Quantitative Proteomics Reveals Subset-Specific Viral Recognition in Dendritic Cells

Abstract

Dendritic cell (DC) populations consist of multiple subsets that are essential orchestrators of the immune system. Technological limitations have so far prevented systems-wide accurate proteome comparison of rare cell populations in vivo. Here, we used high-resolution mass spectrometry-based proteomics, combined with label-free quantitation algorithms, to determine the proteome of mouse splenic conventional and plasmacytoid DC subsets to a depth of 5,780 and 6,664 proteins, respectively. We found mutually exclusive expression of pattern recognition pathways not previously known to be different among conventional DC subsets. Our experiments assigned key viral recognition functions to be exclusively expressed in CD4(+) and double-negative DCs. The CD8alpha(+) DCs largely lack the receptors required to sense certain viruses in the cytoplasm. By avoiding activation via cytoplasmic receptors, including retinoic acid-inducible gene I, CD8alpha(+) DCs likely gain a window of opportunity to process and present viral antigens before activation-induced shutdown of antigen presentation pathways occurs.

From skin dendritic cells to a simplified classification of human and mouse dendritic cell subsets

“…They include (i) a side-by-side comparison of the phenotypes, gene expression programs and proteomes [44,45] [1,2]. pDC detect RNA and DNA from viruses and RNA/DNA/ immunocomplexes through two endosomal sensors, TLR7 and TLR9, respectively, both of which induce secretion of IFN-I through the MyD88-IRF7 signaling pathway [3][4][5].…”

“…Hence, the specific expression of XCR1 on mouse CD8a 1 LT-DC and human BDCA3 1 DC likely contributes to their high ability for CD8 1 T-cell activation [40,41]. Both human BDCA3 1 LT-DC and mouse CD8a 1 LT-DC express high levels of TLR3 and contain low to undetectable levels of the cytosolic RNA or DNA sensors RIG-I, MDA5 and DAI under steady-state conditions, [43,44]. In contrast, human BDCA1 1 and mouse CD11b 1 LT-DC express higher levels of PRR involved in bacteria or fungi recognition such as TLR1, TLR6, and specific members of the lectin and Nod-like receptor families [43,45].…”

Label free quantitative proteomics reveals the role of miR-200b in androgen-independent prostate cancer cells

“…Cysteine carbamidomethylation was defined as a fixed modification, while protein N-terminal acetylation and methionine oxidation were defined as variable modifications for database searching. Label-free quantification was carried out in MaxQuant, as described elsewhere [12]. The peptide spectrum match (PSM) was filtered by Posterior Error Probability (PEP).…”

Dendritic cell subsets involved in type I IFN induction in mouse measles virus infection models

“…In vitro infection assays showed that isolated cell subsets of CD11c + DCs, but not T or B cells, mainly produced (Table I) (Edwards et al, 2003, Luber et al, 2010. Mouse pDCs express most TLRs except TLR3 and therefore respond to a wide range of pathogen-associated molecular patterns including TLR7 ligand (Boonstra et al, 2003, Edwards et al, 2003.…”