gene signatures from the comparison of human and mouse transcriptomes during Th17 cell polarization (Tuomela et al., 2016). To further establish the level of dissimilarity, we made direct comparison with data from a recently published proteomics dataset from mouse Th17 cells cultured for 72 hr (Mohammad et al., 2018). The proteome profiles of CD4+ T cells 72 hr after TCR activation and Th17 polarization were compared using the aforementioned mouse data and the human data from the current study.…”

“…Comparison of the proteins detected in human (5,917 proteins) and mouse (3,731 proteins) revealed high degree of overall overlap as homologs for almost 85% of the mouse proteins were also detected in human (Figure 6A, Table S6). To make the comparison of the differentially regulated proteins more comprehensive, we used a threshold of FDR 0.1 (used in Mohammad et al., 2018) in both datasets to define the DE proteins. In agreement with our previous study (Tuomela et al., 2016), there was very limited overlap between the proteins differentially regulated between Th17 and Th0 cells, respectively, in human and mouse.…”

“…Recently, a number of studies identified a distinct set of differentially regulated proteins when comparing the proteomes of CD4+CD25+ Foxp3 expressing natural Treg cells and induced Treg (iTreg) with CD4+ conventional T cells both in human and mouse (Kubach et al., 2007, Duguet et al., 2017, Cuadrado et al., 2018, Schmidt et al., 2018). Most recently, a study reported Th17 proteome profiles in mouse (Mohammad et al., 2018). Although studies of the molecular profiles and mechanisms governing different Th and Treg cell differentiation have been mostly performed in mouse, previous reports that have compared the transcriptomic profiles of human and mouse have revealed significant differences between the two species (Schwanhüusser et al., 2011, Vogel and Marcotte, 2012).…”

Proteomic Profiling of Mouse Helper T Cell Differentiation

“…However, very few studies have been performed in mouse Th cells. A recent study investigated the differentiation of T cells to Th17 and iTreg subsets providing a valuable resource for further characterization of these cell types. In this study, we set out to perform comprehensive proteome profiling of mouse Th1 and Th2 cells.…”