A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis

Jianting Shi, Xun Wu, Ziyi Wang, Fang Li, Yujiao Meng, Rebecca M. Moore, Jian Cui, Chenyi Xue, Katherine R. Croce, Arif Yurdagul, John G. Doench, Wei Li, Konstantinos S. Zarbalis, Ira Tabas, Ai Yamamoto and Hanrui Zhang ()
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Jianting Shi: Columbia University Irving Medical Center
Xun Wu: Columbia University Irving Medical Center
Ziyi Wang: Columbia University Irving Medical Center
Fang Li: Columbia University Irving Medical Center
Yujiao Meng: Columbia University Irving Medical Center
Rebecca M. Moore: Columbia University Irving Medical Center
Jian Cui: Columbia University Irving Medical Center
Chenyi Xue: Columbia University Irving Medical Center
Katherine R. Croce: Columbia University
Arif Yurdagul: Louisiana State University Health Sciences Center at Shreveport
John G. Doench: Broad Institute of MIT and Harvard
Wei Li: Center for Genetic Medicine Research, Children’s National Hospital
Konstantinos S. Zarbalis: Department of Pathology and Laboratory Medicine
Ira Tabas: Columbia University
Ai Yamamoto: Columbia University
Hanrui Zhang: Columbia University Irving Medical Center

Nature Communications, 2022, vol. 13, issue 1, 1-19

Abstract: Abstract Phagocytic clearance of dying cells, termed efferocytosis, is essential for maintaining tissue homeostasis, yet our understanding of efferocytosis regulation remains incomplete. Here we perform a FACS-based, genome-wide CRISPR knockout screen in primary mouse macrophages to search for novel regulators of efferocytosis. The results show that Wdfy3 knockout in macrophages specifically impairs uptake, but not binding, of apoptotic cells due to defective actin disassembly. Additionally, WDFY3 interacts with GABARAP, thus facilitating LC3 lipidation and subsequent lysosomal acidification to permit the degradation of apoptotic cell components. Mechanistically, while the C-terminus of WDFY3 is sufficient to rescue the impaired degradation induced by Wdfy3 knockout, full-length WDFY3 is required to reconstitute the uptake of apoptotic cells. Finally, WDFY3 is also required for efficient efferocytosis in vivo in mice and in vitro in primary human macrophages. This work thus expands our knowledge of the mechanisms of macrophage efferocytosis, as well as supports genome-wide CRISPR screen as a platform for interrogating complex functional phenotypes in primary macrophages.

Date: 2022
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DOI: 10.1038/s41467-022-35604-8

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