Integrated proteomic and transcriptomic landscape of macrophages in mouse tissues

Jingbo Qie, Yang Liu, Yunzhi Wang, Fan Zhang, Zhaoyu Qin, Sha Tian, Mingwei Liu, Kai Li, Wenhao Shi, Lei Song, Mingjun Sun, Yexin Tong, Ping Hu, Tao Gong, Xiaqiong Wang, Yi Huang, Bolong Lin, Xuesen Zheng, Rongbin Zhou, Jie Lv, Changsheng Du, Yi Wang, Jun Qin, Wenjun Yang (), Fuchu He () and Chen Ding ()
Additional contact information
Jingbo Qie: Fudan University
Yang Liu: Fudan University
Yunzhi Wang: Fudan University
Fan Zhang: Fudan University
Zhaoyu Qin: Fudan University
Sha Tian: Fudan University
Mingwei Liu: National Center for Protein Sciences
Kai Li: National Center for Protein Sciences
Wenhao Shi: National Center for Protein Sciences
Lei Song: National Center for Protein Sciences
Mingjun Sun: Fudan University
Yexin Tong: Fudan University
Ping Hu: Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine
Tao Gong: University of Science and Technology of China
Xiaqiong Wang: University of Science and Technology of China
Yi Huang: University of Science and Technology of China
Bolong Lin: University of Science and Technology of China
Xuesen Zheng: University of Science and Technology of China
Rongbin Zhou: University of Science and Technology of China
Jie Lv: Tongji University
Changsheng Du: Tongji University
Yi Wang: National Center for Protein Sciences
Jun Qin: Fudan University
Wenjun Yang: Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine
Fuchu He: Fudan University
Chen Ding: Fudan University

Nature Communications, 2022, vol. 13, issue 1, 1-23

Abstract: Abstract Macrophages are involved in tissue homeostasis and are critical for innate immune responses, yet distinct macrophage populations in different tissues exhibit diverse gene expression patterns and biological processes. While tissue-specific macrophage epigenomic and transcriptomic profiles have been reported, proteomes of different macrophage populations remain poorly characterized. Here we use mass spectrometry and bulk RNA sequencing to assess the proteomic and transcriptomic patterns, respectively, of 10 primary macrophage populations from seven mouse tissues, bone marrow-derived macrophages and the cell line RAW264.7. The results show distinct proteomic landscape and protein copy numbers between tissue-resident and recruited macrophages. Construction of a hierarchical regulatory network finds cell-type-specific transcription factors of macrophages serving as hubs for denoting tissue and functional identity of individual macrophage subsets. Finally, Il18 is validated to be essential in distinguishing molecular signatures and cellular function features between tissue-resident and recruited macrophages in the lung and liver. In summary, these deposited datasets and our open proteome server ( http://macrophage.mouseprotein.cn ) integrating all information will provide a valuable resource for future functional and mechanistic studies of mouse macrophages.

Date: 2022
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DOI: 10.1038/s41467-022-35095-7

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