title: A Cell-type-resolved Liver Proteome.
abstract: Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level.
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China.
authors: Chen
authors: C
authors: Ding
authors: ¶School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors: Yanyan
authors: Y
authors: Li
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Feifei
authors: F
authors: Guo
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Ying
authors: Y
authors: Jiang
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Wantao
authors: W
authors: Ying
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Dong
authors: D
authors: Li
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Dong
authors: D
authors: Yang
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Xia
authors: X
authors: Xia
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Wanlin
authors: W
authors: Liu
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Yan
authors: Y
authors: Zhao
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ¶School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors: Yangzhige
authors: Y
authors: He
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Xianyu
authors: X
authors: Li
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Wei
authors: W
authors: Sun
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Qiongming
authors: Q
authors: Liu
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Lei
authors: L
authors: Song
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Bei
authors: B
authors: Zhen
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China.
authors: Pumin
authors: P
authors: Zhang
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; qianxh1@163.com jqin@bcm.edu hefc@nic.bmi.ac.cn.
authors: Xiaohong
authors: X
authors: Qian
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China qianxh1@163.com jqin@bcm.edu hefc@nic.bmi.ac.cn.
authors: Jun
authors: J
authors: Qin
authors: From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China qianxh1@163.com jqin@bcm.edu hefc@nic.bmi.ac.cn.
authors: Fuchu
authors: F
authors: He
mesh_terms: D000818:Animals; D063990:Gene Ontology; D008099:Liver / Q000166:cytology* / Q000378:metabolism; D051379:Mice; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D020543:Proteome