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Li J, Tan J, Wang T, Yu S, Guo G, Li K, Yang L, Zeng B, Mei X, Gao S, Lao X, Zhang S, Liao G, Liang Y. cGAS-ISG15-RAGE axis reprogram necroptotic microenvironment and promote lymphatic metastasis in head and neck cancer. Exp Hematol Oncol 2024; 13:63. [PMID: 38926796 PMCID: PMC11200990 DOI: 10.1186/s40164-024-00531-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Cancer cells frequently evolve necroptotic resistance to overcome various survival stress during tumorigenesis. However, we have previously showed that necroptosis is widespread in head and neck squamous cell carcinoma (HNSCC) and contributes to tumor progression and poor survival via DAMPs-induced migration and invasiveness in peri-necroptotic tumor cells. This implicated an alternative strategy that cancers cope with necroptotic stress by reprogramming a pro-invasive necroptotic microenvironment (NME). Here, we aim to decipher how necroptotic cells shape the NME and affect HNSCC progression. METHODS Both our pre-established cellular necroptotic model and newly established Dox-induce intratumoral necroptosis model were used to investigate how necroptosis affect HNSCC progression. Transcriptomic alterations in peri-necroptotic tumor cells were analyzed by RNA-seq and validated in the NME in mice and patients' samples. The differential DAMPs compositon among apopotosis. Necrosis, and necroptosis were analyzed by label-free proteomic technique, and the necroptosis-specific DAMPs were then identified and validated. The potential receptor for ISG15 were simulated using molecular docking and further validated by in vitro assays. Then the ISG15-RAGE axis was blocked by either knockdown of necroptotic-ISG15 release and RAGE inhibitor FPS-ZM1, and the impact on tumor progression were tested. Last, we further tested our findings in a HNSCC-patients cohort. RESULTS Necroptosis played a crucial role in driving tumor-cell invasiveness and lymphatic metastasis via tumor-type dependent DAMPs-releasing. Mechanistically, necroptotic DAMPs induced peri-necroptotic EMT via NF-κB and STAT3 signaling. Furthermore, intrinsic orchestration between necroptotic and cGAS-STING signaling resulted in producing a group of interferon stimulated genes (ISGs) as HNSCC-dependent necroptotic DAMPs. Among them, ISG15 played an essential role in reprogramming the NME. We then identified RAGE as a novel receptor for extracellular ISG15. Either blockage of ISG15 release or ISG15-RAGE interaction dramatically impeded necroptosis-driven EMT and lymphatic metastasis in HNSCC. Lastly, clinicopathological analysis showed high ISG15 expression in NME. Extensive necroptosis and high tumor-cell RAGE expression correlated with tumor progression and poor survival of HNSCC patients. CONCLUSIONS Our data revealed a previously unknown cGAS-ISG15-RAGE dependent reprogramming of the necroptotic microenvironment which converts the necroptotic stress into invasive force to foster HNSCC-cell dissemination. By demonstrating the programmatic production of ISG15 via necroptosis-cGAS orchestration and its downstream signaling through RAGE, we shed light on the unique role of ISG15 in HNSCC progression. Targeting such machineries may hold therapeutic potential for restoring intratumoral survival stress and preventing lymphatic metastasis in HNSCC.
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Affiliation(s)
- Jingyuan Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jun Tan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Tao Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shan Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Guangliang Guo
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Kan Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Le Yang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Bin Zeng
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xueying Mei
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Siyong Gao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xiaomei Lao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Sien Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Guiqing Liao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Sun Yat-Sen University, 56th Lingyuanxi Road, Guangzhou, 510055, Guangdong, China.
| | - Yujie Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Sun Yat-Sen University, 56th Lingyuanxi Road, Guangzhou, 510055, Guangdong, China.
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Liu X, Zheng M, Zhang H, Feng B, Li J, Zhang Y, Zhang J, Zhao N, Li C, Song N, Song B, Yang D, Chen J, Qi A, Zhao L, Luo C, Zang Y, Liu H, Li J, Zhang B, Zhou Y, Zheng J. Characterization and noncovalent inhibition of the K63-deubiquitinase activity of SARS-CoV-2 PLpro. Antiviral Res 2024:105944. [PMID: 38914283 DOI: 10.1016/j.antiviral.2024.105944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/26/2024]
Abstract
SARS-CoV-2 papain-like protease (PLpro) could facilitate viral replication and host immune evasion by respectively hydrolyzing viral polyprotein and host ubiquitin conjugates, thereby rendering itself as an important antiviral target. Yet few noncovalent PLpro inhibitors of SARS-CoV-2 have been reported with improved directed towards pathogenic deubiquitinating activities inhibition. Herein, we report that coronavirus PLpro proteases have distinctive substrate bias and are conserved to deubiquitylate K63-linked polyubiquitination, thereby attenuating host type I interferon response. We identify a noncovalent compound specifically optimized towards halting the K63-deubiquitinase activity of SARS-CoV-2 PLpro, but not other coronavirus (CoV) counterparts or host deubiquitinase. Contrasting with GRL-0617, a SARS-CoV-1 PLpro inhibitor, SIMM-036 is 50-fold and 7-fold (half maximal inhibitory concentration (IC50)) more potent to inhibit viral replication during SARS-CoV-2 infection and restore the host interferon-β (IFN-β) response in human angiotensin-converting enzyme 2 (hACE2)-HeLa cells, respectively. Structure-activity relationship (SAR) analysis further reveals the importance of BL2 groove of PLpro, which could determine the selectivity of K63-deubiquitinase activity of the enzyme.
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Affiliation(s)
- Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Miao Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hongqing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiaqi Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ji Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Na Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chaoqiang Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dongyuan Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jin Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linxiang Zhao
- Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Zang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Hong Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jia Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wu J, Guo J, Xia S, Chen J, Cao M, Xie L, Yang C, Qiu F, Wang J. A Single-Cell Transcriptome Profiling of Triptolide-Induced Nephrotoxicity in Mice. Adv Biol (Weinh) 2024:e2400120. [PMID: 38864263 DOI: 10.1002/adbi.202400120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/16/2024] [Indexed: 06/13/2024]
Abstract
Triptolide (TP), an active component isolated from the traditional Chinese herb Tripterygium wilfordii Hook F (TWHF), shows great promise for treating inflammation-related diseases. However, its potential nephrotoxic effects remain concerning. The mechanism underlying TP-induced nephrotoxicity is inadequately elucidated, particularly at single-cell resolution. Hence, single-cell RNA sequencing (scRNA-seq) of kidney tissues from control and TP-treated mice is performed to generate a thorough description of the renal cell atlas upon TP treatment. Heterogeneous responses of nephron epithelial cells are observed after TP exposure, attributing differential susceptibility of cell subtypes to excessive reactive oxygen species and increased inflammatory responses. Moreover, TP disrupts vascular function by activating endothelial cell immunity and damaging fibroblasts. Severe immune cell damage and the activation of pro-inflammatory Macro_C1 cells are also observed with TP treatment. Additionally, ligand-receptor crosstalk analysis reveals that the SPP1 (osteopontin) signaling pathway targeting Macro_C1 cells is triggered by TP treatment, which may promote the infiltration of Macro_C1 cells to exacerbate renal toxicity. Overall, this study provides comprehensive information on the transcriptomic profiles and cellular composition of TP-associated nephrotoxicity at single-cell resolution, which can strengthen the understanding of the pathogenesis of TP-induced nephrotoxicity and provide valuable clues for the discovery of new therapeutic targets to ameliorate TP-associated nephrotoxicity.
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Affiliation(s)
- Jiangpeng Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Jinan Guo
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Siyu Xia
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Jiayun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Min Cao
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Lulin Xie
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Chuanbin Yang
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jigang Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China
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4
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Davila KMS, Nelli RK, Mora-Díaz JC, Sang Y, Miller LC, Giménez-Lirola LG. Transcriptome Analysis in Air-Liquid Interface Porcine Respiratory Epithelial Cell Cultures Reveals That the Betacoronavirus Porcine Encephalomyelitis Hemagglutinating Virus Induces a Robust Interferon Response to Infection. Viruses 2024; 16:939. [PMID: 38932231 PMCID: PMC11209522 DOI: 10.3390/v16060939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV) replicates in the upper respiratory tract and tonsils of pigs. Using an air-liquid interface porcine respiratory epithelial cells (ALI-PRECs) culture system, we demonstrated that PHEV disrupts respiratory epithelia homeostasis by impairing ciliary function and inducing antiviral, pro-inflammatory cytokine, and chemokine responses. This study explores the mechanisms driving early innate immune responses during PHEV infection through host transcriptome analysis. Total RNA was collected from ALI-PRECs at 24, 36, and 48 h post inoculation (hpi). RNA-seq analysis was performed using an Illumina Hiseq 600 to generate 100 bp paired-end reads. Differential gene expression was analyzed using DeSeq2. PHEV replicated actively in ALI-PRECs, causing cytopathic changes and progressive mucociliary disruption. Transcriptome analysis revealed downregulation of cilia-associated genes such as CILK1, DNAH11, LRRC-23, -49, and -51, and acidic sialomucin CD164L2. PHEV also activated antiviral signaling pathways, significantly increasing the expression of interferon-stimulated genes (RSAD2, MX1, IFIT, and ISG15) and chemokine genes (CCL5 and CXCL10), highlighting inflammatory regulation. This study contributes to elucidating the molecular mechanisms of the innate immune response to PHEV infection of the airway epithelium, emphasizing the critical roles of the mucociliary, interferon, and chemokine responses.
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Affiliation(s)
- Kaitlyn M. Sarlo Davila
- Infectious Bacterial Disease Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA 50010, USA;
| | - Rahul K. Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
| | - Juan C. Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA;
| | - Laura C. Miller
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA 50010, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
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Zhuang Y, Fischer JB, Nishanth G, Schlüter D. Cross-regulation of Listeria monocytogenes and the host ubiquitin system in listeriosis. Eur J Cell Biol 2024; 103:151401. [PMID: 38442571 DOI: 10.1016/j.ejcb.2024.151401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
The facultative intracellular bacterium Listeria (L.) monocytogenes may cause severe diseases in humans and animals. The control of listeriosis/L. monocytogenes requires the concerted action of cells of the innate and adaptive immune systems. In this regard, cell-intrinsic immunity of infected cells, activated by the immune responses, is crucial for the control and elimination intracellular L. monocytogenes. Both the immune response against L. monocytogenes and cell intrinsic pathogen control are critically regulated by post-translational modifications exerted by the host ubiquitin system and ubiquitin-like modifiers (Ubls). In this review, we discuss our current understanding of the role of the ubiquitin system and Ubls in listeriosis, as well as future directions of research.
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Affiliation(s)
- Yuan Zhuang
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover 30625, Germany.
| | - Johanna B Fischer
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover 30625, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover 30625, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover 30625, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
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6
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Gautam D, Sindhu A, Vats A, Rajput S, Roshan M, Pal H, De S. Characterization and expression profiling of buffalo IFN-lambda family. Vet Immunol Immunopathol 2024; 272:110770. [PMID: 38735115 DOI: 10.1016/j.vetimm.2024.110770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Interferon lambda (IFN-λ) is an important type III interferon triggered mainly by viral infection. IFN-λ binds to their heterodimeric receptors and signals through JAK-STAT pathways similar to type I IFN. In this study, we deduced the buffalo IFN-λ sequences through the polymerase chain reaction, and then studied IFN-λ's expression patterns in different tissues, and post induction with poly I:C and live MRSA using RT-qPCR. The full-length sequences of buffalo IFN-λ3, IFN-λ receptors, and a transcript variant of IFN-λ4 were determined. IFN-λ1 is identified as a pseudogene. Virus response elements and a recombination hotspot factor was observed in the regulatory region of IFN-λ. The IFN-λ3 expressed highest in lungs and monocytes but IFN-λ4 did not. The expression of Interferon Lambda Receptor 1 was tissue specific, while Interleukin 10 Receptor subunit beta was ubiquitous. Following poly I:C induction, IFN-λ3 expression was primarily observed in epithelial cells as opposed to fibroblasts, displaying cell type-dependent expression. The cytosolic RNA sensors were expressed highest in endometrial epithelial cells, whereas the endosomal receptor was higher in fibroblasts. 2',5'-oligoadenylate synthetase expressed higher in fibroblasts, myxoma resistance protein 1 and IFN-stimulated gene 56 in epithelial cells, displaying cell-specific antiviral response of the interferon stimulated genes (ISGs). The endometrial epithelial cells expressed IFN-λ3 after live S. aureus infection indicating its importance in bacterial infection. The induction of IFN-λ3 was S. aureus isolate specific at the same multiplicity of infection (MOI). This study elucidates the IFN-λ sequences, diverse expression patterns revealing tissue specificity, and specificity in response to poly I:C and bacterial stimuli, emphasising its crucial role in innate immune response modulation.
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Affiliation(s)
- Devika Gautam
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India; Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat, HR 139031, India
| | - Anil Sindhu
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat, HR 139031, India
| | - Ashutosh Vats
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India
| | - Shiveeli Rajput
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India
| | - Mayank Roshan
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India
| | - Hanshika Pal
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, HR 132001, India.
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Qin Y, Wang M, Meng X, Wang M, Jiang H, Gao Y, Li J, Zhao C, Han C, Zhao W, Zheng X. ISGylation by HERCs facilitates STING activation. Cell Rep 2024; 43:114135. [PMID: 38652662 DOI: 10.1016/j.celrep.2024.114135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Optimal activation of stimulator of interferon genes (STING) protein is crucial for host defenses against pathogens and avoiding detrimental effects. Various post-translational modifications control STING activity. However, the function of interferon (IFN)-stimulated gene (ISG) 15 modification (ISGylation) in controlling STING stability and activation is unclear. Here, we show that the E3 ISGylation ligases HECT domain- and RCC1-like domain-containing proteins (HERCs; HERC5 in humans and HERC6 in mice) facilitate STING activation by mediating ISGylation of STING at K150, preventing its K48-linked ubiquitination and degradation. Concordantly, Herc6 deficiency suppresses herpes simplex virus 1 infection-induced type I IFN responses and facilitates viral replication both in vitro and in vivo. Notably, severe acute respiratory syndrome coronavirus 2 protein papain-like protease cleaves HERC5-mediated ISGylation of STING, suppressing host antiviral responses. These data identify a mechanism by which HERCs-mediated ISGylation controls STING stability and activation and uncover the correlations and interactions of ISGylation and ubiquitination during STING activation.
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Affiliation(s)
- Ying Qin
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Min Wang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xintong Meng
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mengge Wang
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haojia Jiang
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanjie Gao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jingxin Li
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chunyuan Zhao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chaofeng Han
- Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, China
| | - Wei Zhao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, China.
| | - Xuexing Zheng
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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8
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Yang B, Tan X, Chen Y, Lin J, Liang J, Yue X, Qiao D, Wang H, Du S. The neuroprotective effects of caffeic acid phenethyl ester against methamphetamine-induced neurotoxicity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116497. [PMID: 38805827 DOI: 10.1016/j.ecoenv.2024.116497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/05/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Methamphetamine (METH) is a highly abused substance on a global scale and has the capacity to elicit toxicity within the central nervous system. The neurotoxicity induced by METH encompasses neuronal degeneration and cellular demise within the substantia nigra-striatum and hippocampus. Caffeic acid phenethyl ester (CAPE), a constituent of propolis, is a diminutive compound that demonstrates antioxidative and anti-inflammatory characteristics. Numerous investigations have demonstrated the safeguarding effects of CAPE in various neurodegenerative ailments. Our hypothesis posits that CAPE may exert a neuroprotective influence on METH-induced neurotoxicity via specific mechanisms. In order to validate the hypothesis, a series of experimental techniques including behavioral tests, immunofluorescence labeling, RNA sequencing, and western blotting were employed to investigate the neurotoxic effects of METH and the potential protective effects of CAPE. The results of our study demonstrate that CAPE effectively ameliorates cognitive memory deficits and anxiety symptoms induced by METH in mice. Furthermore, CAPE has been observed to attenuate the upregulation of neurotoxicity-associated proteins that are induced by METH exposure and also reduced the loss of hippocampal neurons in mice. Moreover, transcriptomics analysis was conducted to determine alterations in gene expression within the hippocampus of mice. Subsequently, bioinformatics analysis was employed to investigate the divergent outcomes and identify potential key genes. Interferon-stimulated gene 15 (ISG15) was successfully identified and confirmed through RT-qPCR, western blotting, and immunofluorescence techniques. Our research findings unequivocally demonstrated the neuroprotective effect of CAPE against METH-induced neurotoxicity, with ISG15 may have an important role in the underlying protective mechanism. These results offer novel perspectives on the treatment of METH-induced neurotoxicity.
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Affiliation(s)
- Bin Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xiaohui Tan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yuzhen Chen
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jing Lin
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jingjie Liang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xia Yue
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Dongfang Qiao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Huijun Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China.
| | - Sihao Du
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China.
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9
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Abdel-Haq H. Feasibility of Using a Type I IFN-Based Non-Animal Approach to Predict Vaccine Efficacy and Safety Profiles. Vaccines (Basel) 2024; 12:583. [PMID: 38932312 PMCID: PMC11209158 DOI: 10.3390/vaccines12060583] [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: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Animal-based tests are used for the control of vaccine quality. However, because highly purified and safe vaccines are now available, alternative approaches that can replace or reduce animal use for the assessment of vaccine outcomes must be established. In vitro tests for vaccine quality control exist and have already been implemented. However, these tests are specifically designed for some next-generation vaccines, and this makes them not readily available for testing other vaccines. Therefore, universal non-animal tests are still needed. Specific signatures of the innate immune response could represent a promising approach to predict the outcome of vaccines by non-animal methods. Type I interferons (IFNs) have multiple immunomodulatory activities, which are exerted through effectors called interferon stimulated genes (ISGs), and are one of the most important immune signatures that might provide potential candidate molecular biomarkers for this purpose. This paper will mainly examine if this idea might be feasible by analyzing all relevant published studies that have provided type I IFN-related biomarkers for evaluating the safety and efficacy profiles of vaccines using an advanced transcriptomic approach as an alternative to the animal methods. Results revealed that such an approach could potentially provide biomarkers predictive of vaccine outcomes after addressing some limitations.
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Affiliation(s)
- Hanin Abdel-Haq
- Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy
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10
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Liang JJ, Pitsillou E, Lau HLY, Mccubbery CP, Gan H, Hung A, Karagiannis TC. Utilization of the EpiMed Coronabank Chemical Collection to identify potential SARS-CoV-2 antivirals: in silico studies targeting the nsp14 ExoN domain and PL pro naphthalene binding site. J Mol Graph Model 2024; 131:108803. [PMID: 38815531 DOI: 10.1016/j.jmgm.2024.108803] [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: 12/08/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome encodes 29 proteins including four structural, 16 nonstructural (nsps), and nine accessory proteins (https://epimedlab.org/sars-cov-2-proteome/). Many of these proteins contain potential targetable sites for the development of antivirals. Despite the widespread use of vaccinations, the emergence of variants necessitates the investigation of new therapeutics and antivirals. Here, the EpiMed Coronabank Chemical Collection (https://epimedlab.org/crl/) was utilized to investigate potential antivirals against the nsp14 exoribonuclease (ExoN) domain. Molecular docking was performed to evaluate the binding characteristics of our chemical library against the nsp14 ExoN site. Based on the initial screen, trisjuglone, ararobinol, corilagin, and naphthofluorescein were identified as potential lead compounds. Molecular dynamics (MD) simulations were subsequently performed, with the results highlighting the stability of the lead compounds in the nsp14 ExoN site. Protein-RNA docking revealed the potential for the lead compounds to disrupt the interaction with RNA when bound to the ExoN site. Moreover, hypericin, cyanidin-3-O-glucoside, and rutin were previously identified as lead compounds targeting the papain-like protease (PLpro) naphthalene binding site. Through performing MD simulations, the stability and interactions of lead compounds with PLpro were further examined. Overall, given the critical role of the exonuclease activity of nsp14 in ensuring viral fidelity and the multifunctional role of PLpro in viral pathobiology and replication, these nsps represent important targets for antiviral drug development. Our databases can be utilized for in silico studies, such as the ones performed here, and this approach can be applied to other potentially druggable SARS-CoV-2 protein targets.
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Affiliation(s)
- Julia J Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Hannah L Y Lau
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cian P Mccubbery
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hockxuen Gan
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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11
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Baker T, Sharifian H, Newcombe PJ, Gavin PG, Lazarus MN, Ramaswamy M, White WI, Ferrari N, Muthas D, Tummala R, Morand EF, Furie RA, Vital EM, Chamberlain C, Platt A, Al-Mossawi H, Brohawn PZ, Csomor E. Type I interferon blockade with anifrolumab in patients with systemic lupus erythematosus modulates key immunopathological pathways in a gene expression and proteomic analysis of two phase 3 trials. Ann Rheum Dis 2024:ard-2023-225445. [PMID: 38569851 DOI: 10.1136/ard-2023-225445] [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: 12/20/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024]
Abstract
INTRODUCTION Anifrolumab is a type I interferon (IFN) receptor 1 (IFNAR1) blocking antibody approved for treating patients with systemic lupus erythematosus (SLE). Here, we investigated the immunomodulatory mechanisms of anifrolumab using longitudinal transcriptomic and proteomic analyses of the 52-week, randomised, phase 3 TULIP-1 and TULIP-2 trials. METHODS Patients with moderate to severe SLE were enrolled in TULIP-1 and TULIP-2 and received intravenous anifrolumab or placebo alongside standard therapy. Whole-blood expression of 18 017 genes using genome-wide RNA sequencing (RNA-seq) (pooled TULIP; anifrolumab, n=244; placebo, n=258) and 184 plasma proteins using Olink and Simoa panels (TULIP-1; anifrolumab, n=124; placebo, n=132) were analysed. We compared treatment groups via gene set enrichment analysis using MetaBase pathway analysis, blood transcriptome modules, in silico deconvolution of RNA-seq and longitudinal linear mixed effect models for gene counts and protein levels. RESULTS Compared with placebo, anifrolumab modulated >2000 genes by week 24, with overlapping results at week 52, and 41 proteins by week 52. IFNAR1 blockade with anifrolumab downregulated multiple type I and II IFN-induced gene modules/pathways and type III IFN-λ protein levels, and impacted apoptosis-associated and neutrophil extracellular traps-(NET)osis-associated transcriptional pathways, innate cell activating chemokines and receptors, proinflammatory cytokines and B-cell activating cytokines. In silico deconvolution of RNA-seq data indicated an increase from baseline of mucosal-associated invariant and γδT cells and a decrease of monocytes following anifrolumab treatment. DISCUSSION Type I IFN blockade with anifrolumab modulated multiple inflammatory pathways downstream of type I IFN signalling, including apoptotic, innate and adaptive mechanisms that play key roles in SLE immunopathogenesis.
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Affiliation(s)
- Tina Baker
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Hoda Sharifian
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Paul J Newcombe
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Patrick G Gavin
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Mark N Lazarus
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Madhu Ramaswamy
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Wendy I White
- Clinical & Quantitative Pharmacology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Nicola Ferrari
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Daniel Muthas
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Raj Tummala
- Clinical Development, Late Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Eric F Morand
- Centre for Inflammatory Diseases, Monash University, Melbourne, Victoria, Australia
| | - Richard A Furie
- Division of Rheumatology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Great Neck, New York, USA
| | - Edward M Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Chris Chamberlain
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Adam Platt
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Hussein Al-Mossawi
- Clinical Development, Late Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Philip Z Brohawn
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Eszter Csomor
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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12
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Ye L, Li P, Wang M, Wu F, Han S, Ma L. Profiling of Early Immune Responses to Vaccination Using THP-1-Derived Dendritic Cells. Int J Mol Sci 2024; 25:5509. [PMID: 38791547 PMCID: PMC11121899 DOI: 10.3390/ijms25105509] [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: 04/02/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
The COVID-19 pandemic has made assessing vaccine efficacy more challenging. Besides neutralizing antibody assays, systems vaccinology studies use omics technology to reveal immune response mechanisms and identify gene signatures in human peripheral blood mononuclear cells (PBMCs). However, due to their low proportion in PBMCs, profiling the immune response signatures of dendritic cells (DCs) is difficult. Here, we develop a predictive model for evaluating early immune responses in dendritic cells. We establish a THP-1-derived dendritic cell (TDDC) model and stimulate their maturation in vitro with an optimal dose of attenuated yellow fever 17D (YF-17D). Transcriptomic analysis reveals that type I interferon (IFN-I)-induced immunity plays a key role in dendritic cells. IFN-I regulatory biomarkers (IRF7, SIGLEC1) and IFN-I-inducible biomarkers (IFI27, IFI44, IFIT1, IFIT3, ISG15, MX1, OAS2, OAS3) are identified and validated in vitro and in vivo. Furthermore, we apply this TDDC approach to various types of vaccines, providing novel insights into their early immune response signatures and their heterogeneity in vaccine recipients. Our findings suggest that a standardizable TDDC model is a promising predictive approach to assessing early immunity in DCs. Further research into vaccine efficacy assessment approaches on various types of immune cells could lead to a systemic regimen for vaccine development in the future.
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Affiliation(s)
- Lei Ye
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518052, China
| | - Ping Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Mingzhe Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Sanyang Han
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (L.Y.); (P.L.); (M.W.); (F.W.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518052, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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13
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Pilcher WC, Yao L, Gonzalez-Kozlova E, Pita-Juarez Y, Karagkouni D, Acharya CR, Michaud ME, Hamilton M, Nanda S, Song Y, Sato K, Wang JT, Satpathy S, Ma Y, Schulman J, D'Souza D, Jayasinghe RG, Cheloni G, Bakhtiari M, Pabustan N, Nie K, Foltz JA, Saldarriaga I, Alaaeldin R, Lepisto E, Chen R, Fiala MA, Thomas BE, Cook A, Dos Santos JV, Chiang IL, Figueiredo I, Fortier J, Slade M, Oh ST, Rettig MP, Anderson E, Li Y, Dasari S, Strausbauch MA, Simon VA, Rahman AH, Chen Z, Lagana A, DiPersio JF, Rosenblatt J, Kim-Schulze S, Dhodapkar MV, Lonial S, Kumar S, Bhasin SS, Kourelis T, Vij R, Avigan D, Cho HJ, Mulligan G, Ding L, Gnjatic S, Vlachos IS, Bhasin M. A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.593193. [PMID: 38798338 PMCID: PMC11118283 DOI: 10.1101/2024.05.15.593193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Multiple Myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We established a harmonized consortium to generate an Immune Atlas of MM aimed at informing disease etiology, risk stratification, and potential therapeutic strategies. We generated a transcriptome profile of 1,149,344 single cells from the bone marrow of 263 newly diagnosed patients enrolled in the CoMMpass study and characterized immune and hematopoietic cell populations. Associating cell abundances and gene expression with disease progression revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing patients. Furthermore, signaling analyses suggested active intercellular communication involving APRIL-BCMA, potentially promoting tumor growth and survival. Finally, we demonstrate that integrating immune cell levels with genetic information can significantly improve patient stratification.
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Affiliation(s)
- William C. Pilcher
- Coultier Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Edgar Gonzalez-Kozlova
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yered Pita-Juarez
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dimitra Karagkouni
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Marina E Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | | | - Shivani Nanda
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Julia T. Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Sarthak Satpathy
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, GA, USA
| | - Yuling Ma
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Darwin D'Souza
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reyka G. Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | | | - Kai Nie
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer A. Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Rania Alaaeldin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | | | - Rachel Chen
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark A. Fiala
- Bone Marrow Transplantation & Leukemia Section, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Beena E Thomas
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | | | - Junia Vieira Dos Santos
- Tisch Cancer Institute, Department of Immunology and Immunotherapy, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - I-ling Chiang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Igor Figueiredo
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julie Fortier
- Bone Marrow Transplantation & Leukemia Section, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Slade
- Bone Marrow Transplantation & Leukemia Section, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen T. Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael P. Rettig
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Ying Li
- Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Adeeb H Rahman
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihong Chen
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Lagana
- Tisch Cancer Institute, Department of Immunology and Immunotherapy, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F. DiPersio
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jacalyn Rosenblatt
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhav V Dhodapkar
- Department of Hematology Oncology, Emory School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory School of Medicine, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta
| | | | - Swati S Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | | | - Ravi Vij
- Bone Marrow Transplantation & Leukemia Section, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - David Avigan
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Tisch Cancer Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ioannis S Vlachos
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA
| | - Manoj Bhasin
- Coultier Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
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14
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Mantel N, Piras-Douce F, Chautard E, Marcos-Lopez E, Bodinham CL, Cosma A, Courtois V, Dhooge N, Gautheron S, Kaufmann SHE, Pizzoferro K, Lewis DJM, Martinon F, Pagnon A, Raynal F, Dereuddre-Bosquet N, Le Grand R. Cynomolgus macaques as a translational model of human immune responses to yellow fever 17D vaccination. J Virol 2024; 98:e0151623. [PMID: 38567951 PMCID: PMC11092345 DOI: 10.1128/jvi.01516-23] [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: 10/11/2023] [Accepted: 12/22/2023] [Indexed: 05/15/2024] Open
Abstract
The non-human primate (NHP) model (specifically rhesus and cynomolgus macaques) has facilitated our understanding of the pathogenic mechanisms of yellow fever (YF) disease and allowed the evaluation of the safety and efficacy of YF-17D vaccines. However, the accuracy of this model in mimicking vaccine-induced immunity in humans remains to be fully determined. We used a systems biology approach to compare hematological, biochemical, transcriptomic, and innate and antibody-mediated immune responses in cynomolgus macaques and human participants following YF-17D vaccination. Immune response progression in cynomolgus macaques followed a similar course as in adult humans but with a slightly earlier onset. Yellow fever virus neutralizing antibody responses occurred earlier in cynomolgus macaques [by Day 7[(D7)], but titers > 10 were reached in both species by D14 post-vaccination and were not significantly different by D28 [plaque reduction neutralization assay (PRNT)50 titers 3.6 Log vs 3.5 Log in cynomolgus macaques and human participants, respectively; P = 0.821]. Changes in neutrophils, NK cells, monocytes, and T- and B-cell frequencies were higher in cynomolgus macaques and persisted for 4 weeks versus less than 2 weeks in humans. Low levels of systemic inflammatory cytokines (IL-1RA, IL-8, MIP-1α, IP-10, MCP-1, or VEGF) were detected in either or both species but with no or only slight changes versus baseline. Similar changes in gene expression profiles were elicited in both species. These included enriched and up-regulated type I IFN-associated viral sensing, antiviral innate response, and dendritic cell activation pathways D3-D7 post-vaccination in both species. Hematological and blood biochemical parameters remained relatively unchanged versus baseline in both species. Low-level YF-17D viremia (RNAemia) was transiently detected in some cynomolgus macaques [28% (5/18)] but generally absent in humans [except one participant (5%; 1/20)].IMPORTANCECynomolgus macaques were confirmed as a valid surrogate model for replicating YF-17D vaccine-induced responses in humans and suggest a key role for type I IFN.
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Affiliation(s)
| | | | | | - Ernesto Marcos-Lopez
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Caroline L. Bodinham
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - Antonio Cosma
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | | | - Nina Dhooge
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | | | - Stefan H. E. Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany; Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, Texas, USA
| | - Kathleen Pizzoferro
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - David J. M. Lewis
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - Frédéric Martinon
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Anke Pagnon
- Research and Development, Sanofi, Marcy L'Etoile, France
| | - Franck Raynal
- Research and Development, Sanofi, Marcy L'Etoile, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
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15
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Bredow C, Thery F, Wirth EK, Ochs S, Kespohl M, Kleinau G, Kelm N, Gimber N, Schmoranzer J, Voss M, Klingel K, Spranger J, Renko K, Ralser M, Mülleder M, Heuser A, Knobeloch KP, Scheerer P, Kirwan J, Brüning U, Berndt N, Impens F, Beling A. ISG15 blocks cardiac glycolysis and ensures sufficient mitochondrial energy production during Coxsackievirus B3 infection. Cardiovasc Res 2024; 120:644-657. [PMID: 38309955 PMCID: PMC11074791 DOI: 10.1093/cvr/cvae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/10/2023] [Accepted: 12/12/2023] [Indexed: 02/05/2024] Open
Abstract
AIMS Virus infection triggers inflammation and, may impose nutrient shortage to the heart. Supported by type I interferon (IFN) signalling, cardiomyocytes counteract infection by various effector processes, with the IFN-stimulated gene of 15 kDa (ISG15) system being intensively regulated and protein modification with ISG15 protecting mice Coxsackievirus B3 (CVB3) infection. The underlying molecular aspects how the ISG15 system affects the functional properties of respective protein substrates in the heart are unknown. METHODS AND RESULTS Based on the protective properties due to protein ISGylation, we set out a study investigating CVB3-infected mice in depth and found cardiac atrophy with lower cardiac output in ISG15-/- mice. By mass spectrometry, we identified the protein targets of the ISG15 conjugation machinery in heart tissue and explored how ISGylation affects their function. The cardiac ISGylome showed a strong enrichment of ISGylation substrates within glycolytic metabolic processes. Two control enzymes of the glycolytic pathway, hexokinase 2 (HK2) and phosphofructokinase muscle form (PFK1), were identified as bona fide ISGylation targets during infection. In an integrative approach complemented with enzymatic functional testing and structural modelling, we demonstrate that protein ISGylation obstructs the activity of HK2 and PFK1. Seahorse-based investigation of glycolysis in cardiomyocytes revealed that, by conjugating proteins, the ISG15 system prevents the infection-/IFN-induced up-regulation of glycolysis. We complemented our analysis with proteomics-based advanced computational modelling of cardiac energy metabolism. Our calculations revealed an ISG15-dependent preservation of the metabolic capacity in cardiac tissue during CVB3 infection. Functional profiling of mitochondrial respiration in cardiomyocytes and mouse heart tissue by Seahorse technology showed an enhanced oxidative activity in cells with a competent ISG15 system. CONCLUSION Our study demonstrates that ISG15 controls critical nodes in cardiac metabolism. ISG15 reduces the glucose demand, supports higher ATP production capacity in the heart, despite nutrient shortage in infection, and counteracts cardiac atrophy and dysfunction.
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MESH Headings
- Animals
- Humans
- Male
- Coxsackievirus Infections/metabolism
- Coxsackievirus Infections/virology
- Coxsackievirus Infections/genetics
- Cytokines/genetics
- Cytokines/metabolism
- Disease Models, Animal
- Energy Metabolism
- Enterovirus B, Human/pathogenicity
- Enterovirus B, Human/metabolism
- Glycolysis
- Host-Pathogen Interactions
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/virology
- Myocytes, Cardiac/pathology
- Protein Processing, Post-Translational
- Signal Transduction
- Ubiquitins/metabolism
- Ubiquitins/genetics
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Affiliation(s)
- Clara Bredow
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Fabien Thery
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Eva Katrin Wirth
- Deutsches Zentrum für Herz-Kreislauf-Forschung, partner site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Sarah Ochs
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Meike Kespohl
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, partner site Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, Germany
| | - Nicolas Kelm
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Niclas Gimber
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Advanced Medical Bioimaging Core Facility, Berlin, Germany
| | - Jan Schmoranzer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Advanced Medical Bioimaging Core Facility, Berlin, Germany
| | - Martin Voss
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Karin Klingel
- University of Tübingen, Cardiopathology, Institute for Pathology and Neuropathology, Tübingen, Germany
| | - Joachim Spranger
- Deutsches Zentrum für Herz-Kreislauf-Forschung, partner site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Kostja Renko
- German Federal Institute for Risk Assessment (BfR), German Centre for the Protection of Laboratory Animals (Bf3R), Berlin, Germany
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility—High-Throughput Mass Spectrometry, Berlin, Germany
| | - Michael Mülleder
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility—High-Throughput Mass Spectrometry, Berlin, Germany
| | - Arnd Heuser
- Max-Delbrueck-Center (MDC) for Molecular Medicine, Animal Phenotyping Platform, Berlin, Germany
| | - Klaus-Peter Knobeloch
- University of Freiburg, Institute of Neuropathology, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Patrick Scheerer
- Deutsches Zentrum für Herz-Kreislauf-Forschung, partner site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, Germany
| | - Jennifer Kirwan
- Berlin Institute of Health at Charité Universitätsmedizin, Metabolomics, Charitéplatz 1 Berlin 10117, Germany
| | - Ulrike Brüning
- Berlin Institute of Health at Charité Universitätsmedizin, Metabolomics, Charitéplatz 1 Berlin 10117, Germany
| | - Nikolaus Berndt
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Department of Molecular Toxicology, Nuthetal, Germany
- Deutsches Herzzentrum der Charité (DHZC), Institute of Computer-assisted Cardiovascular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Antje Beling
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, partner site Berlin, Berlin, Germany
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16
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Zhang B, Yan L, Lin C, Liu Y, Zhao C, Wang P, Zhang B, Zhang Y, Qiu L. Asymmetric evolution of ISG15 homologs and the immune adaptation to LBUSV infection in spotted seabass (Lateolabrax maculatus). FISH & SHELLFISH IMMUNOLOGY 2024; 148:109441. [PMID: 38354965 DOI: 10.1016/j.fsi.2024.109441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/15/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
The battle between host and viral is ubiquitous across all ecosystems. Despite this, research is scarce on the antiviral characteristics of fish, particularly in those that primarily rely on innate immune responses. This study, comprehensively explored the genetic and antiviral features of ISG15 in spotted seabass, focusing on its response to largemouth bass ulcerative syndrome virus (LBUSV). Through whole-genome BLAST and PCR cloning, two ISG15 homologs, namely LmISG15a and LmISG15b, were identified in spotted seabass, both encoding highly conserved proteins. However, a distinctive contrast emerged in their expression patterns, with LmISG15a exhibiting high expression in immune organs while LmISG15b remained largely silent across various organs. Regulatory elements analysis indicated an asymmetric evolution of the two ISG15s, with the minimal expression of LmISG15b may attribute to the loss of a necessary ISRE and an additional instability "ATTTA" motif. Association analysis demonstrated a significant correlation between LmISG15a expression and LBUSV infection. Subsequent antiviral activity detection revealed that LmISG15a interacted with LBUSV, inhibiting its replication by activating ISGylation and downstream pro-inflammatory mediators. In summary, this study unveils a distinct evolutionary strategy of fish antiviral gene ISG15 and delineates its kinetic characteristics in response to LBUSV infection.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
| | - Lulu Yan
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Changhong Lin
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; College of Aqua-life Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Liu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chao Zhao
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Pengfei Wang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Bo Zhang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
| | - Yanhong Zhang
- Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, China
| | - Lihua Qiu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
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17
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Ba C, Tian C, Bo X, Xu C, Zhang Y, Sun X, Nan Y, Wu C. Porcine HERC6 acts as major E3 ligase for ISGylation and is auto-ISGylated for effective ISGylation in porcine. Microb Pathog 2024; 190:106633. [PMID: 38554778 DOI: 10.1016/j.micpath.2024.106633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Interferon-stimulated gene product 15 (ISG15) can be conjugated to substrates through ISGylation. Currently, the E3 ligase for porcine ISGylation remains unclear. Here, we identified porcine HERC5 and HERC6 (pHERC5/6) as ISGylation E3 ligases with pHERC6 acting as a major one by reconstitution of porcine ISGylation system in HEK-293 T cell via co-transfecting E1, E2 and porcine ISG15(pISG15) genes. Meanwhile, our data demonstrated that co-transfection of pISG15 and pHERC5/6 was sufficient to confer ISGylation, suggesting E1 and E2 of ISGylation are interchangeable between human and porcine. Using an immunoprecipitation based ISGylation analysis, our data revealed pHERC6 was a substrate for ISGylation and confirmed that K707 and K993 of pHERC6 were auto-ISGylation sites. Mutation of these sites reduced pHERC6 half-life and inhibited ISGylation, suggesting that auto-ISGylation of pHERC6 was required for effective ISGylation. Conversely, sustained ISGylation induced by overexpression of pISG15 and pHERC6 could be inhibited by a well-defined porcine ISGylation antagonist, the ovarian tumor (OTU) protease domain of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)-nsp2 and PRRSV-nsp1β, further indicating such method could be used for identification of virus-encoded ISG15 antagonist. In conclusion, our study contributes new insights towards porcine ISGylation system and provides a novel tool for screening viral-encoded ISG15 antagonist.
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Affiliation(s)
- Cuiyu Ba
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chaonan Tian
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xueying Bo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chang Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yi Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiangyu Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chunyan Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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18
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Wang Y, Feng H, Li X, Ruan Y, Guo Y, Cui X, Zhang P, Li Y, Wang X, Wang X, Wei L, Yi Y, Zhang L, Yang X, Liu H. Dampening of ISGylation of RIG-I by ADAP regulates type I interferon response of macrophages to RNA virus infection. PLoS Pathog 2024; 20:e1012230. [PMID: 38776321 PMCID: PMC11111093 DOI: 10.1371/journal.ppat.1012230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
While macrophage is one of the major type I interferon (IFN-I) producers in multiple tissues during viral infections, it also serves as an important target cell for many RNA viruses. However, the regulatory mechanism for the IFN-I response of macrophages to respond to a viral challenge is not fully understood. Here we report ADAP, an immune adaptor protein, is indispensable for the induction of the IFN-I response of macrophages to RNA virus infections via an inhibition of the conjugation of ubiquitin-like ISG15 (ISGylation) to RIG-I. Loss of ADAP increases RNA virus replication in macrophages, accompanied with a decrease in LPS-induced IFN-β and ISG15 mRNA expression and an impairment in the RNA virus-induced phosphorylation of IRF3 and TBK1. Moreover, using Adap-/- mice, we show ADAP deficiency strongly increases the susceptibility of macrophages to RNA-virus infection in vivo. Mechanically, ADAP selectively interacts and functionally cooperates with RIG-I but not MDA5 in the activation of IFN-β transcription. Loss of ADAP results in an enhancement of ISGylation of RIG-I, whereas overexpression of ADAP exhibits the opposite effect in vitro, indicating ADAP is detrimental to the RNA virus-induced ISGylation of RIG-I. Together, our data demonstrate a novel antagonistic activity of ADAP in the cell-intrinsic control of RIG-I ISGylation, which is indispensable for initiating and sustaining the IFN-I response of macrophages to RNA virus infections and replication.
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Affiliation(s)
- Yan Wang
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Haixia Feng
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Xiao Li
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Yina Ruan
- Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Department of Veterinary Medicine, Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Yueping Guo
- Department of Veterinary Medicine, Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Xinxing Cui
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Pengchao Zhang
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Yanli Li
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Xinning Wang
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Xingran Wang
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
| | - Luxin Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Yulan Yi
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Lifeng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaodong Yang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu Province, China
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19
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Ghosh C, Kakar R, Hoyle RG, Liu Z, Guo C, Li J, Wang XY, Sun Y. Type I gamma phosphatidylinositol phosphate 5-kinase i5 controls cell sensitivity to interferon. Dev Cell 2024; 59:1028-1042.e5. [PMID: 38452758 PMCID: PMC11043016 DOI: 10.1016/j.devcel.2024.02.005] [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: 07/08/2023] [Revised: 12/21/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
The interferon signaling pathway is critical for host defense by serving diverse functions in both innate and adaptive immune responses. Here, we show that type I gamma phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme that synthesizes phosphatidylinositol-4,5-bisphosphate (PI4,5P2), controls the sensitivity to interferon in both human and mouse cells. PIPKIγi5 directly binds to the interferon-gamma (IFN-γ) downstream effector signal transducer and activator of transcription 1 (STAT1), which suppresses the STAT1 dimerization, IFN-γ-induced STAT1 nuclear translocation, and transcription of IFN-γ-responsive genes. Depletion of PIPKIγi5 significantly enhances IFN-γ signaling and strengthens an antiviral response. In addition, PIPKIγi5-synthesized PI4,5P2 can bind to STAT1 and promote the PIPKIγi5-STAT1 interaction. Similar to its interaction with STAT1, PIPKIγi5 is capable of interacting with other members of the STAT family, including STAT2 and STAT3, thereby suppressing the expression of genes mediated by these transcription factors. These findings identify the function of PIPKIγi5 in immune regulation.
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Affiliation(s)
- Chinmoy Ghosh
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ruchi Kakar
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Rosalie G Hoyle
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Zheng Liu
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Chunqing Guo
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jiong Li
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yue Sun
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.
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20
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Jové V, Wheeler H, Lee CW, Healy DR, Levine K, Ralph EC, Yamaguchi M, Jiang ZK, Cabral E, Xu Y, Stock J, Yang B, Giddabasappa A, Loria P, Casimiro-Garcia A, Kessler BM, Pinto-Fernández A, Frattini V, Wes PD, Wang F. Type I interferon regulation by USP18 is a key vulnerability in cancer. iScience 2024; 27:109593. [PMID: 38632987 PMCID: PMC11022047 DOI: 10.1016/j.isci.2024.109593] [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: 05/26/2023] [Revised: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Precise regulation of Type I interferon signaling is crucial for combating infection and cancer while avoiding autoimmunity. Type I interferon signaling is negatively regulated by USP18. USP18 cleaves ISG15, an interferon-induced ubiquitin-like modification, via its canonical catalytic function, and inhibits Type I interferon receptor activity through its scaffold role. USP18 loss-of-function dramatically impacts immune regulation, pathogen susceptibility, and tumor growth. However, prior studies have reached conflicting conclusions regarding the relative importance of catalytic versus scaffold function. Here, we develop biochemical and cellular methods to systematically define the physiological role of USP18. By comparing a patient-derived mutation impairing scaffold function (I60N) to a mutation disrupting catalytic activity (C64S), we demonstrate that scaffold function is critical for cancer cell vulnerability to Type I interferon. Surprisingly, we discovered that human USP18 exhibits minimal catalytic activity, in stark contrast to mouse USP18. These findings resolve human USP18's mechanism-of-action and enable USP18-targeted therapeutics.
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Affiliation(s)
- Veronica Jové
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Heather Wheeler
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - David R. Healy
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Kymberly Levine
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Erik C. Ralph
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Masaya Yamaguchi
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Edward Cabral
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | - Yingrong Xu
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Jeffrey Stock
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Bing Yang
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | | | - Paula Loria
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Véronique Frattini
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Paul D. Wes
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Feng Wang
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
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21
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Kahraman K, Robson SA, Göcenler O, Yenici CM, Tozkoparan CD, Klein JM, Dötsch V, Elgin ES, Haas AL, Ziarek JJ, Dağ Ç. Characterizing the monomer-dimer equilibrium of UbcH8/Ube2L6: A combined SAXS and NMR study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.13.536743. [PMID: 37090523 PMCID: PMC10120734 DOI: 10.1101/2023.04.13.536743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain, and the conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins through a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a literal central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral immunity. Depending on the type of conjugated protein and the ultimate target protein, E2 enzymes have been shown to function as monomers, dimers, or both. UbcH8 has been crystalized in both monomeric and dimeric forms, but the functional state is unclear. Here, we used a combined approach of small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy to characterize UbcH8's oligomeric state in solution. SAXS revealed a dimeric UbcH8 structure that could be dissociated when fused N-terminally to glutathione S-transferase. NMR spectroscopy validated the presence of a concentration-dependent monomer-dimer equilibrium and suggested a backside dimerization interface. Chemical shift perturbation and peak intensity analysis further suggest dimer-induced conformational dynamics at E1 and E3 interfaces - providing hypotheses for the protein's functional mechanisms. Our study highlights the power of combining NMR and SAXS techniques in providing structural information about proteins in solution.
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Affiliation(s)
- Kerem Kahraman
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Scott A. Robson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, IL, 460611, USA
| | - Oktay Göcenler
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Cansu M. Yenici
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Cansu D. Tozkoparan
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Jennifer M. Klein
- Department of Biochemistry and Molecular Biology, LSUHSC-School of Medicine, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
| | - Emine Sonay Elgin
- Muğla Sıtkı Koçman University, College of Sciences, Department of Chemistry, Mugla, 48000, Turkey
| | - Arthur L. Haas
- Department of Biochemistry and Molecular Biology, LSUHSC-School of Medicine, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Joshua J. Ziarek
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, IL, 460611, USA
| | - Çağdaş Dağ
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), Koc University, Istanbul, Turkey
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22
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Schneegans S, Löptien J, Mojzisch A, Loreth D, Kretz O, Raschdorf C, Hanssen A, Gocke A, Siebels B, Gunasekaran K, Ding Y, Oliveira-Ferrer L, Brylka L, Schinke T, Schlüter H, Paatero I, Voß H, Werner S, Pantel K, Wikman H. HERC5 downregulation in non-small cell lung cancer is associated with altered energy metabolism and metastasis. J Exp Clin Cancer Res 2024; 43:110. [PMID: 38605423 PMCID: PMC11008035 DOI: 10.1186/s13046-024-03020-z] [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: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Metastasis is the leading cause of cancer-related death in non-small cell lung cancer (NSCLC) patients. We previously showed that low HERC5 expression predicts early tumor dissemination and a dismal prognosis in NSCLC patients. Here, we performed functional studies to unravel the mechanism underlying the "metastasis-suppressor" effect of HERC5, with a focus on mitochondrial metabolism pathways. METHODS We assessed cell proliferation, colony formation potential, anchorage-independent growth, migration, and wound healing in NSCLC cell line models with HERC5 overexpression (OE) or knockout (KO). To study early tumor cell dissemination, we used these cell line models in zebrafish experiments and performed intracardial injections in nude mice. Mass spectrometry (MS) was used to analyze protein changes in whole-cell extracts. Furthermore, electron microscopy (EM) imaging, cellular respiration, glycolytic activity, and lactate production were used to investigate the relationships with mitochondrial energy metabolism pathways. RESULTS Using different in vitro NSCLC cell line models, we showed that NSCLC cells with low HERC5 expression had increased malignant and invasive properties. Furthermore, two different in vivo models in zebrafish and a xenograft mouse model showed increased dissemination and metastasis formation (in particular in the brain). Functional enrichment clustering of MS data revealed an increase in mitochondrial proteins in vitro when HERC5 levels were high. Loss of HERC5 leads to an increased Warburg effect, leading to improved adaptation and survival under prolonged inhibition of oxidative phosphorylation. CONCLUSIONS Taken together, these results indicate that low HERC5 expression increases the metastatic potential of NSCLC in vitro and in vivo. Furthermore, HERC5-induced proteomic changes influence mitochondrial pathways, ultimately leading to alterations in energy metabolism and demonstrating its role as a new potential metastasis suppressor gene.
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Affiliation(s)
- Svenja Schneegans
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Jana Löptien
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Angelika Mojzisch
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Desirée Loreth
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Raschdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Annkathrin Hanssen
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Antonia Gocke
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karthikeyan Gunasekaran
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yi Ding
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Laura Brylka
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ilkka Paatero
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Hannah Voß
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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23
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Tran DT, Batchu SN, Advani A. Interferons and interferon-related pathways in heart disease. Front Cardiovasc Med 2024; 11:1357343. [PMID: 38665231 PMCID: PMC11043610 DOI: 10.3389/fcvm.2024.1357343] [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: 12/17/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Interferons (IFNs) and IFN-related pathways play key roles in the defence against microbial infection. However, these processes may also be activated during the pathogenesis of non-infectious diseases, where they may contribute to organ injury, or function in a compensatory manner. In this review, we explore the roles of IFNs and IFN-related pathways in heart disease. We consider the cardiac effects of type I IFNs and IFN-stimulated genes (ISGs); the emerging role of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway; the seemingly paradoxical effects of the type II IFN, IFN-γ; and the varied actions of the interferon regulatory factor (IRF) family of transcription factors. Recombinant IFNs and small molecule inhibitors of mediators of IFN receptor signaling are already employed in the clinic for the treatment of some autoimmune diseases, infections, and cancers. There has also been renewed interest in IFNs and IFN-related pathways because of their involvement in SARS-CoV-2 infection, and because of the relatively recent emergence of cGAS-STING as a pattern recognition receptor-activated pathway. Whether these advances will ultimately result in improvements in the care of those experiencing heart disease remains to be determined.
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Affiliation(s)
| | | | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
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24
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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25
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Homma H, Yoshioka Y, Fujita K, Shirai S, Hama Y, Komano H, Saito Y, Yabe I, Okano H, Sasaki H, Tanaka H, Okazawa H. Dynamic molecular network analysis of iPSC-Purkinje cells differentiation delineates roles of ISG15 in SCA1 at the earliest stage. Commun Biol 2024; 7:413. [PMID: 38594382 PMCID: PMC11003991 DOI: 10.1038/s42003-024-06066-z] [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: 05/03/2023] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
Better understanding of the earliest molecular pathologies of all neurodegenerative diseases is expected to improve human therapeutics. We investigated the earliest molecular pathology of spinocerebellar ataxia type 1 (SCA1), a rare familial neurodegenerative disease that primarily induces death and dysfunction of cerebellum Purkinje cells. Extensive prior studies have identified involvement of transcription or RNA-splicing factors in the molecular pathology of SCA1. However, the regulatory network of SCA1 pathology, especially central regulators of the earliest developmental stages and inflammatory events, remains incompletely understood. Here, we elucidated the earliest developmental pathology of SCA1 using originally developed dynamic molecular network analyses of sequentially acquired RNA-seq data during differentiation of SCA1 patient-derived induced pluripotent stem cells (iPSCs) to Purkinje cells. Dynamic molecular network analysis implicated histone genes and cytokine-relevant immune response genes at the earliest stages of development, and revealed relevance of ISG15 to the following degradation and accumulation of mutant ataxin-1 in Purkinje cells of SCA1 model mice and human patients.
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Affiliation(s)
- Hidenori Homma
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yuki Yoshioka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Research Center for Child Mental Development, Kanazawa University, 13-1 Takaramachi, Kanazawa-shi, Ishikawa, 920-8640, Japan
| | - Shinichi Shirai
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Yuka Hama
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hajime Komano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yuko Saito
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Ichiro Yabe
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hidenao Sasaki
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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26
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O'Leary K, Zheng D. Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs. NPJ Syst Biol Appl 2024; 10:36. [PMID: 38580667 PMCID: PMC10997786 DOI: 10.1038/s41540-024-00364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as "replicates" for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.
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Affiliation(s)
- Kevin O'Leary
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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27
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Attreed SE, Silva C, Rodriguez-Calzada M, Mogulothu A, Abbott S, Azzinaro P, Canning P, Skidmore L, Nelson J, Knudsen N, Medina GN, de los Santos T, Díaz-San Segundo F. Prophylactic treatment with PEGylated bovine IFNλ3 effectively bridges the gap in vaccine-induced immunity against FMD in cattle. Front Microbiol 2024; 15:1360397. [PMID: 38638908 PMCID: PMC11024232 DOI: 10.3389/fmicb.2024.1360397] [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: 12/23/2023] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
Foot-and-mouth disease (FMD) is a vesicular disease of cloven-hoofed animals with devastating economic implications. The current FMD vaccine, routinely used in enzootic countries, requires at least 7 days to induce protection. However, FMD vaccination is typically not recommended for use in non-enzootic areas, underscoring the need to develop new fast-acting therapies for FMD control during outbreaks. Interferons (IFNs) are among the immune system's first line of defense against viral infections. Bovine type III IFN delivered by a replication defective adenovirus (Ad) vector has effectively blocked FMD in cattle. However, the limited duration of protection-usually only 1-3 days post-treatment (dpt)-diminishes its utility as a field therapeutic. Here, we test whether polyethylene glycosylation (PEGylation) of recombinant bovine IFNλ3 (PEGboIFNλ3) can extend the duration of IFN-induced prevention of FMDV infection in both vaccinated and unvaccinated cattle. We treated groups of heifers with PEGboIFNλ3 alone or in combination with an adenovirus-based FMD O1Manisa vaccine (Adt-O1M) at either 3 or 5 days prior to challenge with homologous wild type FMDV. We found that pre-treatment with PEGboIFNλ3 was highly effective at preventing clinical FMD when administered at either time point, with or without co-administration of Adt-O1M vaccine. PEGboIFNλ3 protein was detectable systemically for >10 days and antiviral activity for 4 days following administration. Furthermore, in combination with Adt-O1M vaccine, we observed a strong induction of FMDV-specific IFNγ+ T cell response, demonstrating its adjuvanticity when co-administered with a vaccine. Our results demonstrate the promise of this modified IFN as a pre-exposure prophylactic therapy for use in emergency outbreak scenarios.
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Affiliation(s)
- Sarah E. Attreed
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
| | - Christina Silva
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
| | - Monica Rodriguez-Calzada
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
- Oak Ridge Institute for Science and Education Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, United States
| | - Aishwarya Mogulothu
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, United States
| | - Sophia Abbott
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
- Animal Biosciences and Biotechnology Laboratory, Northeast Area, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, United States
| | - Paul Azzinaro
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
| | | | | | - Jay Nelson
- Ambrx Biopharma, Inc., La Jolla, CA, United States
| | - Nick Knudsen
- Ambrx Biopharma, Inc., La Jolla, CA, United States
| | - Gisselle N. Medina
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
- National Bio-and Agro-Defense Facility, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS, United States
| | - Teresa de los Santos
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
| | - Fayna Díaz-San Segundo
- Plum Island Animal Disease Center, Plains Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY, United States
- Office of Biodefense, Research Resources and Translational Research, National Institute of Allergy and Infectious Disease, Rockville, MD, United States
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28
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Zhang Y, Qiu H, Duan F, An H, Qiao H, Zhang X, Zhang JR, Ding Q, Na J. A Comparative Study of Human Pluripotent Stem Cell-Derived Macrophages in Modeling Viral Infections. Viruses 2024; 16:552. [PMID: 38675895 PMCID: PMC11053470 DOI: 10.3390/v16040552] [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: 01/30/2024] [Revised: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Macrophages play multiple roles in innate immunity including phagocytosing pathogens, modulating the inflammatory response, presenting antigens, and recruiting other immune cells. Tissue-resident macrophages (TRMs) adapt to the local microenvironment and can exhibit different immune responses upon encountering distinct pathogens. In this study, we generated induced macrophages (iMACs) derived from human pluripotent stem cells (hPSCs) to investigate the interactions between the macrophages and various human pathogens, including the hepatitis C virus (HCV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Streptococcus pneumoniae. iMACs can engulf all three pathogens. A comparison of the RNA-seq data of the iMACs encountering these pathogens revealed that the pathogens activated distinct gene networks related to viral response and inflammation in iMACs. Interestingly, in the presence of both HCV and host cells, iMACs upregulated different sets of genes involved in immune cell migration and chemotaxis. Finally, we constructed an image-based high-content analysis system consisting of iMACs, recombinant GFP-HCV, and hepatic cells to evaluate the effect of a chemical inhibitor on HCV infection. In summary, we developed a human cell-based in vitro model to study the macrophage response to human viral and bacterial infections; the results of the transcriptome analysis indicated that the iMACs were a useful resource for modeling pathogen-macrophage-tissue microenvironment interactions.
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Affiliation(s)
- Yaxuan Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fuyu Duan
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
- Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510000, China
| | - Haoran An
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Medical Technology, Peking University Health Science Center, Peking University, Beijing 100084, China
| | - Huimin Qiao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xingwu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan 030001, China
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Shannon MJ, McNeill GL, Koksal B, Baltayeva J, Wächter J, Castellana B, Peñaherrera MS, Robinson WP, Leung PCK, Beristain AG. Single-cell assessment of primary and stem cell-derived human trophoblast organoids as placenta-modeling platforms. Dev Cell 2024; 59:776-792.e11. [PMID: 38359834 DOI: 10.1016/j.devcel.2024.01.023] [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: 11/10/2022] [Revised: 11/15/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Human trophoblast stem cells (hTSCs) and related trophoblast organoids are state-of-the-art culture systems that facilitate the study of trophoblast development and human placentation. Using single-cell transcriptomics, we evaluate how organoids derived from freshly isolated first-trimester trophoblasts or from established hTSC cell lines reproduce developmental cell trajectories and transcriptional regulatory processes defined in vivo. Although organoids from primary trophoblasts and hTSCs overall model trophoblast differentiation with accuracy, specific features related to trophoblast composition, trophoblast differentiation, and transcriptional drivers of trophoblast development show levels of misalignment. This is best illustrated by the identification of an expanded progenitor state in stem cell-derived organoids that is nearly absent in vivo and transcriptionally shares both villous cytotrophoblast and extravillous trophoblast characteristics. Together, this work provides a comprehensive resource that identifies strengths and limitations of current trophoblast organoid platforms.
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Affiliation(s)
- Matthew J Shannon
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Gina L McNeill
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Burak Koksal
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Jennet Baltayeva
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Jasmin Wächter
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Barbara Castellana
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Maria S Peñaherrera
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Wendy P Robinson
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Peter C K Leung
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Alexander G Beristain
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada.
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30
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Chen SJ, Hashimoto K, Fujio K, Hayashi K, Paul SK, Yuzuriha A, Qiu WY, Nakamura E, Kanashiro MA, Kabata M, Nakamura S, Sugimoto N, Kaneda A, Yamamoto T, Saito H, Takayama N, Eto K. A let-7 microRNA-RALB axis links the immune properties of iPSC-derived megakaryocytes with platelet producibility. Nat Commun 2024; 15:2588. [PMID: 38519457 PMCID: PMC10960040 DOI: 10.1038/s41467-024-46605-0] [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: 07/06/2023] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
We recently achieved the first-in-human transfusion of induced pluripotent stem cell-derived platelets (iPSC-PLTs) as an alternative to standard transfusions, which are dependent on donors and therefore variable in supply. However, heterogeneity characterized by thrombopoiesis-biased or immune-biased megakaryocytes (MKs) continues to pose a bottleneck against the standardization of iPSC-PLT manufacturing. To address this problem, here we employ microRNA (miRNA) switch biotechnology to distinguish subpopulations of imMKCLs, the MK cell lines producing iPSC-PLTs. Upon miRNA switch-based screening, we find imMKCLs with lower let-7 activity exhibit an immune-skewed transcriptional signature. Notably, the low activity of let-7a-5p results in the upregulation of RAS like proto-oncogene B (RALB) expression, which is crucial for the lineage determination of immune-biased imMKCL subpopulations and leads to the activation of interferon-dependent signaling. The dysregulation of immune properties/subpopulations, along with the secretion of inflammatory cytokines, contributes to a decline in the quality of the whole imMKCL population.
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Affiliation(s)
- Si Jing Chen
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuya Hashimoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kosuke Fujio
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Karin Hayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Sudip Kumar Paul
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akinori Yuzuriha
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Wei-Yin Qiu
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Emiri Nakamura
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | | | - Mio Kabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Sou Nakamura
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Naoshi Sugimoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| | - Naoya Takayama
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Koji Eto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
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31
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Lin C, Kuffour EO, Li T, Gertzen CGW, Kaiser J, Luedde T, König R, Gohlke H, Münk C. The ISG15-Protease USP18 Is a Pleiotropic Enhancer of HIV-1 Replication. Viruses 2024; 16:485. [PMID: 38675828 PMCID: PMC11053637 DOI: 10.3390/v16040485] [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: 02/16/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The innate immune response to viruses is formed in part by interferon (IFN)-induced restriction factors, including ISG15, p21, and SAMHD1. IFN production can be blocked by the ISG15-specific protease USP18. HIV-1 has evolved to circumvent host immune surveillance. This mechanism might involve USP18. In our recent studies, we demonstrate that HIV-1 infection induces USP18, which dramatically enhances HIV-1 replication by abrogating the antiviral function of p21. USP18 downregulates p21 by accumulating misfolded dominant negative p53, which inactivates wild-type p53 transactivation, leading to the upregulation of key enzymes involved in de novo dNTP biosynthesis pathways and inactivated SAMHD1. Despite the USP18-mediated increase in HIV-1 DNA in infected cells, it is intriguing to note that the cGAS-STING-mediated sensing of the viral DNA is abrogated. Indeed, the expression of USP18 or knockout of ISG15 inhibits the sensing of HIV-1. We demonstrate that STING is ISGylated at residues K224, K236, K289, K347, K338, and K370. The inhibition of STING K289-linked ISGylation suppresses its oligomerization and IFN induction. We propose that human USP18 is a novel factor that potentially contributes in multiple ways to HIV-1 replication.
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Affiliation(s)
- Chaohui Lin
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Edmund Osei Kuffour
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Taolan Li
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Christoph G. W. Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany;
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
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32
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Hu C, Zhang N, Hong Y, Tie R, Fan D, Lin A, Chen Y, Xiang LX, Shao JZ. Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity. eLife 2024; 13:RP92424. [PMID: 38497789 PMCID: PMC10948150 DOI: 10.7554/elife.92424] [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] [Indexed: 03/19/2024] Open
Abstract
The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of the kidney in fish immune systems remains to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cells types from zebrafish kidneys via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in the kidney, suggesting the kidney acts as a secondary lymphoid organ. These results indicated that the fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune systems, and highlighted the multifaced biology of kidneys in ancient vertebrates.
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Affiliation(s)
- Chongbin Hu
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Nan Zhang
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Yun Hong
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Dongdong Fan
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Aifu Lin
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Ye Chen
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthHangzhouChina
| | - Li-xin Xiang
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Jian-zhong Shao
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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33
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Wardlaw CP, Miele MM, Li Z, Hendrickson RC, Petrini JHJ. Protocol for the quantitative identification of endogenously ISGylated proteins from mammalian cell lines. STAR Protoc 2024; 5:102843. [PMID: 38294909 PMCID: PMC10844860 DOI: 10.1016/j.xpro.2024.102843] [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: 10/31/2023] [Revised: 12/06/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Ubiquitin-like protein ISG15 plays an important role in an array of cellular functions via its covalent attachment to target proteins (ISGylation). Here, we present a protocol for the identification of ISGylated proteins that avoids the caveats associated with ISG15 overexpression and minimizes the likelihood of false positives. We describe steps for the tagging of endogenous ISG15, followed by genotyping and clone selection. We then detail steps for ISGylation induction, the isolation of ISGylated proteins, and their identification via quantitative mass spectrometry. For complete details on the use and execution of this protocol, please refer to Wardlaw and Petrini.1.
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Affiliation(s)
- Christopher P Wardlaw
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
| | - Matthew M Miele
- Proteomics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Zhuoning Li
- Proteomics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Ronald C Hendrickson
- Proteomics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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34
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Das P, Chakrabarti O. ISGylation of DRP1 closely balances other post-translational modifications to mediate mitochondrial fission. Cell Death Dis 2024; 15:184. [PMID: 38431611 PMCID: PMC10908869 DOI: 10.1038/s41419-024-06543-7] [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: 06/27/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Dynamin related protein 1 (DRP1), a pivotal mitochondrial fission protein, is post-translationally modified by multiple mechanisms. Here we identify a new post-translational modification of DRP1 by the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15). DRP1 ISGylation is mediated by ISG15 E3 ligase, HERC5; this promotes mitochondrial fission. DeISGylation of DRP1 however leads to hyperfusion. Heterologous expression of SARS-CoV2 PLpro, a deISGylating enzyme, results in similar mitochondrial filamentation, significant decrease in total DRP1 protein levels and efflux of mtDNA. We report that deISGylated DRP1 gets ubiquitylated and degraded by TRIM25, instead of PARKIN and MITOL. While the cytosolic pool of DRP1 is primarily ISGylated, both mitochondrial and cytosolic fractions may be ubiquitylated. It is known that phosphorylation of DRP1 at S616 residue regulates its mitochondrial localisation; we show that ISGylation of phospho-DRP1 (S616) renders fission competence at mitochondria. This is significant because DRP1 ISGylation affects its functionality and mitochondrial dynamics in Alzheimer's disease pathophysiology.
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Affiliation(s)
- Palamou Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, Mumbai, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhabha National Institute, Mumbai, India.
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Liu L, Kapralov M, Ashton M. Plant-derived compounds as potential leads for new drug development targeting COVID-19. Phytother Res 2024; 38:1522-1554. [PMID: 38281731 DOI: 10.1002/ptr.8105] [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: 08/09/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
COVID-19, which was first identified in 2019 in Wuhan, China, is a respiratory illness caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although some patients infected with COVID-19 can remain asymptomatic, most experience a range of symptoms that can be mild to severe. Common symptoms include fever, cough, shortness of breath, fatigue, loss of taste or smell and muscle aches. In severe cases, complications can arise including pneumonia, acute respiratory distress syndrome, organ failure and even death, particularly in older adults or individuals with underlying health conditions. Treatments for COVID-19 include remdesivir, which has been authorised for emergency use in some countries, and dexamethasone, a corticosteroid used to reduce inflammation in severe cases. Biological drugs including monoclonal antibodies, such as casirivimab and imdevimab, have also been authorised for emergency use in certain situations. While these treatments have improved the outcome for many patients, there is still an urgent need for new treatments. Medicinal plants have long served as a valuable source of new drug leads and may serve as a valuable resource in the development of COVID-19 treatments due to their broad-spectrum antiviral activity. To date, various medicinal plant extracts have been studied for their cellular and molecular interactions, with some demonstrating anti-SARS-CoV-2 activity in vitro. This review explores the evaluation and potential therapeutic applications of these plants against SARS-CoV-2. This review summarises the latest evidence on the activity of different plant extracts and their isolated bioactive compounds against SARS-CoV-2, with a focus on the application of plant-derived compounds in animal models and in human studies.
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Affiliation(s)
- Lingxiu Liu
- Faculty of Medical Sciences, School of Pharmacy, Newcastle University, Newcastle-Upon-Tyne, UK
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Maxim Kapralov
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Mark Ashton
- Faculty of Medical Sciences, School of Pharmacy, Newcastle University, Newcastle-Upon-Tyne, UK
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, UK
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Spiteri AG, Suprunenko T, Cutts E, Suen A, Ashhurst TM, Viengkhou B, King NJC, Hofer MJ. CD8 + T Cells Mediate Lethal Lung Pathology in the Absence of PD-L1 and Type I Interferon Signalling following LCMV Infection. Viruses 2024; 16:390. [PMID: 38543756 PMCID: PMC10975266 DOI: 10.3390/v16030390] [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: 02/08/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 05/23/2024] Open
Abstract
CD8+ T cells are critical to the adaptive immune response against viral pathogens. However, overwhelming antigen exposure can result in their exhaustion, characterised by reduced effector function, failure to clear virus, and the upregulation of inhibitory receptors, including programmed cell death 1 (PD-1). However, exhausted T cell responses can be "re-invigorated" by inhibiting PD-1 or the primary ligand of PD-1: PD-L1. Further, the absence of the type I interferon receptor IFNAR1 also results in T cell exhaustion and virus persistence in lymphocytic choriomeningitis virus Armstrong (LCMV-Arm)-infected mice. In this study, utilizing single- and double-knockout mice, we aimed to determine whether ablation of PD-1 could restore T cell functionality in the absence of IFNAR1 signalling in LCMV-Arm-infected mice. Surprisingly, this did not re-invigorate the T cell response and instead, it converted chronic LCMV-Arm infection into a lethal disease characterized by severe lung inflammation with an infiltration of neutrophils and T cells. Depletion of CD8+ T cells, but not neutrophils, rescued mice from lethal disease, demonstrating that IFNAR1 is required to prevent T cell exhaustion and virus persistence in LCMV-Arm infection, and in the absence of IFNAR1, PD-L1 is required for survival. This reveals an important interplay between IFNAR1 and PD-L1 with implications for therapeutics targeting these pathways.
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Affiliation(s)
- Alanna G. Spiteri
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Tamara Suprunenko
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Erin Cutts
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Andrew Suen
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Thomas M. Ashhurst
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, NSW 2050, Australia
| | - Barney Viengkhou
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Nicholas J. C. King
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, NSW 2050, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2050, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2050, Australia
| | - Markus J. Hofer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2050, Australia
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Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.21.533528. [PMID: 36993393 PMCID: PMC10055223 DOI: 10.1101/2023.03.21.533528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
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Johnston RA, Aracena KA, Barreiro LB, Lea AJ, Tung J. DNA methylation-environment interactions in the human genome. eLife 2024; 12:RP89371. [PMID: 38407202 PMCID: PMC10942648 DOI: 10.7554/elife.89371] [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] [Indexed: 02/27/2024] Open
Abstract
Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here, we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures-one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.
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Affiliation(s)
- Rachel A Johnston
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Zoo New EnglandBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Luis B Barreiro
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
- Committee on Immunology, University of ChicagoChicagoUnited States
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
- Canadian Institute for Advanced ResearchTorontoCanada
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Canadian Institute for Advanced ResearchTorontoCanada
- Duke Population Research Institute, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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Plaça DR, Fonseca DLM, Marques AHC, Zaki Pour S, Usuda JN, Baiocchi GC, Prado CADS, Salgado RC, Filgueiras IS, Freire PP, Rocha V, Camara NOS, Catar R, Moll G, Jurisica I, Calich VLG, Giil LM, Rivino L, Ochs HD, Cabral-Miranda G, Schimke LF, Cabral-Marques O. Immunological signatures unveiled by integrative systems vaccinology characterization of dengue vaccination trials and natural infection. Front Immunol 2024; 15:1282754. [PMID: 38444851 PMCID: PMC10912564 DOI: 10.3389/fimmu.2024.1282754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Dengue virus infection is a global health problem lacking specific therapy, requiring an improved understanding of DENV immunity and vaccine responses. Considering the recent emerging of new dengue vaccines, here we performed an integrative systems vaccinology characterization of molecular signatures triggered by the natural DENV infection (NDI) and attenuated dengue virus infection models (DVTs). Methods and results We analyzed 955 samples of transcriptomic datasets of patients with NDI and attenuated dengue virus infection trials (DVT1, DVT2, and DVT3) using a systems vaccinology approach. Differential expression analysis identified 237 common differentially expressed genes (DEGs) between DVTs and NDI. Among them, 28 and 60 DEGs were up or downregulated by dengue vaccination during DVT2 and DVT3, respectively, with 20 DEGs intersecting across all three DVTs. Enriched biological processes of these genes included type I/II interferon signaling, cytokine regulation, apoptosis, and T-cell differentiation. Principal component analysis based on 20 common DEGs (overlapping between DVTs and our NDI validation dataset) distinguished dengue patients by disease severity, particularly in the late acute phase. Machine learning analysis ranked the ten most critical predictors of disease severity in NDI, crucial for the anti-viral immune response. Conclusion This work provides insights into the NDI and vaccine-induced overlapping immune response and suggests molecular markers (e.g., IFIT5, ISG15, and HERC5) for anti-dengue-specific therapies and effective vaccination development.
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Affiliation(s)
- Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M. Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Alexandre H. C. Marques
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Shahab Zaki Pour
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriela Crispim Baiocchi
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ranieri Coelho Salgado
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology and Cell Therapy, Hospital das Clínicas, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Department of Hematology, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Niels Olsen Saraiva Camara
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT) and Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vera Lúcia Garcia Calich
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lasse M. Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Emerging Infectious Diseases, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children’s Research Institute, Seattle, WA, United States
| | - Gustavo Cabral-Miranda
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lena F. Schimke
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
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Zhao X, Perez JM, Faull PA, Chan C, Munting FW, Canadeo LA, Cenik C, Huibregtse JM. Cellular targets and lysine selectivity of the HERC5 ISG15 ligase. iScience 2024; 27:108820. [PMID: 38303729 PMCID: PMC10831901 DOI: 10.1016/j.isci.2024.108820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
ISG15 is a type I interferon-induced ubiquitin-like modifier that functions in innate immune responses. The major human ISG15 ligase is hHERC5, a ribosome-associated HECT E3 that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 2,000 modified lysines in over 1,100 proteins in IFN-β-stimulated cells. In parallel, we compared the substrate selectivity hHERC5 to the major mouse ISG15 ligase, mHERC6, and analysis of sequences surrounding ISGylation sites revealed that hHERC5 and mHERC6 have distinct preferences for amino acid sequence context. Several features of the datasets were consistent with ISGylation of ribosome-tethered nascent chains, and mHERC6, like hHERC5, cotranslationally modified nascent polypeptides. The ISGylome datasets presented here represent the largest numbers of protein targets and modification sites attributable to a single Ub/Ubl ligase and the lysine selectivities of the hHERC5 and mHERC6 enzymes may have implications for the activities of HECT domain ligases, generally.
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Affiliation(s)
- Xu Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jessica M. Perez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter A. Faull
- Biological Mass Spectrometry Facility, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Chan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Femke W. Munting
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Larissa A. Canadeo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jon M. Huibregtse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- John Ring LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
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Espada CE, da Rocha EL, Ricciardi-Jorge T, dos Santos AA, Soares ZG, Malaquias G, Patrício DO, Gonzalez Kozlova E, dos Santos PF, Bordignon J, Sanford TJ, Fajardo T, Sweeney TR, Báfica A, Mansur DS. ISG15/USP18/STAT2 is a molecular hub regulating IFN I-mediated control of Dengue and Zika virus replication. Front Immunol 2024; 15:1331731. [PMID: 38384473 PMCID: PMC10879325 DOI: 10.3389/fimmu.2024.1331731] [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: 11/01/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
The establishment of a virus infection is the result of the pathogen's ability to replicate in a hostile environment generated by the host's immune system. Here, we found that ISG15 restricts Dengue and Zika viruses' replication through the stabilization of its binding partner USP18. ISG15 expression was necessary to control DV replication driven by both autocrine and paracrine type one interferon (IFN-I) signaling. Moreover, USP18 competes with NS5-mediated STAT2 degradation, a major mechanism for establishment of flavivirus infection. Strikingly, reconstitution of USP18 in ISG15-deficient cells was sufficient to restore the STAT2's stability and restrict virus growth, suggesting that the IFNAR-mediated ISG15 activity is also antiviral. Our results add a novel layer of complexity in the virus/host interaction interface and suggest that NS5 has a narrow window of opportunity to degrade STAT2, therefore suppressing host's IFN-I mediated response and promoting virus replication.
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Affiliation(s)
- Constanza Eleonora Espada
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Edroaldo Lummertz da Rocha
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Taissa Ricciardi-Jorge
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Adara Aurea dos Santos
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Zamira Guerra Soares
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Greicy Malaquias
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Daniel Oliveira Patrício
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Edgar Gonzalez Kozlova
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Paula Fernandes dos Santos
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Juliano Bordignon
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Instituto Carlos Chagas (ICC)/Fiocruz-PR, Curitiba, Brazil
| | - Thomas J. Sanford
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Teodoro Fajardo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Trevor R. Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Viral Gene Expression Group, The Pirbright Institute, Guildford, United Kingdom
| | - André Báfica
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Daniel Santos Mansur
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Han P, Zhang W, Wang D, Wu Y, Li X, Zhao S, Zhu M. Comparative transcriptome analysis of T lymphocyte subpopulations and identification of critical regulators defining porcine thymocyte identity. Front Immunol 2024; 15:1339787. [PMID: 38384475 PMCID: PMC10879363 DOI: 10.3389/fimmu.2024.1339787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. Method Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. Results The comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. Discussion Our findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.
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Affiliation(s)
- Pingping Han
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yalan Wu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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Khalil AM, Nogales A, Martínez-Sobrido L, Mostafa A. Antiviral responses versus virus-induced cellular shutoff: a game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1. Front Cell Infect Microbiol 2024; 14:1357866. [PMID: 38375361 PMCID: PMC10875036 DOI: 10.3389/fcimb.2024.1357866] [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: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Following virus recognition of host cell receptors and viral particle/genome internalization, viruses replicate in the host via hijacking essential host cell machinery components to evade the provoked antiviral innate immunity against the invading pathogen. Respiratory viral infections are usually acute with the ability to activate pattern recognition receptors (PRRs) in/on host cells, resulting in the production and release of interferons (IFNs), proinflammatory cytokines, chemokines, and IFN-stimulated genes (ISGs) to reduce virus fitness and mitigate infection. Nevertheless, the game between viruses and the host is a complicated and dynamic process, in which they restrict each other via specific factors to maintain their own advantages and win this game. The primary role of the non-structural protein 1 (NS1 and Nsp1) of influenza A viruses (IAV) and the pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively, is to control antiviral host-induced innate immune responses. This review provides a comprehensive overview of the genesis, spatial structure, viral and cellular interactors, and the mechanisms underlying the unique biological functions of IAV NS1 and SARS-CoV-2 Nsp1 in infected host cells. We also highlight the role of both non-structural proteins in modulating viral replication and pathogenicity. Eventually, and because of their important role during viral infection, we also describe their promising potential as targets for antiviral therapy and the development of live attenuated vaccines (LAV). Conclusively, both IAV NS1 and SARS-CoV-2 Nsp1 play an important role in virus-host interactions, viral replication, and pathogenesis, and pave the way to develop novel prophylactic and/or therapeutic interventions for the treatment of these important human respiratory viral pathogens.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Madrid, Spain
| | - Luis Martínez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
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Álvarez E, Falqui M, Sin L, McGrail JP, Perdiguero B, Coloma R, Marcos-Villar L, Tárrega C, Esteban M, Gómez CE, Guerra S. Unveiling the Multifaceted Roles of ISG15: From Immunomodulation to Therapeutic Frontiers. Vaccines (Basel) 2024; 12:153. [PMID: 38400136 PMCID: PMC10891536 DOI: 10.3390/vaccines12020153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
The Interferon Stimulated Gene 15 (ISG15), a unique Ubiquitin-like (Ubl) modifier exclusive to vertebrates, plays a crucial role in the immune system. Primarily induced by interferon (IFN) type I, ISG15 functions through diverse mechanisms: (i) covalent protein modification (ISGylation); (ii) non-covalent intracellular action; and (iii) exerting extracellular cytokine activity. These various roles highlight its versatility in influencing numerous cellular pathways, encompassing DNA damage response, autophagy, antiviral response, and cancer-related processes, among others. The well-established antiviral effects of ISGylation contrast with its intriguing dual role in cancer, exhibiting both suppressive and promoting effects depending on the tumour type. The multifaceted functions of ISG15 extend beyond intracellular processes to extracellular cytokine signalling, influencing immune response, chemotaxis, and anti-tumour effects. Moreover, ISG15 emerges as a promising adjuvant in vaccine development, enhancing immune responses against viral antigens and demonstrating efficacy in cancer models. As a therapeutic target in cancer treatment, ISG15 exhibits a double-edged nature, promoting or suppressing oncogenesis depending on the tumour context. This review aims to contribute to future studies exploring the role of ISG15 in immune modulation and cancer therapy, potentially paving the way for the development of novel therapeutic interventions, vaccine development, and precision medicine.
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Affiliation(s)
- Enrique Álvarez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
| | - Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.F.); (J.P.M.); (R.C.); (C.T.)
| | - Laura Sin
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Joseph Patrick McGrail
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.F.); (J.P.M.); (R.C.); (C.T.)
| | - Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Rocío Coloma
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.F.); (J.P.M.); (R.C.); (C.T.)
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Céline Tárrega
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.F.); (J.P.M.); (R.C.); (C.T.)
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (E.Á.); (L.S.); (B.P.); (L.M.-V.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.F.); (J.P.M.); (R.C.); (C.T.)
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Lee EJ, Kim JY, Yeo JH, Park S, Bae YJ, Kwon IJ, Seong SH, Lee J, Oh SH. ISG15-USP18 Dysregulation by Oxidative Stress Promotes IFN-γ Secretion from CD8+ T Cells in Vitiligo. J Invest Dermatol 2024; 144:273-283.e11. [PMID: 37625543 DOI: 10.1016/j.jid.2023.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/28/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023]
Abstract
Excessive oxidative stress is thought to play pathologic roles in cellular senescence and autoimmune disorders by inducing inflammation and breaking down immune tolerance. In this study, we sought to identify the factors linking oxidative stress to autoimmunity and cellular senescence in vitiligo, where elevated oxidative stress plays an important role. RNA sequencing analysis of hydrogen peroxide-treated melanocytes revealed upregulation of ISG15. The upregulation of ISG15 was observed in vitiligo skin tissues as well as in the blood of patients with vitiligo, whereas USP18 downregulation was observed in vitiligo melanocytes and vitiligo skin tissues. Oxidative stress induced hypermethylation of the USP18 promoter region in keratinocytes and melanocytes, and USP18 promoter hypermethylation was also confirmed in vitiligo skin tissues. Our results indicate that USP18 promoter hypermethylation caused by oxidative stress increases ISG15 expression in keratinocytes and melanocytes along with senescence changes, leading CD8+ T cells to produce IFN-γ, the main pathogenic cytokine in vitiligo. Therefore, the ISG15-USP18 network may be important in oxidative stress-induced autoimmunity and cellular senescence in vitiligo pathogenesis.
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Affiliation(s)
- Eun Jung Lee
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Young Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Joo Hye Yeo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Sujin Park
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Jeong Bae
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Il Joo Kwon
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seol Hwa Seong
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jinu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Sang Ho Oh
- Department of Dermatology and Cutaneous Biology Research Institute, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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47
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Zhao Z, Han S, Zhang Q, Wang Y, Yue K, Abbas S, He H. Impaired influenza A virus replication by the host restriction factor SAMHD1 which inhibited by PA-mediated dephosphorylation of the host transcription factor IRF3. Virol J 2024; 21:33. [PMID: 38287375 PMCID: PMC10826253 DOI: 10.1186/s12985-024-02295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Influenza A virus (IAV) can cause severe and life-threatening illness in humans and animals. Therefore, it is important to search for host antiviral proteins and elucidate their antiviral mechanisms for the development of potential treatments. As a part of human innate immunity, host restriction factors can inhibit the replication of viruses, among which SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) can restrict the replication of viruses, such as HIV and enterovirus EV71. Viruses also developed countermeasures in the arms race with their hosts. There are few reports about whether SAMHD1 has a restriction effect on IAV. METHODS To investigate the impact of IAV infection on SAMHD1 expression in A549 cells, we infected A549 cells with a varying multiplicity of infection (MOI) of IAV and collected cell samples at different time points for WB and RT-qPCR analysis to detect viral protein and SAMHD1 levels. The virus replication level in the cell culture supernatant was determined using TCID50 assay. Luciferase assay was used to reveal that H5N1 virus polymerase acidic protein (PA) affected the activity of the SAMHD1 promoter. To assess the antiviral capacity of SAMHD1, we generated a knockdown and overexpressed cell line for detecting H5N1 replication. RESULTS In this study, we observed that SAMHD1 can restrict the intracellular replication of H5N1 and that the H5N1 viral protein PA can downregulate the expression of SAMHD1 by affecting SAMHD1 transcriptional promoter activity. We also found that SAMHD1's ability to restrict H5N1 is related to phosphorylation at 592-tyrosine. CONCLUSIONS In conclusion, we found that SAMHD1 may affect the replication of IAVs as a host restriction factor and be countered by PA. Furthermore, SAMHD1 may be a potential target for developing antiviral drugs.
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Affiliation(s)
- Zhilei Zhao
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingxun Zhang
- Beijing Milu Ecological Research Center, Beijing, 100076, China
| | - Ye Wang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Kening Yue
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Salbia Abbas
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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48
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Meng Y, Bian L, Zhang M, Zhou P, Zhang S, Ying Y, Yang S, Liu Y, Yao Y, Li D. ISG15 Promotes Progression and Gemcitabine Resistance of Pancreatic Cancer Cells Through ATG7. Int J Biol Sci 2024; 20:1180-1193. [PMID: 38385083 PMCID: PMC10878160 DOI: 10.7150/ijbs.85424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024] Open
Abstract
Chemoresistance is an obstacle of improving pancreatic cancer (PC) prognosis. However, the biological function of ISG15 in PC and whether it correlates with the resistance to chemotherapy are still unknown. Here, we aimed to reveal the clinical significance of ISG15 in PC and its regulatory mechanism in cancer progression and resistance to therapy. The level of ISG15, a protein involved in post-translational modifications, is elevated in PC tissues. Clinically, higher ISG15 expression correlates with higher PC grades, stronger resistance to treatment and poorer prognosis. Moreover, ISG15 promotes the proliferation, migration, invasion, colony formation of PC cells and resistance to Gemcitabine, a classic chemotherapeutics for PC, both in vitro and in vivo. ISG15 promotes progression and resistance to therapy in PC cells by binding to ATG7, reducing its degradation, and thereby leading to enhanced autophagy in PC cells. ISG15 may be used as both a potential diagnosis marker and sensitizer for chemotherapeutics such as Gemcitabine during PC intervention.
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Affiliation(s)
- Yiling Meng
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lei Bian
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meichao Zhang
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Pingting Zhou
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Suning Zhang
- Department of Emergency, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yingxia Ying
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sunhu Yang
- Department of General Surgery, Shanghai university of TCM Shanghai TCM-integrated hospital, Shanghai, China
| | - Yuanhua Liu
- Department of Chemotherapy, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, Jiangsu, China
| | - Yuan Yao
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dong Li
- Department of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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49
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Zierhut C. Potential cGAS-STING pathway functions in DNA damage responses, DNA replication and DNA repair. DNA Repair (Amst) 2024; 133:103608. [PMID: 38056369 DOI: 10.1016/j.dnarep.2023.103608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
The major innate immune responder to the DNA of pathogens is the cyclic GMP-AMP (cGAMP) synthase (cGAS) - stimulator of interferon genes (STING) pathway. Most prominently, the outcome of cGAS signalling is the activation of inflammatory transcription through interferon regulatory factor 3 (IRF3) and nuclear factor kappa B (NF-kB). In addition, the cGAS-STING pathway can lead to the direct modulation of cellular processes independently of transcription, such as activation of autophagy. Under unperturbed conditions, several mechanisms are in place to prevent the activation of cGAS by self-DNA, chiefly its sequestration on chromatin, which interferes with binding to stimulatory DNA. However, under conditions of genotoxic stress and chromosomal instability, this inhibition breaks down, resulting in the activation of cGAS, which drives sterile inflammation, as well as cell fate and immune responses in cancer. Recently, several studies have suggested that cGAS, STING, or downstream pathway components can also regulate the DNA damage response, DNA damage checkpoint signalling, DNA repair and DNA replication. Here, I review these proposed mechanisms, and discuss some unanswered questions relating to them.
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Affiliation(s)
- Christian Zierhut
- The Institute of Cancer Research, Division of Cancer Biology, 237 Fulham Road, London SW3 6JB, UK.
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50
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Hu M, Liu L. Choline regulation of triglycerides synthesis through ubiquintination pathway in MAC-T cells. PeerJ 2023; 11:e16611. [PMID: 38144203 PMCID: PMC10740596 DOI: 10.7717/peerj.16611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
This study aims to investigate the regulatory mechanism of choline (CH) on triglyceride (TG) synthesis in cows, with a specific focus on its potential association with high milk fat percentage in the gut of the Zhongdian yak. By employing combined metagenomics and metabolomics analysis, we establish a correlation between CH and milk fat production in yaks. Bovine mammary epithelial cells (MAC-T) were exposed to varying CH concentrations, and after 24 h, we analyzed the expression levels of key proteins (membrane glycoprotein CD36 (CD36); adipose differentiation-related protein (ADFP); and ubiquintin (UB)), cellular TG content, lipid droplets, and cell vitality. Additionally, we evaluated the genes potentially related to the CH-mediated regulation of TG synthesis using real-time qPCR. CH at 200 μM significantly up-regulated CD36, ADFP, UB, and TG content. Pathway analysis reveals the involvement of the ubiquitination pathway in CH-mediated regulation of TG synthesis. These findings shed light on the role of CH in controlling TG synthesis in MAC-T cells and suggest its potential as a feed additive for cattle, offering possibilities to enhance milk fat production efficiency and economic outcomes in the dairy industry.
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Affiliation(s)
- Mengxue Hu
- College of Life Science, Southwest Forestry University, Kunming, Yunnan Province, China
| | - Lily Liu
- College of Life Science, Southwest Forestry University, Kunming, Yunnan Province, China
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