Proteomics of protein trafficking by in vivo tissue-specific labeling

Ilia A. Droujinine (), Amanda S. Meyer, Dan Wang, Namrata D. Udeshi, Yanhui Hu, David Rocco, Jill A. McMahon, Rui Yang, JinJin Guo, Luye Mu, Dominique K. Carey, Tanya Svinkina, Rebecca Zeng, Tess Branon, Areya Tabatabai, Justin A. Bosch, John M. Asara, Alice Y. Ting, Steven A. Carr, Andrew P. McMahon and Norbert Perrimon ()
Additional contact information
Ilia A. Droujinine: Department of Genetics, Blavatnik Institute, Harvard Medical School
Amanda S. Meyer: University of Southern California
Dan Wang: Department of Genetics, Blavatnik Institute, Harvard Medical School
Namrata D. Udeshi: Broad Institute of Harvard and MIT
Yanhui Hu: Department of Genetics, Blavatnik Institute, Harvard Medical School
David Rocco: Department of Genetics, Blavatnik Institute, Harvard Medical School
Jill A. McMahon: University of Southern California
Rui Yang: University of Southern California
JinJin Guo: University of Southern California
Luye Mu: Yale University
Dominique K. Carey: Broad Institute of Harvard and MIT
Tanya Svinkina: Broad Institute of Harvard and MIT
Rebecca Zeng: Department of Genetics, Blavatnik Institute, Harvard Medical School
Tess Branon: Chan Zuckerberg Biohub
Areya Tabatabai: Department of Genetics, Blavatnik Institute, Harvard Medical School
Justin A. Bosch: Department of Genetics, Blavatnik Institute, Harvard Medical School
John M. Asara: Department of Medicine, Harvard Medical School
Alice Y. Ting: Chan Zuckerberg Biohub
Steven A. Carr: Broad Institute of Harvard and MIT
Andrew P. McMahon: University of Southern California
Norbert Perrimon: Department of Genetics, Blavatnik Institute, Harvard Medical School

Nature Communications, 2021, vol. 12, issue 1, 1-22

Abstract: Abstract Conventional approaches to identify secreted factors that regulate homeostasis are limited in their abilities to identify the tissues/cells of origin and destination. We established a platform to identify secreted protein trafficking between organs using an engineered biotin ligase (BirA*G3) that biotinylates, promiscuously, proteins in a subcellular compartment of one tissue. Subsequently, biotinylated proteins are affinity-enriched and identified from distal organs using quantitative mass spectrometry. Applying this approach in Drosophila, we identify 51 muscle-secreted proteins from heads and 269 fat body-secreted proteins from legs/muscles, including CG2145 (human ortholog ENDOU) that binds directly to muscles and promotes activity. In addition, in mice, we identify 291 serum proteins secreted from conditional BirA*G3 embryo stem cell-derived teratomas, including low-abundance proteins with hormonal properties. Our findings indicate that the communication network of secreted proteins is vast. This approach has broad potential across different model systems to identify cell-specific secretomes and mediators of interorgan communication in health or disease.

Date: 2021
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DOI: 10.1038/s41467-021-22599-x

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