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Cell type-selective secretome profiling in vivo


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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Fig. 1: Biotinylation of secreted polypeptides in cell culture.
Fig. 2: In vivo labeling of the hepatocyte secretome.
Fig. 3: Proteomics of hepatocyte-secreted plasma proteins.
Fig. 4: Dynamic and nutrient-dependent reprogramming of the hepatocyte secretome.
Fig. 5: Nutrient-induced unconventional secretion of hepatocyte BHMT.
Fig. 6: A secretome atlas across four diverse cell types in mice.

Data availability

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 14. 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).

Author information




W.W. generated all constructs used for this study and performed all mouse experiments. N.M.R. performed all proteomic analyses. A.C.Y. and S.M.T. performed histological and immunofluorescence analyses of livers. J.T.K., V.L.L. and M.G.-C. assisted in tissue collection and processing for mouse experiments. C.R.B. and J.Z.L. supervised the work. W.W., N.M.R. and J.Z.L. conceived experiments and wrote the manuscript.

Corresponding author

Correspondence to Jonathan Z. Long.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–13

Reporting Summary

Supplementary Table 1

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.

Supplementary Table 2

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.

Supplementary Table 3

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.

Supplementary Table 4

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.

Source data

Source Data Fig. 1

Uncropped gel images for Fig. 1.

Source Data Fig. 2

Uncropped gel images for Fig. 2.

Source Data Fig. 4

Uncropped gel images for Fig. 4.

Source Data Fig. 5

Uncropped gel images for Fig. 5.

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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).

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