A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis
Authors
Jianting Shi, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Xun Wu, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Ziyi Wang, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Fang Li, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Yujiao Meng, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Rebecca M. Moore, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Jian Cui, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Chenyi Xue, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
Katherine R. Croce, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
Arif Yurdagul, Department of Molecular & Cellular Physiology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, LA, USA.
John G. Doench, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Wei Li, Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
Konstantinos S. Zarbalis, University of California at Davis, Department of Pathology and Laboratory Medicine, Sacramento, CA, 95817, USA.
Ira Tabas, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
Ai Yamamoto, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
Hanrui Zhang, Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA. hz2418@cumc.columbia.edu.
Document Type
Journal Article
Publication Date
12-24-2022
Journal
Nature communications
DOI
10.1038/s41467-022-35604-8
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.
APA Citation
Shi, Jianting; Wu, Xun; Wang, Ziyi; Li, Fang; Meng, Yujiao; Moore, Rebecca M.; Cui, Jian; Xue, Chenyi; Croce, Katherine R.; Yurdagul, Arif; Doench, John G.; Li, Wei; Zarbalis, Konstantinos S.; Tabas, Ira; Yamamoto, Ai; and Zhang, Hanrui, "A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis" (2022). GW Authored Works. Paper 2059.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/2059
Department
Genomics and Precision Medicine
