Secreted polypeptides are a fundamental axis of intercellular and endocrine communication. However, a global understanding of the composition and dynamics of cellular secretomes in intact mammalian organisms has been lacking. Here, we introduce a proximity biotinylation strategy that enables labeling, detection and enrichment of secreted polypeptides in a cell type-selective manner in mice. We generate a proteomic atlas of hepatocyte, myocyte, pericyte and myeloid cell secretomes by direct purification of biotinylated secreted proteins from blood plasma. Our secretome dataset validates known cell type–protein pairs, reveals secreted polypeptides that distinguish between cell types and identifies new cellular sources for classical plasma proteins. Lastly, we uncover a dynamic and previously undescribed nutrient-dependent reprogramming of the hepatocyte secretome characterized by the increased unconventional secretion of the cytosolic enzyme betaine–homocysteine S-methyltransferase (BHMT). This secretome profiling strategy enables dynamic and cell type-specific dissection of the plasma proteome and the secreted polypeptides that mediate intercellular signaling.
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The authors declare that data supporting the findings of this study are available within the paper and its Supplementary Information files. Figs. 3, 5 and 6 have associated raw data provided in Supplementary Tables 1–4. All proteomic data generated here are publicly available on ProteomeXchange under project accession no. PXD021602. Source data are provided with this paper.
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We thank members of the Long, Bertozzi, Svensson and Abu-Remaileh labs for helpful discussions. We gratefully acknowledge the staff at the Penn Vector Core for the production of AAVs. This work was supported by the US National Institutes of Health (DK105203 and DK124265 to J.Z.L. and K00CA21245403 to N.M.R.) and the Stanford Diabetes Research Center (P30DK116074).
The authors declare no competing interests.
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Supplementary Figs. 1–13
LC–MS/MS proteomic analysis of streptavidin-purified plasma proteins from mice transduced with AAV-Tbg-Mem, AAV-Tbg-Cyto or AAV-Tbg-ER viruses or control mice. Statistical comparisons were made using ANOVA and Student’s two-way t-test.
LC–MS/MS proteomic analysis of streptavidin-purified liver proteins from mice transduced with AAV-Tbg-Mem, AAV-Tbg-Cyto or AAV-Tbg-ER viruses.
LC–MS/MS proteomic analysis of streptavidin-purified plasma from control mice (chow) without viral transduction or mice transduced with AAV-Tbg-Cyto after 2 weeks of chow or HFHS diet. Statistical comparisons were made using ANOVA and Student’s two-way t-test.
LC–MS/MS proteomic analysis of streptavidin-purified plasma from mice. The following cell types correspond to the following mouse genotypes and viruses: hepatocytes (albumin-Cre, AAV-FLEx), myocytes (WT mice, AAV-tMCK), pericytes (Pdgfrb-creERT2, AAV-FLEx), myeloid cells (LysM-creERT2, AAV-FLEx). Statistical comparisons were made using ANOVA.
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Wei, W., Riley, N.M., Yang, A.C. et al. Cell type-selective secretome profiling in vivo. Nat Chem Biol 17, 326–334 (2021). https://doi.org/10.1038/s41589-020-00698-y
Nature Communications (2021)