Genome-scale CRISPR screen identifies TRIM2 and SLC35A1 associated with porcine epidemic diarrhoea virus infection

Jieru Wang; Hailong Liu; Yuqing Yang; Yubei Tan; Limeng Sun; Zishi Guo; Xiaoyu Zeng; Zichang Wang; Sheng Li; Lei Yin; Dongdong Yin; Xuehuai Shen; Yin Dai; Xiangdong Liu; Jinxue Ruan; Xinyun Li; Shuhong Zhao; Guiqing Peng; Xiaocheng Pan; Chonglong Wang; Shengsong Xie

doi:10.1016/j.ijbiomac.2023.125962

Genome-scale CRISPR screen identifies TRIM2 and SLC35A1 associated with porcine epidemic diarrhoea virus infection

Int J Biol Macromol. 2023 Oct 1:250:125962. doi: 10.1016/j.ijbiomac.2023.125962. Epub 2023 Jul 25.

Authors

Jieru Wang¹, Hailong Liu², Yuqing Yang², Yubei Tan³, Limeng Sun³, Zishi Guo², Xiaoyu Zeng¹, Zichang Wang², Sheng Li², Lei Yin¹, Dongdong Yin¹, Xuehuai Shen¹, Yin Dai¹, Xiangdong Liu², Jinxue Ruan², Xinyun Li⁴, Shuhong Zhao⁴, Guiqing Peng⁵, Xiaocheng Pan⁶, Chonglong Wang⁷, Shengsong Xie⁸

Affiliations

¹ Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
² Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.
³ Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Wuhan 430070, China.
⁴ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
⁵ Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Wuhan 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: penggq@mail.hzau.edu.cn.
⁶ Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China. Electronic address: pxcpyq@sina.com.
⁷ Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China. Electronic address: ahwchl@163.com.
⁸ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Wuhan 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: ssxie@mail.hzau.edu.cn.

PMID: 37499712
DOI: 10.1016/j.ijbiomac.2023.125962

Abstract

Porcine epidemic diarrhoea (PED) caused by the porcine epidemic diarrhoea virus (PEDV) is the most devastating disease in the global pig industry due to its high mortality rate in piglets. The host factors critical for PEDV replication are poorly understood. Here, we designed a pooled African green monkey genome-scale CRISPR/Cas9 knockout (VeroCKO) library containing 75,608 single guide RNAs targeting 18,993 protein-coding genes. Subsequently, we use the VeroCKO library to identify key host factors facilitating PEDV infection in Vero E6 cells. Several previously unreported genes associated with PEDV infection are highly enriched post-PEDV selection. We discovered that knocking out the tripartite motif 2 (TRIM2) and the solute carrier family 35 member A1 (SLC35A1) inhibited PEDV replication. Virtual screening and molecular docking approaches showed that chem-80,048,685 (M2) s ignificantly inhibited PEDV attachment and late replication by impeding SLC35A1. Furthermore, we found that knocking out SLC35A1 in Vero E6 cells upregulated a disintegrin and metalloprotease protein-17 (ADAM17) by splicing porcine aminopeptidase N (pAPN) and angiotensin-converting enzyme 2 (ACE2) ectodomains to reduce PEDV-infection in a CMP-Sialic Acid (CMP-SA) cell entry-independent manner. These findings provide a new perspective for a better understanding of host-pathogen interactions and new therapeutic targets for PEDV infection.

Keywords: CRISPR screen; PEDV; SLC35A1; Small-molecule inhibitors; TRIM2.