1
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Zhang W, Tang Y, Yang P, Chen Y, Xu Z, Qi C, Huang H, Liu R, Qin H, Ke H, Huang C, Xu F, Pang P, Zhao Z, Shan H, Xiao F. TMX2 potentiates cell viability of hepatocellular carcinoma by promoting autophagy and mitophagy. Autophagy 2024:1-18. [PMID: 38797513 DOI: 10.1080/15548627.2024.2358732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
The dysregulation of membrane protein expression has been implicated in tumorigenesis and progression, including hepatocellular carcinoma (HCC). In this study, we aimed to identify membrane proteins that modulate HCC viability. To achieve this, we performed a CRISPR activation screen targeting human genes encoding membrane-associated proteins, revealing TMX2 as a potential driver of HCC cell viability. Gain- and loss-of-function experiments demonstrated that TMX2 promoted growth and tumorigenesis of HCC. Clinically, TMX2 was an independent prognostic factor for HCC patients. It was significantly upregulated in HCC tissues and associated with poor prognosis of HCC patients. Mechanistically, TMX2 was demonstrated to promote macroautophagy/autophagy by facilitating KPNB1 nuclear export and TFEB nuclear import. In addition, TMX2 interacted with VDAC2 and VADC3, assisting in the recruitment of PRKN to defective mitochondria to promote cytoprotective mitophagy during oxidative stress. Most interestingly, HCC cells responded to oxidative stress by upregulating TMX2 expression and cell autophagy. Knockdown of TMX2 enhanced the anti-tumor effect of lenvatinib. In conclusion, our findings emphasize the pivotal role of TMX2 in driving the HCC cell viability by promoting both autophagy and mitophagy. These results suggest that TMX2 May serve as a prognostic marker and promising therapeutic target for HCC treatment.Abbreviation: CCCP: Carbonyl cyanide 3-chlorophenylhydrazone; Co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeat; ER: endoplasmic reticulum; HCC: hepatocellular carcinoma; KPNB1: karyopherin subunit beta 1; PRKN: parkin RBR E3 ubiquitin protein ligase; ROS: reactive oxygen species; TFEB: transcription factor EB; TMX2: thioredoxin related transmembrane protein 2; VDAC2: voltage dependent anion channel 2; VDAC3: voltage dependent anion channel 3; WB: western blot.
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Affiliation(s)
- Weiyu Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Yao Tang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Pengfei Yang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Yutong Chen
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Abdominal Oncology, Cancer Center of The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Zhijie Xu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Chunhui Qi
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Hongbin Huang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Ruiyang Liu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Haorui Qin
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Haoying Ke
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Caini Huang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Fuyuan Xu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Pengfei Pang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Zhiju Zhao
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Hong Shan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Fei Xiao
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Kashi Guangdong Institute of Science and Technology, The First People's Hospital of Kashi, Kashi, Xinjiang Uygur Autonomous Region, China
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2
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Clark T, Waller MA, Loo L, Moreno CL, Denes CE, Neely GG. CRISPR activation screens: navigating technologies and applications. Trends Biotechnol 2024:S0167-7799(24)00036-2. [PMID: 38493051 DOI: 10.1016/j.tibtech.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) has become an integral part of the molecular biology toolkit. CRISPRa genetic screens are an exciting high-throughput means of identifying genes the upregulation of which is sufficient to elicit a given phenotype. Activation machinery is continually under development to achieve greater, more robust, and more consistent activation. In this review, we offer a succinct technological overview of available CRISPRa architectures and a comprehensive summary of pooled CRISPRa screens. Furthermore, we discuss contemporary applications of CRISPRa across broad fields of research, with the aim of presenting a view of exciting emerging applications for CRISPRa screening.
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Affiliation(s)
- Teleri Clark
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Christopher E Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia.
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3
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Yang L, Sheets TP, Feng Y, Yu G, Bajgain P, Hsu KS, So D, Seaman S, Lee J, Lin L, Evans CN, Guest MR, Chari R, St. Croix B. Uncovering receptor-ligand interactions using a high-avidity CRISPR activation screening platform. SCIENCE ADVANCES 2024; 10:eadj2445. [PMID: 38354234 PMCID: PMC10866537 DOI: 10.1126/sciadv.adj2445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The majority of clinically approved drugs target proteins that are secreted or cell surface bound. However, further advances in this area have been hindered by the challenging nature of receptor deorphanization, as there are still many secreted and cell-bound proteins with unknown binding partners. Here, we developed an advanced screening platform that combines CRISPR-CAS9 guide-mediated gene activation (CRISPRa) and high-avidity bead-based selection. The CRISPRa platform incorporates serial enrichment and flow cytometry-based monitoring, resulting in substantially improved screening sensitivity for well-known yet weak interactions of the checkpoint inhibitor family. Our approach has successfully revealed that siglec-4 exerts regulatory control over T cell activation through a low affinity trans-interaction with the costimulatory receptor 4-1BB. Our highly efficient screening platform holds great promise for identifying extracellular interactions of uncharacterized receptor-ligand partners, which is essential to develop next-generation therapeutics, including additional immune checkpoint inhibitors.
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Affiliation(s)
- Liping Yang
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Timothy P. Sheets
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Yang Feng
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Guojun Yu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Pradip Bajgain
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Kuo-Sheng Hsu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Daeho So
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Steven Seaman
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Jaewon Lee
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Ling Lin
- Proteomic Instability of Cancer Section, MCGP, NCI, NIH, Frederick, MD 21702, USA
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Mary R. Guest
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Brad St. Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
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Zhou Y, Wang D, Zhou L, Zhou N, Wang Z, Chen J, Pang R, Fu H, Huang Q, Dong F, Cheng H, Zhang H, Tang K, Ma J, Lv J, Cheng T, Fiskesund R, Zhang X, Huang B. Cell softness renders cytotoxic T lymphocytes and T leukemic cells resistant to perforin-mediated killing. Nat Commun 2024; 15:1405. [PMID: 38360940 PMCID: PMC10869718 DOI: 10.1038/s41467-024-45750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 02/03/2024] [Indexed: 02/17/2024] Open
Abstract
Mechanical force contributes to perforin pore formation at immune synapses, thus facilitating the cytotoxic T lymphocytes (CTL)-mediated killing of tumor cells in a unidirectional fashion. How such mechanical cues affect CTL evasion of perforin-mediated autolysis remains unclear. Here we show that activated CTLs use their softness to evade perforin-mediated autolysis, which, however, is shared by T leukemic cells to evade CTL killing. Downregulation of filamin A is identified to induce softness via ZAP70-mediated YAP Y357 phosphorylation and activation. Despite the requirements of YAP in both cell types for softness induction, CTLs are more resistant to YAP inhibitors than malignant T cells, potentially due to the higher expression of the drug-resistant transporter, MDR1, in CTLs. As a result, moderate inhibition of YAP stiffens malignant T cells but spares CTLs, thus allowing CTLs to cytolyze malignant cells without autolysis. Our findings thus hint a mechanical force-based immunotherapeutic strategy against T cell leukemia.
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Affiliation(s)
- Yabo Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Dianheng Wang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Li Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Nannan Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Zhenfeng Wang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Jie Chen
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Ruiyang Pang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Haixia Fu
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease; Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Beijing, China
| | - Qiusha Huang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease; Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Beijing, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Huafeng Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwei Ma
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiadi Lv
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Roland Fiskesund
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Xiaohui Zhang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease; Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Beijing, China.
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China.
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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5
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Lee DH, Ahn H, Sim HI, Choi E, Choi S, Jo Y, Yun B, Song HK, Oh SJ, Denda-Nagai K, Park CS, Irimura T, Park Y, Jin HS. A CRISPR activation screen identifies MUC-21 as critical for resistance to NK and T cell-mediated cytotoxicity. J Exp Clin Cancer Res 2023; 42:272. [PMID: 37858248 PMCID: PMC10588101 DOI: 10.1186/s13046-023-02840-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Immunotherapy has significantly advanced cancer treatments, but many patients do not respond to it, partly due to immunosuppressive mechanisms used by tumor cells. These cells employ immunosuppressive ligands to evade detection and elimination by the immune system. Therefore, the discovery and characterization of novel immunosuppressive ligands that facilitate immune evasion are crucial for developing more potent anti-cancer therapies. METHODS We conducted gain-of-function screens using a CRISPRa (CRISPR activation) library that covered the entire human transmembrane sub-genome to identify surface molecules capable of hindering NK-mediated cytotoxicity. The immunosuppressive role and mechanism of MUC21 were validated using NK and T cell mediated cytotoxicity assays. Bioinformatics tools were employed to assess the clinical implications of mucin-21 (MUC21) in cancer cell immunity. RESULTS Our genetic screens revealed that MUC21 expression on cancer cell surfaces inhibits both the cytotoxic activity of NK cells and antibody-dependent cellular cytotoxicity, but not affecting complement-dependent cytotoxicity. Additionally, MUC21 expression hinders T cell activation by impeding antigen recognition, thereby diminishing the effectiveness of the immune checkpoint inhibitor, anti-PD-L1. Moreover, MUC21 expression suppress the antitumor function of both CAR-T cells and CAR-NK cells. Mechanistically, MUC21 facilitates immune evasion by creating steric hindrance, preventing interactions between cancer and immune cells. Bioinformatics analysis revealed elevated MUC21 expression in lung cancer, which correlated with reduced infiltration and activation of cytotoxic immune cells. Intriguingly, MUC21 expression was higher in non-small cell lung cancer (NSCLC) tumors that were non-responsive to anti-PD-(L)1 treatment compared to responsive tumors. CONCLUSIONS These findings indicate that surface MUC21 serves as a potent immunosuppressive ligand, shielding cancer cells from NK and CD8+T cell attacks. This suggests that inhibiting MUC21 could be a promising strategy to improve cancer immunotherapy.
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Affiliation(s)
- Dong-Hee Lee
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hyejin Ahn
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hye-In Sim
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Eunji Choi
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Seunghyun Choi
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Yunju Jo
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Bohwan Yun
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Soo Jin Oh
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Kaori Denda-Nagai
- Division of Glycobiologics, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Chan-Sik Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Tatsuro Irimura
- Division of Glycobiologics, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoon Park
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea.
| | - Hyung-Seung Jin
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea.
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6
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Peng R, Deng M. Mapping the protein-protein interactome in the tumor immune microenvironment. Antib Ther 2023; 6:311-321. [PMID: 38098892 PMCID: PMC10720949 DOI: 10.1093/abt/tbad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/01/2023] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
The cell-to-cell communication primarily occurs through cell-surface and secreted proteins, which form a sophisticated network that coordinates systemic immune function. Uncovering these protein-protein interactions (PPIs) is indispensable for understanding the molecular mechanism and elucidating immune system aberrances under diseases. Traditional biological studies typically focus on a limited number of PPI pairs due to the relative low throughput of commonly used techniques. Encouragingly, classical methods have advanced, and many new systems tailored for large-scale protein-protein screening have been developed and successfully utilized. These high-throughput PPI investigation techniques have already made considerable achievements in mapping the immune cell interactome, enriching PPI databases and analysis tools, and discovering therapeutic targets for cancer and other diseases, which will definitely bring unprecedented insight into this field.
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Affiliation(s)
- Rui Peng
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, PR China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, PR China
| | - Mi Deng
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, PR China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, PR China
- Peking University Cancer Hospital and Institute, Peking University, Beijing 100142, PR China
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7
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Nogo-A and LINGO-1: Two Important Targets for Remyelination and Regeneration. Int J Mol Sci 2023; 24:ijms24054479. [PMID: 36901909 PMCID: PMC10003089 DOI: 10.3390/ijms24054479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) that causes progressive neurological disability in most patients due to neurodegeneration. Activated immune cells infiltrate the CNS, triggering an inflammatory cascade that leads to demyelination and axonal injury. Non-inflammatory mechanisms are also involved in axonal degeneration, although they are not fully elucidated yet. Current therapies focus on immunosuppression; however, no therapies to promote regeneration, myelin repair, or maintenance are currently available. Two different negative regulators of myelination have been proposed as promising targets to induce remyelination and regeneration, namely the Nogo-A and LINGO-1 proteins. Although Nogo-A was first discovered as a potent neurite outgrowth inhibitor in the CNS, it has emerged as a multifunctional protein. It is involved in numerous developmental processes and is necessary for shaping and later maintaining CNS structure and functionality. However, the growth-restricting properties of Nogo-A have negative effects on CNS injury or disease. LINGO-1 is also an inhibitor of neurite outgrowth, axonal regeneration, oligodendrocyte differentiation, and myelin production. Inhibiting the actions of Nogo-A or LINGO-1 promotes remyelination both in vitro and in vivo, while Nogo-A or LINGO-1 antagonists have been suggested as promising therapeutic approaches for demyelinating diseases. In this review, we focus on these two negative regulators of myelination while also providing an overview of the available data on the effects of Nogo-A and LINGO-1 inhibition on oligodendrocyte differentiation and remyelination.
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8
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Heidersbach AJ, Dorighi KM, Gomez JA, Jacobi AM, Haley B. A versatile, high-efficiency platform for CRISPR-based gene activation. Nat Commun 2023; 14:902. [PMID: 36804928 PMCID: PMC9938141 DOI: 10.1038/s41467-023-36452-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with an optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.
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Affiliation(s)
- Amy J Heidersbach
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Kristel M Dorighi
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | | | | | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
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9
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Yang HW, Ju SP, Tseng TF. Design the RNA aptamer of PCA3 long non-coding ribonucleic acid by the coarse-grained molecular mechanics. J Biomol Struct Dyn 2022; 40:13833-13847. [PMID: 34693888 DOI: 10.1080/07391102.2021.1994881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The stochastic tunneling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to predict the tertiary structure of the prostate cancer marker PCA3 using two respective secondary structures predicted by the Vienna RNA package and Mathews lab package. The RNA CG force field with the geometrical restraints for maintaining PCA3 secondary structures is used. For each secondary structure, 5000 PCA3 structures were predicted by using 5000 independent initial structures. These structures were then evaluated by a scoring function, considering the contributions from the radius of gyration, contact energy, and surface fraction of complementary nucleotides to ASO683 and ASO735 used in the related experiment. For each secondary structure, the PCA3 structures with the highest three scores were selected for aptamer design and further adsorption simulation. The ASOs complementary to PCA3 surface segments possessing relatively higher RMSF values are selected to be the potential PCA3 aptamers. After the adsorption simulation, the adsorption energies of ASO961, ASO3181, ASO3533, and ASO3595 are higher than or comparable to those of ASO683 and ASO735 used in the experiment. The NEB method was used to obtain MEPs for the adsorption process of all predicted ASOs onto PCA3. The adsorption barriers range between 29 ∼ 39 kcal/mol, while the desorption barriers range between 112 ∼ 352 kcal/mol, indicating these aptamer/PCA3 complexes are very stable. Using PCA3 surface segments with relatively higher RMSF values, longer ASOs can be also obtained and most longer ASOs possess lower binding energy, ranging between -486.1 and -618.2 kcal/mol.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hung-Wei Yang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Feng Tseng
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
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10
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Lala T, Doan JK, Takatsu H, Hartzell HC, Shin HW, Hall RA. Phosphatidylserine exposure modulates adhesion GPCR BAI1 (ADGRB1) signaling activity. J Biol Chem 2022; 298:102685. [PMID: 36370845 PMCID: PMC9723945 DOI: 10.1016/j.jbc.2022.102685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022] Open
Abstract
Brain-specific angiogenesis inhibitor 1 (BAI1; also called ADGRB1 or B1) is an adhesion G protein-coupled receptor known from studies on macrophages to bind to phosphatidylserine (PS) on apoptotic cells via its N-terminal thrombospondin repeats. A separate body of work has shown that B1 regulates postsynaptic function and dendritic spine morphology via signaling pathways involving Rac and Rho. However, it is unknown if PS binding by B1 has any effect on the receptor's signaling activity. To shed light on this subject, we studied G protein-dependent signaling by B1 in the absence and presence of coexpression with the PS flippase ATP11A in human embryonic kidney 293T cells. ATP11A expression reduced the amount of PS exposed extracellularly and also strikingly reduced the signaling activity of coexpressed full-length B1 but not a truncated version of the receptor lacking the thrombospondin repeats. Further experiments with an inactive mutant of ATP11A showed that the PS flippase function of ATP11A was required for modulation of B1 signaling. In coimmunoprecipitation experiments, we made the surprising finding that ATP11A not only modulates B1 signaling but also forms complexes with B1. Parallel studies in which PS in the outer leaflet was reduced by an independent method, deletion of the gene encoding the endogenous lipid scramblase anoctamin 6 (ANO6), revealed that this manipulation also markedly reduced B1 signaling. These findings demonstrate that B1 signaling is modulated by PS exposure and suggest a model in which B1 serves as a PS sensor at synapses and in other cellular contexts.
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Affiliation(s)
- Trisha Lala
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Juleva K Doan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hiroyuki Takatsu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - H Criss Hartzell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hye-Won Shin
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Randy A Hall
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA.
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11
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Rodriguez CM, Bechek SC, Jones GL, Nakayama L, Akiyama T, Kim G, Solow-Cordero DE, Strittmatter SM, Gitler AD. Targeting RTN4/NoGo-Receptor reduces levels of ALS protein ataxin-2. Cell Rep 2022; 41:111505. [PMID: 36288715 PMCID: PMC9664481 DOI: 10.1016/j.celrep.2022.111505] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/30/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023] Open
Abstract
Gene-based therapeutic strategies to lower ataxin-2 levels are emerging for the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2). Additional strategies to lower levels of ataxin-2 could be beneficial. Here, we perform a genome-wide arrayed small interfering RNA (siRNA) screen in human cells and identify RTN4R, the gene encoding the RTN4/NoGo-Receptor, as a potent modifier of ataxin-2 levels. RTN4R knockdown, or treatment with a peptide inhibitor, is sufficient to lower ataxin-2 protein levels in mouse and human neurons in vitro, and Rtn4r knockout mice have reduced ataxin-2 levels in vivo. We provide evidence that ataxin-2 shares a role with the RTN4/NoGo-Receptor in limiting axonal regeneration. Reduction of either protein increases axonal regrowth following axotomy. These data define the RTN4/NoGo-Receptor as a novel therapeutic target for ALS and SCA2 and implicate the targeting of ataxin-2 as a potential treatment following nerve injury.
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Affiliation(s)
- Caitlin M Rodriguez
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophia C Bechek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Graham L Jones
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Nakayama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garam Kim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Neurosciences Interdepartmental Program, Stanford University School of Medicine, Stanford, CA, USA
| | - David E Solow-Cordero
- High-Throughput Bioscience Center, Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Stephen M Strittmatter
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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12
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Chong ZS, Ohnishi S, Yusa K, Wright GJ. Author Correction: Pooled extracellular receptor-ligand interaction screening using CRISPR activation. Genome Biol 2022; 23:224. [PMID: 36271468 DOI: 10.1186/s13059-022-02797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Zheng-Shan Chong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Shuhei Ohnishi
- Stem Cell Genetics Laboratory, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Stem Cell Genetics Laboratory, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
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13
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Lala T, Hall RA. Adhesion G protein-coupled receptors: structure, signaling, physiology, and pathophysiology. Physiol Rev 2022; 102:1587-1624. [PMID: 35468004 PMCID: PMC9255715 DOI: 10.1152/physrev.00027.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/11/2022] [Accepted: 04/16/2022] [Indexed: 01/17/2023] Open
Abstract
Adhesion G protein-coupled receptors (AGPCRs) are a family of 33 receptors in humans exhibiting a conserved general structure but diverse expression patterns and physiological functions. The large NH2 termini characteristic of AGPCRs confer unique properties to each receptor and possess a variety of distinct domains that can bind to a diverse array of extracellular proteins and components of the extracellular matrix. The traditional view of AGPCRs, as implied by their name, is that their core function is the mediation of adhesion. In recent years, though, many surprising advances have been made regarding AGPCR signaling mechanisms, activation by mechanosensory forces, and stimulation by small-molecule ligands such as steroid hormones and bioactive lipids. Thus, a new view of AGPCRs has begun to emerge in which these receptors are seen as massive signaling platforms that are crucial for the integration of adhesive, mechanosensory, and chemical stimuli. This review article describes the recent advances that have led to this new understanding of AGPCR function and also discusses new insights into the physiological actions of these receptors as well as their roles in human disease.
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Affiliation(s)
- Trisha Lala
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia
| | - Randy A Hall
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia
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14
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Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC. Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. eLife 2022; 11:e81398. [PMID: 36178190 PMCID: PMC9578707 DOI: 10.7554/elife.81398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors ('orphans') or are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening are not optimized for extracellular interactions. Cell-based screening is a promising technology for the deorphanization of ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high-value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass transmembrane (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding assays. The newly deorphanized ligands include three receptor protein tyrosine phosphatase (RPTP) ligands and a chemokine-like protein that binds to killer immunoglobulin-like receptors (KIRs). These new interactions provide a resource for future investigations of interactions between the human-secreted and membrane proteomes.
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Affiliation(s)
- Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Lukas T Henneberg
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gaelen T Hess
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Michael C Bassik
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
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15
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Mei H, Gu Q, Wang W, Meng Y, Jiang L, Liu J. CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins. Comput Struct Biotechnol J 2022; 20:3833-3838. [PMID: 35891797 PMCID: PMC9307495 DOI: 10.1016/j.csbj.2022.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-based genome-editing tools have emerged as an efficient tool for functional genomics studies. Online tools and databases have been developed to facilitate the design and selection of CRISPR single guide RNA (sgRNA) for gene modifications. However, to the best of our knowledge, none of these tools or database are designated to cell surface proteins. In a previous study, we described the development and application of surfaceome CRISPR libraries targeting to cell surface proteins on human cells. Here, we present the design and construction of an online tool and database (https://crispr-surfaceome.siais.shanghaitech.edu.cn/home), named CRISPR-Surfaceome, for the design of highly efficient sgRNA targeting to the surface proteins on human cells. To show case and validate the efficiencies of sgRNAs designed by this online tool, we chose ICAM-1 gene for knockout studies and found that all the 10 designed ICAM-1 sgRNAs could efficiently generate knockout cells, with more than 80% gene disruption rates. These ICAM-1 knockout cells were found to be resistant to the infection of rhinovirus (RV), which utilizes ICAM-1 as the receptor. Therefore, CRISPR-Surfaceome can serve the research community for the functional genomics studies on cell surface proteins, such as identification of pathogen receptors and discovery of drug targets.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qian Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yu Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
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16
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Application of Gene Editing Technology in Resistance Breeding of Livestock. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071070. [PMID: 35888158 PMCID: PMC9325061 DOI: 10.3390/life12071070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023]
Abstract
As a new genetic engineering technology, gene editing can precisely modify the specific gene sequence of the organism’s genome. In the last 10 years, with the rapid development of gene editing technology, zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR/Cas9 systems have been applied to modify endogenous genes in organisms accurately. Now, gene editing technology has been used in mice, zebrafish, pigs, cattle, goats, sheep, rabbits, monkeys, and other species. Breeding for disease-resistance in agricultural animals tends to be a difficult task for traditional breeding, but gene editing technology has made this easier. In this work, we overview the development and application of gene editing technology in the resistance breeding of livestock. Also, we further discuss the prospects and outlooks of gene editing technology in disease-resistance breeding.
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17
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Embigin is a fibronectin receptor that affects sebaceous gland differentiation and metabolism. Dev Cell 2022; 57:1453-1465.e7. [DOI: 10.1016/j.devcel.2022.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 03/19/2022] [Accepted: 05/16/2022] [Indexed: 12/25/2022]
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18
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Wang J, Miao Y, Wicklein R, Sun Z, Wang J, Jude KM, Fernandes RA, Merrill SA, Wernig M, Garcia KC, Südhof TC. RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development. Cell 2021; 184:5869-5885.e25. [PMID: 34758294 PMCID: PMC8620742 DOI: 10.1016/j.cell.2021.10.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/01/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022]
Abstract
RTN4-binding proteins were widely studied as "NoGo" receptors, but their physiological interactors and roles remain elusive. Similarly, BAI adhesion-GPCRs were associated with numerous activities, but their ligands and functions remain unclear. Using unbiased approaches, we observed an unexpected convergence: RTN4 receptors are high-affinity ligands for BAI adhesion-GPCRs. A single thrombospondin type 1-repeat (TSR) domain of BAIs binds to the leucine-rich repeat domain of all three RTN4-receptor isoforms with nanomolar affinity. In the 1.65 Å crystal structure of the BAI1/RTN4-receptor complex, C-mannosylation of tryptophan and O-fucosylation of threonine in the BAI TSR-domains creates a RTN4-receptor/BAI interface shaped by unusual glycoconjugates that enables high-affinity interactions. In human neurons, RTN4 receptors regulate dendritic arborization, axonal elongation, and synapse formation by differential binding to glial versus neuronal BAIs, thereby controlling neural network activity. Thus, BAI binding to RTN4/NoGo receptors represents a receptor-ligand axis that, enabled by rare post-translational modifications, controls development of synaptic circuits.
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Affiliation(s)
- Jie Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rebecca Wicklein
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zijun Sun
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinzhao Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean A Merrill
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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19
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Chulanov V, Kostyusheva A, Brezgin S, Ponomareva N, Gegechkori V, Volchkova E, Pimenov N, Kostyushev D. CRISPR Screening: Molecular Tools for Studying Virus-Host Interactions. Viruses 2021; 13:v13112258. [PMID: 34835064 PMCID: PMC8618713 DOI: 10.3390/v13112258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas is a powerful tool for studying the role of genes in viral infections. The invention of CRISPR screening technologies has made it possible to untangle complex interactions between the host and viral agents. Moreover, whole-genome and pathway-specific CRISPR screens have facilitated identification of novel drug candidates for treating viral infections. In this review, we highlight recent developments in the fields of CRISPR/Cas with a focus on the use of CRISPR screens for studying viral infections and identifying new candidate genes to aid development of antivirals.
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Affiliation(s)
- Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Natalia Ponomareva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Gegechkori
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Elena Volchkova
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Nikolay Pimenov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
- Correspondence:
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20
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Mei H, Zha Z, Wang W, Xie Y, Huang Y, Li W, Wei D, Zhang X, Qu J, Liu J. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Genome Biol 2021; 22:297. [PMID: 34686207 PMCID: PMC8532573 DOI: 10.1186/s13059-021-02513-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02513-w.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Yusang Xie
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuege Huang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Shanghai Clinical Research and Trial Center, 201210, Shanghai, People's Republic of China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510182, Guangdong Province, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, People's Republic of China. .,Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou Interntional Bio Island, Guangdong Province, 510005, Guangzhou, China.
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21
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Rosa M, Noel T, Harris M, Ladds G. Emerging roles of adhesion G protein-coupled receptors. Biochem Soc Trans 2021; 49:1695-1709. [PMID: 34282836 PMCID: PMC8421042 DOI: 10.1042/bst20201144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) form a sub-group within the GPCR superfamily. Their distinctive structure contains an abnormally large N-terminal, extracellular region with a GPCR autoproteolysis-inducing (GAIN) domain. In most aGPCRs, the GAIN domain constitutively cleaves the receptor into two fragments. This process is often required for aGPCR signalling. Over the last two decades, much research has focussed on aGPCR-ligand interactions, in an attempt to deorphanize the family. Most ligands have been found to bind to regions N-terminal to the GAIN domain. These receptors may bind a variety of ligands, ranging across membrane-bound proteins and extracellular matrix components. Recent advancements have revealed a conserved method of aGPCR activation involving a tethered ligand within the GAIN domain. Evidence for this comes from increased activity in receptor mutants exposing the tethered ligand. As a result, G protein-coupling partners of aGPCRs have been more extensively characterised, making use of their tethered ligand to create constitutively active mutants. This has led to demonstrations of aGPCR function in, for example, neurodevelopment and tumour growth. However, questions remain around the ligands that may bind many aGPCRs, how this binding is translated into changes in the GAIN domain, and the exact mechanism of aGPCR activation following GAIN domain conformational changes. This review aims to examine the current knowledge around aGPCR activation, including ligand binding sites, the mechanism of GAIN domain-mediated receptor activation and how aGPCR transmembrane domains may relate to activation. Other aspects of aGPCR signalling will be touched upon, such as downstream effectors and physiological roles.
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Affiliation(s)
- Matthew Rosa
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Timothy Noel
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
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22
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van der Weyden L, Harle V, Turner G, Offord V, Iyer V, Droop A, Swiatkowska A, Rabbie R, Campbell AD, Sansom OJ, Pardo M, Choudhary JS, Ferreira I, Tullett M, Arends MJ, Speak AO, Adams DJ. CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation. Commun Biol 2021; 4:395. [PMID: 33758365 PMCID: PMC7987976 DOI: 10.1038/s42003-021-01912-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/25/2021] [Indexed: 02/08/2023] Open
Abstract
Melanoma represents ~5% of all cutaneous malignancies, yet accounts for the majority of skin cancer deaths due to its propensity to metastasise. To develop new therapies, novel target molecules must to be identified and the accessibility of cell surface proteins makes them attractive targets. Using CRISPR activation technology, we screened a library of guide RNAs targeting membrane protein-encoding genes to identify cell surface molecules whose upregulation enhances the metastatic pulmonary colonisation capabilities of tumour cells in vivo. We show that upregulated expression of the cell surface protein LRRN4CL led to increased pulmonary metastases in mice. Critically, LRRN4CL expression was elevated in melanoma patient samples, with high expression levels correlating with decreased survival. Collectively, our findings uncover an unappreciated role for LRRN4CL in the outcome of melanoma patients and identifies a potential therapeutic target and biomarker.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- CRISPR-Cas Systems
- Cell Line, Tumor
- Cell Movement
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/secondary
- Male
- Melanoma, Experimental/genetics
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/secondary
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Neoplasm Invasiveness
- Skin Neoplasms/genetics
- Skin Neoplasms/metabolism
- Skin Neoplasms/pathology
- Up-Regulation
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Affiliation(s)
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gemma Turner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alastair Droop
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Roy Rabbie
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ingrid Ferreira
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mark Tullett
- Western Sussex NHS Foundation Trust, Chichester, West Sussex, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Edinburgh Cancer Research UK Cancer Centre, Institute of Genetics & Molecular Medicine, Edinburgh, UK
| | - Anneliese O Speak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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23
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Rahman MM, Tollefsbol TO. Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects. Methods 2021; 187:77-91. [PMID: 32315755 PMCID: PMC7572534 DOI: 10.1016/j.ymeth.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer therapeutics is an ever-evolving field due to incessant demands for effective and precise treatment options. Over the last few decades, cancer treatment strategies have shifted somewhat from surgery to targeted precision medicine. CRISPR-dCas9 is an emerging version of precision cancer therapy that has been adapted from the prokaryotic CRISPR-Cas system. Once ligated to epigenetic effectors (EE), CRISPR-dCas9 can function as an epigenetic editing tool and CRISPR-dCas9-EE complexes could be exploited to alter cancerous epigenetic features associated with different cancer hallmarks. In this article, we discuss the rationale of epigenetic editing as a therapeutic strategy against cancer. We also outline how sgRNA-dCas9 was derived from the CRISPR-Cas system. In addition, the current status of sgRNA-dCas9 use (in vivo and in vitro) in cancer is updated with a molecular illustration of CRISPR-dCas9-mediated epigenetic and transcriptional modulation. As sgRNA-dCas9 is still at the developmental phase, challenges are inherent to its use. We evaluate major challenges in targeting cancer with sgRNA-dCas9 such as off-target effects, lack of sgRNA designing rubrics, target site selection dilemmas and deficient sgRNA-dCas9 delivery systems. Finally, we appraise the sgRNA-dCas9 as a prospective cancer therapeutic by summarizing ongoing improvements of sgRNA-dCas9 methodology.
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Affiliation(s)
- Mohammad Mijanur Rahman
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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24
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Bianchi E, Sun Y, Almansa-Ordonez A, Woods M, Goulding D, Martinez-Martin N, Wright GJ. Control of oviductal fluid flow by the G-protein coupled receptor Adgrd1 is essential for murine embryo transit. Nat Commun 2021; 12:1251. [PMID: 33623007 PMCID: PMC7902839 DOI: 10.1038/s41467-021-21512-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Dysfunction of embryo transport causes ectopic pregnancy which affects approximately 2% of conceptions in the US and Europe, and is the most common cause of pregnancy-related death in the first trimester. Embryo transit involves a valve-like tubal-locking phenomenon that temporarily arrests oocytes at the ampullary-isthmic junction (AIJ) where fertilisation occurs, but the mechanisms involved are unknown. Here we show that female mice lacking the orphan adhesion G-protein coupled receptor Adgrd1 are sterile because they do not relieve the AIJ restraining mechanism, inappropriately retaining embryos within the oviduct. Adgrd1 is expressed on the oviductal epithelium and the post-ovulatory attenuation of tubal fluid flow is dysregulated in Adgrd1-deficient mice. Using a large-scale extracellular protein interaction screen, we identified Plxdc2 as an activating ligand for Adgrd1 displayed on cumulus cells. Our findings demonstrate that regulating oviductal fluid flow by Adgrd1 controls embryo transit and we present a model where embryo arrest at the AIJ is due to the balance of abovarial ciliary action and the force of adovarial tubal fluid flow, and in wild-type oviducts, fluid flow is gradually attenuated through Adgrd1 activation to enable embryo release. Our findings provide important insights into the molecular mechanisms involved in embryo transport in mice. Lack of correct embryo transport can cause ectopic pregnancy. Here, the authors show that female mice lacking the adhesion G-protein coupled receptor Adgrd1 are infertile, due to embryos being trapped in the ampulla as the result of dysregulated oviductal fluid flow.
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Affiliation(s)
- Enrica Bianchi
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Yi Sun
- Receptor Discovery Group, Microchemistry, Proteomics and Lipidomics Department, San Francisco, CA, USA.,Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
| | | | - Michael Woods
- Mouse Production Team, Wellcome Sanger Institute, Cambridge, UK
| | - David Goulding
- Electron and Advanced Light Microscopy Suite, Wellcome Sanger Institute, Cambridge, UK
| | - Nadia Martinez-Martin
- Receptor Discovery Group, Microchemistry, Proteomics and Lipidomics Department, San Francisco, CA, USA
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK. .,Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, Wentworth Way, York, UK.
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25
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Wang JL, Chen WG, Zhang JJ, Xu CJ. Nogo-A-Δ20/EphA4 interaction antagonizes apoptosis of neural stem cells by integrating p38 and JNK MAPK signaling. J Mol Histol 2021; 52:521-537. [PMID: 33555537 DOI: 10.1007/s10735-021-09960-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Nogo-A protein consists of two main extracellular domains: Nogo-66 (rat amino acid [aa] 1019-1083) and Nogo-A-Δ20 (extracellular, active 180 amino acid Nogo-A region), which serve as strong inhibitors of axon regeneration in the adult CNS (Central Nervous System). Although receptors S1PR2 and HSPGs have been identified as Nogo-A-Δ20 binding proteins, it remains at present elusive whether other receptors directly interacting with Nogo-A-Δ20 exist, and decrease cell death. On the other hand, the key roles of EphA4 in the regulation of glioblastoma, axon regeneration and NSCs (Neural Stem Cells) proliferation or differentiation are well understood, but little is known the relationship between EphA4 and Nogo-A-Δ20 in NSCs apoptosis. Thus, we aim to determine whether Nogo-A-Δ20 can bind to EphA4 and affect survival of NSCs. Here, we discover that EphA4, belonging to a member of erythropoietin-producing hepatocellular (Eph) receptors family, could be acting as a high affinity ligand for Nogo-A-Δ20. Trans-membrane protein of EphA4 is needed for Nogo-A-Δ20-triggered inhibition of NSCs apoptosis, which are mediated by balancing p38 inactivation and JNK MAPK pathway activation. Finally, we predict at the atomic level that essential residues Lys-205, Ile-190, Pro-194 in Nogo-A-Δ20 and EphA4 residues Gln-390, Asn-425, Pro-426 might play critical roles in Nogo-A-Δ20/EphA4 binding via molecular docking.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wei-Guang Chen
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jia-Jia Zhang
- School of 1St Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China.
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26
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Casas-Mollano JA, Zinselmeier MH, Erickson SE, Smanski MJ. CRISPR-Cas Activators for Engineering Gene Expression in Higher Eukaryotes. CRISPR J 2020; 3:350-364. [PMID: 33095045 PMCID: PMC7580621 DOI: 10.1089/crispr.2020.0064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR-Cas-based transcriptional activators allow genetic engineers to specifically induce expression of one or many target genes in trans. Here we review the many design variations of these versatile tools and compare their effectiveness in different eukaryotic systems. Lastly, we highlight several applications of programmable transcriptional activation to interrogate and engineer complex biological processes.
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Affiliation(s)
- J. Armando Casas-Mollano
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Matthew H. Zinselmeier
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Samuel E. Erickson
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
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27
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Vizurraga A, Adhikari R, Yeung J, Yu M, Tall GG. Mechanisms of adhesion G protein-coupled receptor activation. J Biol Chem 2020; 295:14065-14083. [PMID: 32763969 DOI: 10.1074/jbc.rev120.007423] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Adhesion G protein-coupled receptors (AGPCRs) are a thirty-three-member subfamily of Class B GPCRs that control a wide array of physiological processes and are implicated in disease. AGPCRs uniquely contain large, self-proteolyzing extracellular regions that range from hundreds to thousands of residues in length. AGPCR autoproteolysis occurs within the extracellular GPCR autoproteolysis-inducing (GAIN) domain that is proximal to the N terminus of the G protein-coupling seven-transmembrane-spanning bundle. GAIN domain-mediated self-cleavage is constitutive and produces two-fragment holoreceptors that remain bound at the cell surface. It has been of recent interest to understand how AGPCRs are activated in relation to their two-fragment topologies. Dissociation of the AGPCR fragments stimulates G protein signaling through the action of the tethered-peptide agonist stalk that is occluded within the GAIN domain in the holoreceptor form. AGPCRs can also signal independently of fragment dissociation, and a few receptors possess GAIN domains incapable of self-proteolysis. This has resulted in complex theories as to how these receptors are activated in vivo, complicating pharmacological advances. Currently, there is no existing structure of an activated AGPCR to support any of the theories. Further confounding AGPCR research is that many of the receptors remain orphans and lack identified activating ligands. In this review, we provide a detailed layout of the current theorized modes of AGPCR activation with discussion of potential parallels to mechanisms used by other GPCR classes. We provide a classification means for the ligands that have been identified and discuss how these ligands may activate AGPCRs in physiological contexts.
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Affiliation(s)
- Alexander Vizurraga
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Rashmi Adhikari
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Jennifer Yeung
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Maiya Yu
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Gregory G Tall
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
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28
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Chong ZS, Wright GJ, Sharma S. Investigating Cellular Recognition Using CRISPR/Cas9 Genetic Screening. Trends Cell Biol 2020; 30:619-627. [DOI: 10.1016/j.tcb.2020.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
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29
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Galaway F, Wright GJ. Rapid and sensitive large-scale screening of low affinity extracellular receptor protein interactions by using reaction induced inhibition of Gaussia luciferase. Sci Rep 2020; 10:10522. [PMID: 32601498 PMCID: PMC7324543 DOI: 10.1038/s41598-020-67468-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular protein interactions mediated by cell surface receptors are essential for intercellular communication in multicellular organisms. Assays to detect extracellular interactions must account for their often weak binding affinities and also the biochemical challenges in solubilising membrane-embedded receptors in an active form. Methods based on detecting direct binding of soluble recombinant receptor ectodomains have been successful, but genome-scale screening is limited by the usual requirement of producing sufficient amounts of each protein in two different forms, usually a "bait" and "prey". Here, we show that oligomeric receptor ectodomains coupled to concatenated units of the light-generating Gaussia luciferase enzyme robustly detected low affinity interactions and reduced the amount of protein required by several orders of magnitude compared to other reporter enzymes. Importantly, we discovered that this flash-type luciferase exhibited a reaction-induced inhibition that permitted the use of a single protein preparation as both bait and prey thereby halving the number of expression plasmids and recombinant proteins required for screening. This approach was tested against a benchmarked set of quantified extracellular interactions and shown to detect extremely weak interactions (KDs ≥ μM). This method will facilitate large-scale receptor interaction screening and contribute to the goal of mapping networks of cellular communication.
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Affiliation(s)
- Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
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30
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Sandoval A, Elahi H, Ploski JE. Genetically Engineering the Nervous System with CRISPR-Cas. eNeuro 2020; 7:ENEURO.0419-19.2020. [PMID: 32098761 PMCID: PMC7096538 DOI: 10.1523/eneuro.0419-19.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/16/2022] Open
Abstract
The multitude of neuronal subtypes and extensive interconnectivity of the mammalian brain presents a substantial challenge to those seeking to decipher its functions. While the molecular mechanisms of several neuronal functions remain poorly characterized, advances in next-generation sequencing (NGS) and gene-editing technology have begun to close this gap. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (CRISPR-Cas) system has emerged as a powerful genetic tool capable of manipulating the genome of essentially any organism and cell type. This technology has advanced our understanding of complex neurologic diseases by enabling the rapid generation of novel, disease-relevant in vitro and transgenic animal models. In this review, we discuss recent developments in the rapidly accelerating field of CRISPR-mediated genome engineering. We begin with an overview of the canonical function of the CRISPR platform, followed by a functional review of its many adaptations, with an emphasis on its applications for genetic interrogation of the normal and diseased nervous system. Additionally, we discuss limitations of the CRISPR editing system and suggest how future modifications to existing platforms may advance our understanding of the brain.
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Affiliation(s)
- Alfredo Sandoval
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
| | - Hajira Elahi
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
| | - Jonathan E Ploski
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
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31
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Wood L, Wright GJ. High-Content Imaging for Large-Scale Detection of Low-Affinity Extracellular Protein Interactions. SLAS DISCOVERY 2019; 24:987-999. [PMID: 31578119 PMCID: PMC6873222 DOI: 10.1177/2472555219879053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extracellular protein interactions coordinate cellular responses with their local
environment and have important roles in pathogen invasion and disease. Due to
technical challenges associated with studying binding events at the cell
surface, the systematic and reliable identification of novel ligand–receptor
pairs remains difficult. Here, we describe the development of a cell-based assay
using large-scale transient transfections and high-content imaging (HCI) to
detect extracellular binding events. We optimized the parameters for efficient
transfection of human cells with cDNA plasmids encoding full-length cell surface
receptors in 384-well plates. Using a range of well-characterized structurally
diverse low-affinity cell surface interactions, we show that transfected cells
probed with highly avid ligands can be used to successfully identify
ligand–receptor pairs using an HCI platform and automated image analysis
software. To establish the high-throughput potential of this approach, we also
screened a pool of ligands against a collection of 2455 cell surface expression
clones and found that known ligand–receptor interactions could be robustly and
consistently detected across the library using this technology.
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Affiliation(s)
- Laura Wood
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, UK
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32
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Li QV, Rosen BP, Huangfu D. Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1464. [PMID: 31407519 DOI: 10.1002/wsbm.1464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/31/2019] [Accepted: 07/17/2019] [Indexed: 01/25/2023]
Abstract
Pluripotent stem cells have the ability to unlimitedly self-renew and differentiate to any somatic cell lineage. A number of systems biology approaches have been used to define this pluripotent state. Complementary to systems level characterization, genetic screens offer a unique avenue to functionally interrogate the pluripotent state and identify the key players in pluripotency acquisition and maintenance, exit of pluripotency, and lineage differentiation. Here we review how genetic screens have helped us decode pluripotency regulation. We will summarize results from RNA interference (RNAi) based screens, discuss recent advances in CRISPR/Cas-based genetic perturbation methods, and how these advances have made it possible to more comprehensively interrogate pluripotency and differentiation through genetic screens. Such investigations will not only provide a better understanding of this unique developmental state, but may enhance our ability to use pluripotent stem cells as an experimental model to study human development and disease progression. Functional interrogation of pluripotency also provides a valuable roadmap for utilizing genetic perturbation to gain systems level understanding of additional cellular states, from later stages of development to pathological disease states. This article is categorized under: Developmental Biology > Stem Cell Biology and Regeneration Developmental Biology > Developmental Processes in Health and Disease Biological Mechanisms > Cell Fates.
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Affiliation(s)
- Qing V Li
- Sloan Kettering Institute, New York, New York.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bess P Rosen
- Sloan Kettering Institute, New York, New York.,Weill Graduate School of Medical Sciences at Cornell University, New York, New York
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33
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Langenhan T. Adhesion G protein–coupled receptors—Candidate metabotropic mechanosensors and novel drug targets. Basic Clin Pharmacol Toxicol 2019; 126 Suppl 6:5-16. [DOI: 10.1111/bcpt.13223] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Langenhan
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty Leipzig University Leipzig Germany
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34
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Olaniru OE, Persaud SJ. Adhesion G-protein coupled receptors: Implications for metabolic function. Pharmacol Ther 2019; 198:123-134. [PMID: 30825474 DOI: 10.1016/j.pharmthera.2019.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adhesion G-protein coupled receptors (aGPCRs) are emerging as important actors in energy homeostasis. Recent biochemical and functional studies using transgenic mice indicate that aGPCRs play important roles in endocrine and metabolic functions including β-cell differentiation, insulin secretion, adipogenesis and whole body fuel homeostasis. Most aGPCRs are orphans, for which endogenous ligands have not yet been identified, and many of the endogenous ligands of the already de-orphanised aGPCRs are components of the extracellular matrix (ECM). In this review we focus on aGPCR expression in metabolically active tissues, their activation by ECM proteins, and current knowledge of their potential roles in islet development, insulin secretion, adipogenesis and muscle function.
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Affiliation(s)
- Oladapo E Olaniru
- Diabetes Research Group, Department of Diabetes, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Shanta J Persaud
- Diabetes Research Group, Department of Diabetes, King's College London, Guy's Campus, London SE1 1UL, UK.
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