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Jia X, Chen J, Li C, Li J, Su M, Yang K, Zhang Y, Li Z. Glycogen synthase kinase 3 promotes the proliferation of porcine epidemic diarrhoea virus by phosphorylating the nucleocapsid protein. Virulence 2025; 16:2506504. [PMID: 40391683 PMCID: PMC12101597 DOI: 10.1080/21505594.2025.2506504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 04/10/2025] [Accepted: 04/27/2025] [Indexed: 05/22/2025] Open
Abstract
Porcine epidemic diarrhoea virus (PEDV) is a highly pathogenic porcine enteric coronavirus that causes severe watery diarrhoea and mortality in piglets. The nucleocapsid protein (N) is the most abundant viral protein and is highly phosphorylated, with the phosphorylation level directly affecting infection and proliferation. Here, we characterized the phosphorylation level of the N protein and found that its SR (Ser and Arg) motif was highly phosphorylated. The phosphorylation level significantly decreased after mutation of threonine (Thr) to serine (Ser). Through screening, it was determined that GSK3α/β plays a major role in phosphorylating the SR motif. Using GSK3α/β inhibitors or directly knocking out the GSK3α/β gene significantly inhibit PEDV proliferation. Finally, we used yeast recombination technology to develop a reverse genetics system for assessing PEDV and confirmed that no differences existed between the wild-type strain and the rescued virus. Using this platform, we generated a PEDV N protein SR motif mutant strain. We found that, compared to the wild-type strain, the proliferation of the mutant strain was significantly weakened, confirming that the phosphorylation of the SR motif is crucial for PEDV proliferation. In summary, we verified the phosphorylation sites of the PEDV N protein and the associated protein kinases, providing new insights into the development of relevant therapeutic strategies.
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Affiliation(s)
- Xiangchao Jia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chenxi Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jian Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Min Su
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Kang Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, China
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2
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Perfilova KV, Matyuta IO, Minyaev ME, Boyko KM, Cooley RB, Sluchanko NN. High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness. Biochem Biophys Res Commun 2025; 767:151915. [PMID: 40318379 DOI: 10.1016/j.bbrc.2025.151915] [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: 04/21/2025] [Accepted: 04/27/2025] [Indexed: 05/07/2025]
Abstract
Replication of many viruses depends on phosphorylation of viral proteins by host protein kinases and subsequent recruitment of host protein partners. The nucleoprotein (N) of SARS-CoV-2 is heavily phosphorylated and recruits human phosphopeptide-binding 14-3-3 proteins early in infection, which is reversed prior to nucleocapsid assembly in new virions. Among the multiple phosphosites of N, which are particularly dense in the serine/arginine-rich interdomain region, phospho-Thr205 is highly relevant for 14-3-3 recruitment by SARS-CoV-2 N. The context of this site is mutated in most SARS-CoV-2 variants of concern. Among mutations that increase infectious virus titers, the S202R mutation (B.1.526 Iota) causes a striking replication boost (∼166-fold), although its molecular consequences have remained unclear. Here, we show that the S202R-mutated N phosphopeptide exhibits a 5-fold higher affinity for human 14-3-3ζ than the Wuhan variant and we rationalize this effect by solving a high-resolution crystal structure of the complex. The structure revealed an enhanced 14-3-3/N interface contributed by the Arg202 side chain that, in contrast to Ser202, formed multiple stabilizing contacts with 14-3-3, including water-mediated H-bonds and guanidinium pi-pi stacking. These findings provide a compelling link between the replicative fitness of SARS-CoV-2 and the N protein's affinity for host 14-3-3 proteins.
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Affiliation(s)
- Kristina V Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Ilya O Matyuta
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Moscow Center for Advanced Studies, Kulakova Str. 20, 123592, Moscow, Russia
| | - Mikhail E Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Richard B Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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Aw DZH, Zhang DX, Vignuzzi M. Strategies and efforts in circumventing the emergence of antiviral resistance against conventional antivirals. NPJ ANTIMICROBIALS AND RESISTANCE 2025; 3:54. [PMID: 40490516 DOI: 10.1038/s44259-025-00125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 05/21/2025] [Indexed: 06/11/2025]
Abstract
Antiviral resistance stemming from rapid viral evolution and adaptation is a major challenge faced in treating viral infections. Here, we describe the mechanisms and factors underlying antiviral resistance and their implications to future drug development. Current improvements to conventional methods provide viable options to overcome antiviral resistance. Ongoing efforts in developing new antiviral strategies are also discussed. Examples from across virology are used to illustrate how virus evolution and antiviral therapy influence each other.
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Affiliation(s)
- Daryl Zheng Hao Aw
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Denzel Xugeng Zhang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Marco Vignuzzi
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore.
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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4
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Peng W, Wei X, Wu Y, Shi C, Liu X, Wu J, Yang H, Rong N, Zhao B, Zhang G, Zhang W, Liu J, Liu J, Yang J. Dynamic Molecular Changes in Brain, Lung, and Heart of Hamsters Infected With SARS-CoV-2: Insights From a Severe and Recovery Phase Model. J Med Virol 2025; 97:e70410. [PMID: 40432336 DOI: 10.1002/jmv.70410] [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: 01/07/2025] [Revised: 04/13/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025]
Abstract
The Global pandemic of coronavirus disease 2019 was initiated by the emergence of severe acute respiratory syndrome coronavirus 2. In addition to conventional pulmonary lesions, a range of neurological injury symptoms have been identified in clinical practice, but the aetiology of neurological disorders linked to SARS-CoV-2 infection remains poorly understood. Syrian hamsters, which are highly susceptible to SARS-CoV-2 infection, exhibit a disease phenotype similar to that observed in human COVID-19 patients. In this study, a hamster model of COVID-19 infection was used to analyze molecular changes in different tissues at various time points post infection with distinct strains using proteomic and phosphoproteomic approaches. Multi-omics analysis showed that SARS-COV-2 infection triggers sustained downregulation of the abundance and phosphorylation levels of neuronal and synapse-associated proteins in the brain, suggesting that neuronal damage persists even during the recovery period. Additionally, infections with SARS-CoV-2 may contribute to the onset of long-term symptoms of COVID-19 by impacting energy metabolism, neurotransmitter release, and synaptic transmission pathways. This study provides a comprehensive molecular profile of hamsters infected with different SARS-CoV-2 strains in different tissues, offering foundational insights into the pathogenic mechanisms of COVID-19.
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Grants
- This study was supported by the National Key R&D Program of China (2023YFC2507102), the CAMS Innovation Fund for Medical Sciences (CIFMS) grant (2022-I2M-1-020, 2022-12M-CoV19-002, 2022-I2M-2-001, 2022-I2M-1-011, 2021-I2M-1-057, 2021-I2M-1-049, 2021-I2M-1-044, 2021-I2M-1-016, 2021-I2M-1-001 and 2022-I2M-CoV19-003), the Haihe Laboratory of Cell Ecosystem Innovation Fund (22HHXBSS00008 and 22HHKYZX0034), State Key Laboratory Special Fund 2060204, and the National Natural Science Foundation of China (Grants 32070543 and 82341064).
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Affiliation(s)
- Wanjun Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Xiaohui Wei
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Yue Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Chunmei Shi
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Jing Wu
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Hekai Yang
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Na Rong
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Binbin Zhao
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Gengxin Zhang
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Wei Zhang
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Laboratory Animal Science, Beijing, China
| | - Juntao Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Pathogen Biology, Beijing, China
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5
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Eltayeb A, Adilović M, Golzardi M, Hromić-Jahjefendić A, Rubio-Casillas A, Uversky VN, Redwan EM. Intrinsic factors behind long COVID: exploring the role of nucleocapsid protein in thrombosis. PeerJ 2025; 13:e19429. [PMID: 40416618 PMCID: PMC12101441 DOI: 10.7717/peerj.19429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 04/15/2025] [Indexed: 05/27/2025] Open
Abstract
COVID-19, caused by the SARS-CoV-2, poses significant global health challenges. A key player in its pathogenesis is the nucleocapsid protein (NP), which is crucial for viral replication and assembly. While NPs from other coronaviruses, such as SARS-CoV and MERS-CoV, are known to increase inflammation and cause acute lung injury, the specific effects of the SARS-CoV-2 NP on host cells remain largely unexplored. Recent findings suggest that the NP acts as a pathogen-associated molecular pattern (PAMP) that binds to Toll-like receptor 2 (TLR2), activating NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) and MAPK (mitogen-activated protein kinase) signaling pathways. This activation is particularly pronounced in severe COVID-19 cases, leading to elevated levels of soluble ICAM-1 (intercellular adhesion molecule 1) and VCAM-1 (vascular cell adhesion molecule 1), which contribute to endothelial dysfunction and multiorgan damage. Furthermore, the NP is implicated in hyperinflammation and thrombosis-key factors in COVID-19 severity and long COVID. Its potential to bind with MASP-2 (mannan-binding lectin serine protease 2) may also be linked to persistent symptoms in long COVID patients. Understanding these mechanisms, particularly the role of the NP in thrombosis, is essential for developing targeted therapies to manage both acute and chronic effects of COVID-19 effectively. This comprehensive review aims to elucidate the multifaceted roles of the NP, highlighting its contributions to viral pathogenesis, immune evasion, and the exacerbation of thrombotic events, thereby providing insights into potential therapeutic targets for mitigating the severe and long-term impacts of COVID-19.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhamed Adilović
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Maryam Golzardi
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America
| | - Elrashdy M. Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, Alexandria, Egypt
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6
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Xu C, Yu F, Xue M, Huang Z, Jiang N, Li Y, Meng Y, Liu W, Zheng Y, Fan Y, Zhou Y. Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry. J Virol 2025; 99:e0196024. [PMID: 40172206 PMCID: PMC12090726 DOI: 10.1128/jvi.01960-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 02/10/2025] [Indexed: 04/04/2025] Open
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is the main pathogen responsible for the development of herpesviral hematopoietic necrosis disease (HVHND) in crucian carp (Carassius auratus). The CyHV-2 genome encodes approximately 150 genes that are expressed in a well-defined manner during productive infection. However, CyHV-2 open reading frames (ORFs) are primarily derived from sequence and homology analyses, and most lack protein-level evidence to support their properties. In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2. Based on our results, a total of 1,683 MS/MS spectra could be mapped to the CyHV-2 genome through six-frame translation, with 1,665 corresponding to 117 currently annotated protein-coding ORFs. Three of the remaining 18 peptides were mapped to the N-terminal extension region of known ORFs. However, 12 novel CyHV-2 ORFs, designated nORF1-12, were identified and characterized for the first time based on the remaining 15 peptides that could be mapped to previously unannotated regions of the viral genome. And the sequence differences of the novel phosphorylated nORF1, also referred to as ORF25E, in different CyHV-2 strains indicated that the nORF1 is a prospective molecular marker that can monitor the evolution from the Japan (J) to the China (C) genotype of CyHV-2. These findings further validate existing annotations, expand the genomic landscape of CyHV-2, and provide a rich resource for aquatic virology research.IMPORTANCECyHV-2 is a viral pathogen that poses a significant threat to crucian carp farming. CyHV-2 has a large genome with complex sequence features and diverse coding mechanisms, which complicates accurate genome annotation in the absence of protein-level evidence. Here, we employed various protein extraction and separation methods to increase viral protein coverage and performed an integrated proteogenomic analysis to refine the CyHV-2 genome annotation. A total of 129 viral genes were confidently identified, including 117 currently annotated genes and 12 novel genes. For the first time, we present large-scale evidence of peptide presence and levels in the genome of aquatic viruses and confirm the majority of the predicted proteins in CyHV-2. Our findings enhance the understanding of the CyHV-2 genome structure and provide valuable insights for future studies on CyHV-2 biology.
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Affiliation(s)
- Chen Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Fangxing Yu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Zhenyu Huang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ya Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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7
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Pipart J, Holstein T, Martens L, Muth T. MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics. J Proteome Res 2025. [PMID: 40384001 DOI: 10.1021/acs.jproteome.4c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
Abstract
The global SARS-CoV-2 pandemic emphasized the need for accurate pathogen diagnostics. While genomics is the gold standard, integrating mass spectrometry-based proteomics offers additional benefits. However, current proteomic and genomic reference databases are often biased toward specific taxa, such as pathogenic strains or model organisms, and proteomic databases are less comprehensive. These biases and gaps can lead to inaccurate identifications. To address these issues, we introduce MultiStageSearch, a multistep database search method that combines proteome and genome databases for taxonomic analysis. Initially, a generalist proteome database is used to infer potential species. Then, MultiStageSearch generates a specialized proteogenomic database for precise identification. This database is preprocessed to filter duplicates and cluster identical open reading frames to reduce genomic database biases. The workflow operates independently of strain-level NCBI taxonomy, enabling the identification of strains not represented in existing taxonomies. We benchmarked the workflow on viral and bacterial samples, demonstrating its superior performance in strain-level taxonomic inference compared to existing methods. MultiStageSearch offers a flexible and accurate approach for pathogen research and diagnostics, overcoming incomplete search spaces and biases inherent in reference databases.
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Affiliation(s)
- Julian Pipart
- Data Competence Center MF 2, Robert Koch Institute, Berlin 13353, Germany
| | - Tanja Holstein
- Data Competence Center MF 2, Robert Koch Institute, Berlin 13353, Germany
- CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent 9000, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, Strasbourg 67000, France
- Infrastructure Nationale de Protéomique ProFIFR2048, Strasbourg 67087, France
| | - Lennart Martens
- CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent 9000, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, Strasbourg 67000, France
- Infrastructure Nationale de Protéomique ProFIFR2048, Strasbourg 67087, France
| | - Thilo Muth
- Data Competence Center MF 2, Robert Koch Institute, Berlin 13353, Germany
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8
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Walter Z, Li M, Molho M, Berish L, Isopi A, O'Mara M, Dittmar M, Nwaezeapu C, Richards A, McCullagh M, Krogan NJ, Cherry S, Johnson JR, Ramage H. An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection. Cell Rep 2025; 44:115728. [PMID: 40381193 DOI: 10.1016/j.celrep.2025.115728] [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: 05/02/2024] [Revised: 03/22/2025] [Accepted: 04/30/2025] [Indexed: 05/20/2025] Open
Abstract
Upon infection, viruses alter the proteome, creating a hospitable environment for infection. Cells respond to limit viral replication, including through protein regulation by post-translational modifications. We use mass spectrometry to define proteome alterations during West Nile virus (WNV) infection. Our studies identify upregulation of HERPUD1, which restricts WNV replication through a mechanism independent of its role in endoplasmic reticulum (ER)-associated degradation (ERAD). We also identify modifications on viral proteins, including a WNV NS3 phosphorylation site that impacts viral replication. Finally, we reveal activation of two host kinases with antiviral activity. We identify phosphorylation at S108 of AMPKβ1, a non-catalytic subunit that regulates activity of the AMPK complex. We also show activation of PAK2 by phosphorylation at S141, which restricts translation of the viral genome. This work contributes to our understanding of the interplay between host and virus while providing a resource to define the changes to the proteome that regulate viral infection.
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Affiliation(s)
- Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Minghua Li
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Melissa Molho
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew Isopi
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mary O'Mara
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chike Nwaezeapu
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Alicia Richards
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; The J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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9
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Loonen S, van Steenis L, Bauer M, Šoštarić N. Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA. Proteins 2025. [PMID: 40375582 DOI: 10.1002/prot.26842] [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: 11/05/2024] [Revised: 05/01/2025] [Accepted: 05/07/2025] [Indexed: 05/18/2025]
Abstract
The SARS-CoV-2 nucleocapsid protein, or N-protein, is a structural protein that plays an important role in the SARS-CoV-2 life cycle. The N-protein takes part in the regulation of viral RNA replication and drives highly specific packaging of full-length genomic RNA prior to virion formation. One regulatory mechanism that is proposed to drive the switch between these two operating modes is the phosphorylation state of the N-protein. Here, we assess the dynamic behavior of non-phosphorylated and phosphorylated versions of the N-protein homodimer through atomistic molecular dynamics simulations. We show that the introduction of phosphorylation yields a more dynamic protein structure and decreases the binding affinity between the N-protein and RNA. Furthermore, we find that secondary structure is essential for the preferential binding of particular RNA elements from the 5' UTR of the viral genome to the N-terminal domain of the N-protein. Altogether, we provide detailed molecular insights into N-protein dynamics, N-protein:RNA interactions, and phosphorylation. Our results corroborate the hypothesis that phosphorylation of the N-protein serves as a regulatory mechanism that determines N-protein function.
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Affiliation(s)
- Stefan Loonen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands
| | - Lina van Steenis
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands
| | - Marianne Bauer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands
| | - Nikolina Šoštarić
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands
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10
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Krüger N, Laufer SA, Pillaiyar T. An overview of progress in human metapneumovirus (hMPV) research: Structure, function, and therapeutic opportunities. Drug Discov Today 2025; 30:104364. [PMID: 40286981 DOI: 10.1016/j.drudis.2025.104364] [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: 02/27/2025] [Revised: 04/09/2025] [Accepted: 04/22/2025] [Indexed: 04/29/2025]
Abstract
The human metapneumovirus (hMPV), a member of the Pneumoviridae family, is a significant respiratory pathogen that causes severe infections in infants, children, the elderly, adults with chronic illnesses, and individuals with immunocompromised conditions. Globally, hMPV is recognized as the second leading cause of bronchiolitis and pneumonia among children under five. The absence of targeted antiviral treatments or vaccines for hMPV significantly strains the global health-care system. This review summarizes recent advances and scientific findings on hMPV by reviewing the current literature on its life cycle, structure, function, prevention, and treatment options.
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Affiliation(s)
- Nadine Krüger
- Platform Infection Models, German Primate Center, Leibniz Institute for Primate Research Göttingen 37077 Göttingen, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University of Tübingen 72076 Tübingen, Germany; Cluster of Excellence 'Image Guided and Functionally Instructed Tumor Therapies' (iFIT), Eberhard Karls University of Tübingen, Tübingen 72076, Germany; Tübingen Center for Academic Drug Discovery, Eberhard Karls University of Tübingen 72076 Tübingen, Germany
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University of Tübingen 72076 Tübingen, Germany; Tübingen Center for Academic Drug Discovery, Eberhard Karls University of Tübingen 72076 Tübingen, Germany.
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11
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Li Y, Wang B, Zheng Y, Kang H, He A, Zhao L, Guo N, Liu H, Mardinoglu A, Mamun M, Gao Y, Chen X. The multifaceted role of post-translational modifications of LSD1 in cellular processes and disease pathogenesis. Genes Dis 2025; 12:101307. [PMID: 40028036 PMCID: PMC11870172 DOI: 10.1016/j.gendis.2024.101307] [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: 10/02/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 03/05/2025] Open
Abstract
Post-translational modifications (PTMs) of proteins play a crucial role in living organisms, altering the properties and functions of proteins. There are over 450 known PTMs involved in various life activities. LSD1 (lysine-specific demethylase 1) is the first identified histone demethylase that can remove monomethylation or dimethylation modifications from histone H3 lysine K4 (H3K4) and histone H3 lysine K9 (H3K9). This ability of LSD1 allows it to inhibit or activate transcription. LSD1 has been found to abnormally express at the protein level in various tumors, making it relevant to multiple diseases. As a PTM enzyme, LSD1 itself undergoes various PTMs, including phosphorylation, acetylation, ubiquitination, methylation, SUMOylation, and S-nitrosylation, influencing its activity and function. Dysregulation of these PTMs has been implicated in a wide range of diseases, including cancer, metabolic disorders, neurological disorders, cardiovascular diseases, and bone diseases. Understanding the species of PTMs and functions regulated by various PTMs of LSD1 provides insights into its involvement in diverse physiological and pathological processes. In this review, we discuss the structural characteristics of LSD1 and amino acid residues that affect its enzyme activity. We also summarize the potential PTMs that occur on LSD1 and their involvement in cellular processes. Furthermore, we describe human diseases associated with abnormal expression of LSD1. This comprehensive analysis sheds light on the intricate interplay between PTMs and the functions of LSD1, highlighting their significance in health and diseases.
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Affiliation(s)
- Yinrui Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yichao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Huiqin Kang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ang He
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Lijuan Zhao
- Henan Institute of Medical and Pharmaceutical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ningjie Guo
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Hongmin Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm SE-100 44, Sweden
- Faculty of Dentistry, Oral & Craniofacial Sciences, Centre for Host-Microbiome Interactions, King's College London, London WC2R 2LS, UK
| | - M.A.A. Mamun
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Zhengzhou, Henan 450001, China
- Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaobing Chen
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, Henan 450008, China
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12
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Wang Z, Cao G, Collier MP, Qiu X, Broadway-Stringer S, Šaman D, Ng JZY, Sen N, Azad AJ, Hooper C, Zimmermann J, McDonough MA, Brem J, Rabe P, Song H, Alderson TR, Schofield CJ, Bolla JR, Djinovic-Carugo K, Fürst DO, Warscheid B, Degiacomi MT, Allison TM, Hochberg GKA, Robinson CV, Gehmlich K, Benesch JLP. Filamin C dimerisation is regulated by HSPB7. Nat Commun 2025; 16:4090. [PMID: 40312381 PMCID: PMC12046049 DOI: 10.1038/s41467-025-58889-x] [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: 01/11/2024] [Accepted: 04/02/2025] [Indexed: 05/03/2025] Open
Abstract
The biomechanical properties and responses of tissues underpin a variety important of physiological functions and pathologies. In striated muscle, the actin-binding protein filamin C (FLNC) is a key protein whose variants causative for a wide range of cardiomyopathies and musculoskeletal pathologies. FLNC is a multi-functional protein that interacts with a variety of partners, however, how it is regulated at the molecular level is not well understood. Here we investigate its interaction with HSPB7, a cardiac-specific molecular chaperone whose absence is embryonically lethal. We find that FLNC and HSPB7 interact in cardiac tissue under biomechanical stress, forming a strong hetero-dimer whose structure we solve by X-ray crystallography. Our quantitative analyses show that the hetero-dimer out-competes the FLNC homo-dimer interface, potentially acting to abrogate the ability of the protein to cross-link the actin cytoskeleton, and to enhance its diffusive mobility. We show that phosphorylation of FLNC at threonine 2677, located at the dimer interface and associated with cardiac stress, acts to favour the homo-dimer. Conversely, phosphorylation at tyrosine 2683, also at the dimer interface, has the opposite effect and shifts the equilibrium towards the hetero-dimer. Evolutionary analysis and ancestral sequence reconstruction reveals this interaction and its mechanisms of regulation to date around the time primitive hearts evolved in chordates. Our work therefore shows, structurally, how HSPB7 acts as a specific molecular chaperone that regulates FLNC dimerisation.
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Affiliation(s)
- Zihao Wang
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Guodong Cao
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Miranda P Collier
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Xingyu Qiu
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | | | - Dominik Šaman
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jediael Z Y Ng
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Navoneel Sen
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Amar J Azad
- Cardiovascular Sciences, School of Medical Sciences, University of Birmingham, Birmingham, UK
- Center of Biological Design, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Charlotte Hooper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, UK
| | - Johannes Zimmermann
- Biochemistry II, Theodor Boveri-Institute, Biocenter, Chemistry and Pharmacy, University of Würzburg, Würzburg, Germany
| | | | - Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory, Oxford, UK
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Patrick Rabe
- Department of Chemistry, Chemistry Research Laboratory, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Haigang Song
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - T Reid Alderson
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, Germany
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, Oxford, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Jani R Bolla
- Department of Biology, University of Oxford, Oxford, UK
| | - Kristina Djinovic-Carugo
- European Molecular Biology Laboratory, Grenoble, France
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Dieter O Fürst
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Bettina Warscheid
- Biochemistry II, Theodor Boveri-Institute, Biocenter, Chemistry and Pharmacy, University of Würzburg, Würzburg, Germany
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Durham, UK
- School of Informatics and EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Carol V Robinson
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Katja Gehmlich
- Cardiovascular Sciences, School of Medical Sciences, University of Birmingham, Birmingham, UK.
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, UK.
| | - Justin L P Benesch
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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13
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Keskitalo S, Seppänen MRJ, Del Sol A, Varjosalo M. From rare to more common: The emerging role of omics in improving understanding and treatment of severe inflammatory and hyperinflammatory conditions. J Allergy Clin Immunol 2025; 155:1435-1450. [PMID: 39978687 DOI: 10.1016/j.jaci.2025.02.011] [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: 10/07/2024] [Revised: 01/31/2025] [Accepted: 02/11/2025] [Indexed: 02/22/2025]
Abstract
Inflammation is a pathogenic driver of many diseases, including atherosclerosis and rheumatoid arthritis. Hyperinflammation can be seen as any inflammatory response that is deleterious to the host, regardless of cause. In medicine, hyperinflammation is defined as severe, deleterious, and fluctuating systemic or local inflammation with presence of a cytokine storm. It has been associated with rare autoinflammatory disorders. However, advances in omics technologies, including genomics, proteomics, and metabolomics, have revealed it to be more common, occurring in sepsis and severe coronavirus disease 2019. With a focus on proteomics, this review highlights the key role of omics in this shift. Through an exploration of research, we present how omics technologies have contributed to improved diagnostics, prognostics, and targeted therapeutics in the field of hyperinflammation. We also discuss the integration of advanced technologies, multiomics approaches, and artificial intelligence in analyzing complex datasets to develop targeted therapies, and we address their potential for revolutionizing the clinical aspects of hyperinflammation. We emphasize personalized medicine approaches for effective treatments and outline challenges, including the need for standardized methodologies, robust bioinformatics tools, and ethical considerations regarding data privacy. This review aims to provide a comprehensive overview of the molecular mechanisms underpinning hyperinflammation and underscores the potential of omics technologies in enabling successful clinical management.
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Affiliation(s)
- Salla Keskitalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Mikko R J Seppänen
- Pediatric Research Center, New Children's Hospital, University of Helsinki and HUS Helsinki University Hospital, Helsinki, Finland; Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; European Reference Network Rare Immunodeficiency Autoinflammatory and Autoimmune Diseases Network (ERN RITA) Core Center, Helsinki, The Netherlands
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; Computational Biology Group, Basque Research and Technology Alliance (CIC bioGUNE-BRTA), Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Developmental Biology and Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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14
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Petrillo M, Querci M, Brogna C, Ponti J, Cristoni S, Markov PV, Valsesia A, Leoni G, Benedetti A, Wiss T, Van den Eede G. Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota. F1000Res 2025; 11:292. [PMID: 40444030 PMCID: PMC12120431 DOI: 10.12688/f1000research.109236.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2025] [Indexed: 06/02/2025] Open
Abstract
Background In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a 'bacteriophage-like' behaviour of SARS-CoV-2. Methods We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of a subject positive to SARS-CoV-2; (2) mass spectrometric analysis of these cultures to assess the eventual de novo synthesis of SARS-CoV-2 spike protein; (3) sequencing of SARS-CoV-2 collected from plaques obtained from two different gut microbial bacteria inoculated with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Results Immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirmed presence of SARS-CoV-2 both outside and inside bacteria. De novo synthesis of SARS-CoV-2 spike protein was observed, as evidence that SARS-CoV-2 RNA is translated in the bacterial cultures. In addition, phage-like plaques were spotted on faecal bacteria cultures after inoculation with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Bioinformatic analyses on the reads obtained by sequencing RNA extracted from the plaques revealed nucleic acid polymorphisms, suggesting different replication environment in the two bacterial cultures. Conclusions Based on these results we conclude that, in addition to its well-documented interactions with eukaryotic cells, SARS-CoV-2 may act as a bacteriophage when interacting with at least two bacterial species known to be present in the human microbiota. If the hypothesis proposed, i.e., that under certain conditions SARS-CoV-2 may multiply at the expense of human gut bacteria, is further substantiated, it would drastically change the model of acting and infecting of SARS-CoV-2, and most likely that of other human pathogenic viruses.
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Affiliation(s)
| | | | | | - Jessica Ponti
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | | | - Peter V Markov
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | - Andrea Valsesia
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | - Gabriele Leoni
- European Commission Joint Research Centre, Ispra, 21027, Italy
- International School for Advanced Studies (SISSA), Trieste, 34136, Italy
| | | | - Thierry Wiss
- European Commission Joint Research Centre, Karlsruhe, 76344, Germany
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15
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Petrillo M, Querci M, Brogna C, Ponti J, Cristoni S, Markov PV, Valsesia A, Leoni G, Benedetti A, Wiss T, Van den Eede G. Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota. F1000Res 2025; 11:292. [PMID: 40444030 PMCID: PMC12120431 DOI: 10.12688/f1000research.109236.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2025] [Indexed: 06/11/2025] Open
Abstract
BACKGROUND In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a 'bacteriophage-like' behaviour of SARS-CoV-2. METHODS We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of a subject positive to SARS-CoV-2; (2) mass spectrometric analysis of these cultures to assess the eventual de novo synthesis of SARS-CoV-2 spike protein; (3) sequencing of SARS-CoV-2 collected from plaques obtained from two different gut microbial bacteria inoculated with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. RESULTS Immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirmed presence of SARS-CoV-2 both outside and inside bacteria. De novo synthesis of SARS-CoV-2 spike protein was observed, as evidence that SARS-CoV-2 RNA is translated in the bacterial cultures. In addition, phage-like plaques were spotted on faecal bacteria cultures after inoculation with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Bioinformatic analyses on the reads obtained by sequencing RNA extracted from the plaques revealed nucleic acid polymorphisms, suggesting different replication environment in the two bacterial cultures. CONCLUSIONS Based on these results we conclude that, in addition to its well-documented interactions with eukaryotic cells, SARS-CoV-2 may act as a bacteriophage when interacting with at least two bacterial species known to be present in the human microbiota. If the hypothesis proposed, i.e., that under certain conditions SARS-CoV-2 may multiply at the expense of human gut bacteria, is further substantiated, it would drastically change the model of acting and infecting of SARS-CoV-2, and most likely that of other human pathogenic viruses.
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Affiliation(s)
| | | | | | - Jessica Ponti
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | | | - Peter V Markov
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | - Andrea Valsesia
- European Commission Joint Research Centre, Ispra, 21027, Italy
| | - Gabriele Leoni
- European Commission Joint Research Centre, Ispra, 21027, Italy
- International School for Advanced Studies (SISSA), Trieste, 34136, Italy
| | | | - Thierry Wiss
- European Commission Joint Research Centre, Karlsruhe, 76344, Germany
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16
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Janevska M, Naessens E, Verhasselt B. Impact of SARS-CoV-2 Wuhan and Omicron Variant Proteins on Type I Interferon Response. Viruses 2025; 17:569. [PMID: 40285011 PMCID: PMC12031613 DOI: 10.3390/v17040569] [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: 03/08/2025] [Revised: 04/08/2025] [Accepted: 04/09/2025] [Indexed: 04/29/2025] Open
Abstract
SARS-CoV-2 has demonstrated a remarkable capacity for immune evasion. While initial studies focused on the Wuhan variant and adaptive immunity, later emerging strains such as Omicron exhibit mutations that may alter their immune-modulatory properties. We performed a comprehensive review of immune evasion mechanisms associated with SARS-CoV-2 viral proteins to focus on the evolutionary dynamics of immune modulation. We systematically analyzed and compared the impact of all currently known Wuhan and Omicron SARS-CoV-2 proteins on type I interferon (IFN) responses using a dual-luciferase reporter assay carrying an interferon-inducible promoter. Results revealed that Nsp1, Nsp5, Nsp14, and ORF6 are potent type I IFN inhibitors conserved across Wuhan and Omicron strains. Notably, we identified strain-specific differences, with Nsp6 and Spike proteins exhibiting enhanced IFN suppression in Omicron, whereas the Envelope protein largely retained this function. To extend these findings, we investigated selected proteins in primary human endothelial cells and also observed strain-specific differences in immune response with higher type I IFN response in cells expressing the Wuhan strain variant, suggesting that Omicron's adaptational mutations may contribute to a damped type I IFN response in the course of the pandemic's trajectory.
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Affiliation(s)
- Marija Janevska
- Department of Diagnostic Sciences, Ghent University, B9000 Ghent, Belgium;
| | - Evelien Naessens
- Department of Laboratory Medicine, Ghent University Hospital, B9000 Ghent, Belgium;
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University, B9000 Ghent, Belgium;
- Department of Laboratory Medicine, Ghent University Hospital, B9000 Ghent, Belgium;
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17
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Zhao C, Hao M, Bian T, Zhao X, Chi X, Chen Z, Fu G, Zhu Z, Fang T, Yu C, Li J, Chen W. Screening of Neutralizing Antibodies Targeting Gc Protein of RVFV. Viruses 2025; 17:559. [PMID: 40285002 PMCID: PMC12031069 DOI: 10.3390/v17040559] [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: 02/25/2025] [Revised: 04/06/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-transmitted bunyavirus that can cause substantial morbidity and mortality in livestock and humans, for which there are no currently available licensed human therapeutics or vaccines. Therefore, the development of safe and effective antivirals is both necessary and urgent. The Gc protein is the primary target of the neutralizing antibody response related to Rift Valley fever virus. Here, we report one Gc-specific neutralizing antibody (NA137) isolated from an alpaca and one bispecific antibody (E2-NA137), the protective efficacies of which we evaluated in A129 mice. In this prophylactic study, the survival rates of the NA137 and E2-NA137 groups were both 80%, and in the treatment study, the survival rates were 20% and 60%, respectively. Altogether, our results emphasize that NA137 and E2-NA137 provide a potential approach for treating RVFV either prophylactically or therapeutically.
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Affiliation(s)
- Chuanyi Zhao
- School of Medicine, Zhejiang University, Hangzhou 310058, China;
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Meng Hao
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Ting Bian
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Xiaofan Zhao
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Xiangyang Chi
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Zhengshan Chen
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Guangcheng Fu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Zheng Zhu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Ting Fang
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Changming Yu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Jianmin Li
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
| | - Wei Chen
- School of Medicine, Zhejiang University, Hangzhou 310058, China;
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China; (M.H.); (T.B.); (X.Z.); (X.C.); (Z.C.); (G.F.); (Z.Z.); (T.F.); (C.Y.)
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18
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Hagbi-Levi S, Abraham M, Gamaev L, Mishaelian I, Hay O, Zorde-Khevalevsky E, Wald O, Wald H, Olam D, Weiss L, Peled A. Identification of Dinaciclib and Ganetespib as anti-inflammatory drugs using a novel HTP screening assay that targets IFNγ-dependent PD-L1. Front Immunol 2025; 16:1502094. [PMID: 40264756 PMCID: PMC12011776 DOI: 10.3389/fimmu.2025.1502094] [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: 09/26/2024] [Accepted: 03/19/2025] [Indexed: 04/24/2025] Open
Abstract
Introduction IFNγ plays both positive and negative roles in the regulation of innate and adaptive immune responses against tumors and virally infected tissues by upregulating CXCL10 and PD-L1 expression. Methods To identify novel pathways and drugs that regulate the IFNγ-dependent PD-L1, we expressed GFP under the control of mouse PD-L1 promoter in mouse cancer cells that up regulate PD-L1 and CXCL10 in response to IFNγ stimulation. Using these cells, we screened an FDA approved library of 1496 small molecules known for their ability to inhibit IFNγ-dependent increase in PD-L1. Results We identified 46 drugs that up regulated and 4 that down regulated IFNγ-dependent PD-L1 expression. We discovered that in addition to the known JAK inhibitors Ruxolitinib and Baricitinib, Dinaciclib, a CDK1/2/5/9 inhibitor, and Ganetespib, a Hsp90 inhibitor, significantly inhibit both PD-L1 and CXCL10 expression in the model cells. Furthermore, both drugs suppressed IFNγ-dependent CXCL10 and PD-L1 expression in-vitro in primary human lung cells and human cancer cells. These drugs also significantly inhibited delayed-type hypersensitivity (DTH) in-vivo in an inflammation mouse model. Discussion Our novel screening platform can therefore be used in the future to identify novel immunomodulators and pathways in cancer and inflammation, expanding therapeutic horizons.
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Affiliation(s)
- Shira Hagbi-Levi
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Lika Gamaev
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Inbal Mishaelian
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ophir Hay
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Elina Zorde-Khevalevsky
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ori Wald
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hanna Wald
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Devorah Olam
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Lola Weiss
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Amnon Peled
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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19
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Chen H, Charles PD, Gu Q, Liberatori S, Robertson DL, Palmarini M, Wilson SJ, Mohammed S, Castello A. Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States. Mol Cell Proteomics 2025; 24:100966. [PMID: 40204275 DOI: 10.1016/j.mcpro.2025.100966] [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: 11/15/2024] [Revised: 03/24/2025] [Accepted: 04/04/2025] [Indexed: 04/11/2025] Open
Abstract
The capacity of host cells to sustain or restrict virus infection is influenced by their proteome. Understanding the compendium of proteins defining cellular permissiveness is key to many questions in fundamental virology. Here, we apply a multi-omic approach to determine the proteins that are associated with highly permissive, intermediate, and hostile cellular states. We observed two groups of differentially regulated genes: (i) with robust changes in mRNA and protein levels and (ii) with protein/RNA discordances. While many of the latter are classified as interferon-stimulated genes (ISGs), most exhibit no antiviral effects in overexpression screens. This suggests that IFN-dependent protein changes can be better indicators of antiviral function than mRNA levels. Phosphoproteomics revealed an additional regulatory layer involving non-signaling proteins with altered phosphorylation. Indeed, we confirmed that several permissiveness-associated proteins with changes in abundance or phosphorylation regulate infection fitness. Altogether, our study provides a comprehensive and systematic map of the cellular alterations driving virus susceptibility.
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Affiliation(s)
- Honglin Chen
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Sam J Wilson
- Cambridge Institute of Therapeutic Immunol & Infect Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK; The Rosalind Franklin Institute, Oxfordshire, UK; Department of Chemistry, University of Oxford, Oxford, UK.
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
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20
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Liu J, Guo L, Zhong J, Wu Y, Wang X, Tang X, Min K, Yang Y, Peng W, Wang Q, Ding T, Gu X, Zhang H, Liu Y, Huang C, Cao B, Wang J, Ren L, Yang J. Proteomic Analysis of 442 Clinical Plasma Samples From Individuals With Symptom Records Revealed Subtypes of Convalescent Patients Who Had COVID-19. J Med Virol 2025; 97:e70203. [PMID: 40207927 PMCID: PMC11984345 DOI: 10.1002/jmv.70203] [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: 09/30/2024] [Revised: 01/11/2025] [Accepted: 01/21/2025] [Indexed: 04/11/2025]
Abstract
After the coronavirus disease 2019 (COVID-19) pandemic, the postacute effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have gradually attracted attention. To precisely evaluate the health status of convalescent patients with COVID-19, we analyzed symptom and proteome data of 442 plasma samples from healthy controls, hospitalized patients, and convalescent patients 6 or 12 months after SARS-CoV-2 infection. Symptoms analysis revealed distinct relationships in convalescent patients. Results of plasma protein expression levels showed that C1QA, C1QB, C2, CFH, CFHR1, and F10, which regulate the complement system and coagulation, remained highly expressed even at the 12-month follow-up compared with their levels in healthy individuals. By combining symptom and proteome data, 442 plasma samples were categorized into three subtypes: S1 (metabolism-healthy), S2 (COVID-19 retention), and S3 (long COVID). We speculated that convalescent patients reporting hair loss could have a better health status than those experiencing headaches and dyspnea. Compared to other convalescent patients, those reporting sleep disorders, appetite decrease, and muscle weakness may need more attention because they were classified into the S2 subtype, which had the most samples from hospitalized patients with COVID-19. Subtyping convalescent patients with COVID-19 may enable personalized treatments tailored to individual needs. This study provides valuable plasma proteomic datasets for further studies associated with long COVID.
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Grants
- This work was supported by grants from the National Key R&D Program of China (2023YFC2507102), the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences, China (CIFMS2022-I2M-1-011, CIFMS2022-I2M-2-001, CIFMS2021-I2M-1-057, CIFMS2021-I2M-1-049, CIFMS2021-I2M-1-044, CIFMS2021-I2M-1-016, CIFMS2021-I2M-1-001, 2022-I2M-CoV19-003, and CIFMS2022-I2M-JB-003), the National Natural Science Foundation of China (82341064), the Haihe Laboratory of Cell Ecosystem Innovation Fund (22HHXBSS00008 and 22HHKYZX0034), and State Key Laboratory Special Fund 2060204.
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Affiliation(s)
- Jiangfeng Liu
- Haihe Laboratory of Cell EcosystemTianjinChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux LaboratoryInstitute of Pathogen Biology, Chinese Academy of Medical SciencesBeijingChina
| | - Jingchuan Zhong
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux LaboratoryInstitute of Pathogen Biology, Chinese Academy of Medical SciencesBeijingChina
| | - Yue Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux LaboratoryInstitute of Pathogen Biology, Chinese Academy of Medical SciencesBeijingChina
| | - Xiaoyue Tang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Kaiyuan Min
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yehong Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Wanjun Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Qiaochu Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tao Ding
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xiaoying Gu
- Tsinghua University‐Peking University Joint Center for Life SciencesBeijingChina
- Department of Pulmonary and Critical Care MedicineNational Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Pulmonary and Critical Care MedicineCapital Medical UniversityBeijingChina
| | - Hui Zhang
- Tsinghua University‐Peking University Joint Center for Life SciencesBeijingChina
- Department of Pulmonary and Critical Care MedicineNational Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Pulmonary and Critical Care MedicineCapital Medical UniversityBeijingChina
| | - Ying Liu
- Medical DepartmentJin Yin‐Tan HospitalWuhanHubeiChina
- Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical SciencesWuhanHubeiChina
| | - Chaolin Huang
- Medical DepartmentJin Yin‐Tan HospitalWuhanHubeiChina
- Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical SciencesWuhanHubeiChina
| | - Bin Cao
- Tsinghua University‐Peking University Joint Center for Life SciencesBeijingChina
- Department of Pulmonary and Critical Care MedicineNational Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Pulmonary and Critical Care MedicineCapital Medical UniversityBeijingChina
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux LaboratoryInstitute of Pathogen Biology, Chinese Academy of Medical SciencesBeijingChina
- Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux LaboratoryInstitute of Pathogen Biology, Chinese Academy of Medical SciencesBeijingChina
- Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Juntao Yang
- Haihe Laboratory of Cell EcosystemTianjinChina
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular BiologySchool of Basic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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21
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Singh M, Shanmukha S, Eldesouki RE, Harraz MM. FDA-approved drug repurposing screen identifies inhibitors of SARS-CoV-2 pseudovirus entry. Front Pharmacol 2025; 16:1537912. [PMID: 40166473 PMCID: PMC11955658 DOI: 10.3389/fphar.2025.1537912] [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: 12/02/2024] [Accepted: 02/17/2025] [Indexed: 04/02/2025] Open
Abstract
Background and purpose The coronavirus disease 2019 (COVID-19) pandemic has devastated global health and the economy, underscoring the urgent need for extensive research into the mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral entry and the development of effective therapeutic interventions. Experimental approach We established a cell line expressing human angiotensin-converting enzyme 2 (ACE2). We used it as a model of pseudotyped viral entry using murine leukemia virus (MLV) expressing SARS-CoV-2 spike (S) protein on its surface and firefly luciferase as a reporter. We screened an U.S. Food and Drug Administration (FDA)-approved compound library for inhibiting ACE2-dependent SARS-CoV-2 pseudotyped viral entry and identified several drug-repurposing candidates. Key results We identified 18 drugs and drug candidates, including 14 previously reported inhibitors of viral entry and four novel candidates. Pyridoxal 5'-phosphate, Dovitinib, Adefovir dipivoxil, and Biapenem potently inhibit ACE2-dependent viral entry with inhibitory concentration 50% (IC50) values of 57nM, 74 nM, 130 nM, and 183 nM, respectively. Conclusion and implications We identified four novel FDA-approved candidate drugs for anti-SARS-CoV-2 combination therapy. Our findings contribute to the growing body of evidence supporting drug repurposing as a viable strategy for rapidly developing COVID-19 treatments.
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Affiliation(s)
- Manisha Singh
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shruthi Shanmukha
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Raghda E. Eldesouki
- Genetics Unit, Histology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Maged M. Harraz
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Pharmacology and Physiology, University of Maryland School of Medicine, Baltimore, MD, United States
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22
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Abou Mansour M, El Rassi C, Sleem B, Borghol R, Arabi M. Thromboembolic Events in the Era of COVID-19: A Detailed Narrative Review. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2025; 2025:3804576. [PMID: 40226433 PMCID: PMC11986918 DOI: 10.1155/cjid/3804576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 02/14/2025] [Indexed: 04/15/2025]
Abstract
COVID-19, caused by the SARS-CoV-2 virus, is not only characterized by respiratory symptoms but is also associated with a wide range of systemic complications, including significant hematologic abnormalities. This is a comprehensive review of the current literature, using PubMed and Google Scholar, on the pathophysiology and incidence of thromboembolic events in COVID-19 patients and thromboprophylaxis. COVID-19 infection induces a prothrombotic state in patients through the dysregulation of the renin-angiotensin-aldosterone system (RAAS), endothelial dysfunction, elevated von Willebrand factor (vWF), and a dysregulated immune response involving the complement system and neutrophil extracellular traps (NETs). As a result, thromboembolic complications have emerged in COVID-19 cases, occurring more frequently in severe cases and hospitalized patients. These thrombotic events affect both venous and arterial circulation, with increased incidences of deep venous thrombosis (DVT), pulmonary embolism (PE), systemic arterial thrombosis, and myocardial infarction (MI). While DVT and PE are more common, the literature highlights the potential lethal consequences of arterial thromboembolism (ATE). This review also briefly examines the ongoing discussions regarding the use of anticoagulants for the prevention of thrombotic events in COVID-19 patients. While theoretically promising, current studies have yielded varied outcomes: Some suggest potential benefits, whereas others report an increased risk of bleeding events among hospitalized patients. Therefore, further large-scale studies are needed to assess the efficacy and safety of anticoagulants for thromboprophylaxis in COVID-19 patients.
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Affiliation(s)
- Maria Abou Mansour
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Christophe El Rassi
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Bshara Sleem
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Raphah Borghol
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Pediatric Department, Division of Pediatric Hematology-Oncology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mariam Arabi
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Pediatric Department, Division of Pediatric Cardiology, American University of Beirut Medical Center, Beirut, Lebanon
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23
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Krogsaeter EK, McKetney J, Valiente-Banuet L, Marquez A, Willis A, Cakir Z, Stevenson E, Jang GM, Rao A, Li E, Zhou A, Attili A, Chang TS, Kampmann M, Huang Y, Krogan NJ, Swaney DL. Lysosomal proteomics reveals mechanisms of neuronal apoE4-associated lysosomal dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.10.02.560519. [PMID: 37873080 PMCID: PMC10592882 DOI: 10.1101/2023.10.02.560519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
ApoE4 is the primary risk factor for Alzheimer Disease (AD). Early AD pathological events first affect the neuronal endolysosomal system, which in turn causes neuronal protein aggregation and cell death. Despite the crucial influence of lysosomes upon AD pathophysiology, and that apoE4 localizes to lysosomes, the influence of apoE4 on lysosomal function remains unexplored. We find that expression of apoE4 in neuronal cell lines results in lysosomal alkalinization and impaired lysosomal function. To identify driving factors for these defects, we performed quantitative lysosomal proteome profiling. This revealed that apoE4 expression results in differential regulation of numerous lysosomal proteins, correlating with apoE allele status and disease severity in AD brains. In particular, apoE4 expression results in the depletion of lysosomal Lgals3bp and the accumulation of lysosomal Tmed5. We additionally validated that these lysosomal protein changes can be targeted to modulate lysosomal function. Taken together, this work thereby reveals that apoE4 causes widespread lysosomal defects through remodeling the lysosomal proteome, with the lysosomal Tmed5 accumulation and Lgals3bp depletion manifesting as lysosomal alkalinization in apoE4 neurons.
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Affiliation(s)
- Einar K. Krogsaeter
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- These authors contributed equally
| | - Justin McKetney
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- These authors contributed equally
| | - Leopoldo Valiente-Banuet
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Angelica Marquez
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Alexandra Willis
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Zeynep Cakir
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Erica Stevenson
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Gwendolyn M. Jang
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Antara Rao
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, USA
| | - Anton Zhou
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
| | - Anjani Attili
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, USA
- Biosciences Internship Program, City College of San Francisco, USA
| | - Timothy S. Chang
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, The J. David Gladstone Institutes, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, USA
- Neuroscience Graduate Program, University of California, San Francisco, USA
- Gladstone Center for Translational Advancement, Gladstone Institutes, San Francisco, USA
- Departments of Neurology and Pathology, University of California, San Francisco, USA
| | - Nevan J. Krogan
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
| | - Danielle L. Swaney
- Gladstone Data Science and Biotechnology Institute, The J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Bioscience Institute, University of California, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
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24
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Vallejo-Arróliga M, Villalobos-Agüero RA, Zamora-Sanabria R, Karkashian-Córdoba J. Molecular analysis of 4/91-like variants of avian infectious bronchitis virus (IBV) obtained after the introduction of a 4/91 live-attenuated vaccine in Costa Rica during 2017. Virusdisease 2025; 36:81-92. [PMID: 40290772 PMCID: PMC12021757 DOI: 10.1007/s13337-025-00910-4] [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: 10/12/2024] [Accepted: 01/18/2025] [Indexed: 04/30/2025] Open
Abstract
Avian infectious bronchitis virus (IBV) belongs to family Coronaviridae, genus Gammacoronavirus and is one of the most predominant causes of respiratory disease in poultry. Its high mutation rate constantly leads to the emergence of novel variants that complicate disease control. In 2016, a GA13-like IBV outbreak occurred in Costa Rica, prompting the introduction of the 4/91 live-attenuated vaccine. The objective of this research was to perform a molecular characterization of IBV variants circulating in the country six years after the introduction of the 4/91 vaccine. A total of 177 samples from symptomatic birds were analyzed, with 43 testing positive for IBV. Seven complete S1 sequences were obtained and clustered within the GI-13 lineage by phylogenetic analysis. Sequence analysis showed high genetic similarity to the 4/91 vaccine strain, with nucleotide and amino acid sequence identities over 99.13% and 97.96%, respectively, despite these samples being taken from unvaccinated birds. Post-translational modification analysis of the S1 protein revealed conserved N-glycosylation and palmitoylation sites, while two serine phosphorylation changes were predicted between the obtained sequences and the vaccine strain. Selective pressure analysis identified 10 sites under positive selection, mainly located within the receptor-binding domain and hypervariable regions of the S1 subunit. The presence of 4/91-like variants in unvaccinated birds needs attention, and its relation to observed pathology requires further research. Continuous surveillance is essential to monitor for potential vaccine escape mutants and mitigate their impact. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-025-00910-4.
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25
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Schreiber A, Ludwig S. Host-targeted antivirals against SARS-CoV-2 in clinical development - Prospect or disappointment? Antiviral Res 2025; 235:106101. [PMID: 39923941 DOI: 10.1016/j.antiviral.2025.106101] [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: 12/29/2024] [Revised: 02/05/2025] [Accepted: 02/06/2025] [Indexed: 02/11/2025]
Abstract
The global response to the COVID-19 pandemic, caused by the novel SARS-CoV-2 virus, has seen an unprecedented increase in the development of antiviral therapies. Traditional antiviral strategies have primarily focused on direct-acting antivirals (DAAs), which specifically target viral components. In recent years, increasing attention was given to an alternative approach aiming to exploit host cellular pathways or immune responses to inhibit viral replication, which has led to development of so-called host-targeted antivirals (HTAs). The emergence of SARS-CoV-2 and COVID-19 has promoted a boost in this field. Numerous HTAs have been tested and demonstrated their potential against SARS-CoV-2 through in vitro and in vivo studies. However, in striking contrast, only a limited number have successfully progressed to advanced clinical trial phases (2-4), and even less have entered clinical practice. This review aims to explore the current landscape of HTAs targeting SARS-CoV-2 that have reached phase 2-4 clinical trials. Additionally, it will explore the challenges faced in the development of HTAs and in gaining regulatory approval and market availability.
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Affiliation(s)
- André Schreiber
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster, University of Muenster, Muenster, Germany.
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San Felipe CJ, Batra J, Muralidharan M, Malpotra S, Anand D, Bauer R, Verba KA, Swaney DL, Krogan NJ, Grabe M, Fraser JS. Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.16.638509. [PMID: 40027672 PMCID: PMC11870501 DOI: 10.1101/2025.02.16.638509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Open Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and -2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom70). Previous structural studies of Orf9b in isolation revealed a β-sheet-rich homodimer, however, structures of Orf9b in complex with Tom70 revealed a monomeric helical fold. Here, we developed a biophysical model that quantifies how Orf9b switches between these conformations and binds to Tom70, a requirement for suppressing the type 1 interferon response. We used this model to characterize the effect of lipid binding and mutations in variants of concern to the Orf9b:Tom70 equilibrium. We found that the binding of a lipid to the Orf9b homodimer biases the Orf9b monomer:dimer equilibrium towards the dimer by reducing the dimer dissociation rate ∼100-fold. We also found that mutations in variants of concern can alter different microscopic rate constants without significantly affecting binding to Tom70. Together our results highlight how perturbations to different steps in these coupled equilibria can affect the apparent affinity of Orf9b to Tom70, with potential downstream implications for interferon signaling in coronavirus infection.
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Affiliation(s)
- CJ San Felipe
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | - Jyoti Batra
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Monita Muralidharan
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Shivali Malpotra
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Durga Anand
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Rachel Bauer
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Kliment A Verba
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Danielle L. Swaney
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Nevan J. Krogan
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, 94158, California,USA
- Department of Cellular and Molecular Pharmacology,University of California San Francisco, San Francisco, CA 94158
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158
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Wang J, Xiao M, Hu Z, Lin Y, Li K, Chen P, Lu C, Dong Z, Pan M. Bombyx mori nucleopolyhedrovirus LEF-2 disrupts the cell cycle in the G2/M phase by triggering a host cell DNA damage response. INSECT MOLECULAR BIOLOGY 2025; 34:81-93. [PMID: 39150688 DOI: 10.1111/imb.12951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]
Abstract
It is a common strategy for viruses to block the host cell cycle to favour their DNA replication. Baculovirus, being a double-stranded DNA virus, can arrest the cell cycle in the G2/M phase to facilitate its replication. However, the key viral genes and mechanisms crucial for inducing cell cycle arrest remain poorly understood. Here, we initially examined the impacts of several Bombyx mori nucleopolyhedrovirus (BmNPV) DNA replication-associated genes: ie1, lef-1, lef-2, lef-3, lef-4, odv-ec27 and dbp. We assessed their effects on both the host cells' DNA replication and cell cycle. Our findings reveal that when the lef-2 gene was overexpressed, it led to a significant increase in the number of cells in the G2/M phase and a reduction in the number of cells in the S phase. Furthermore, we discovered that the LEF-2 protein is located in the virogenic stroma and confirmed its involvement in viral DNA replication. Additionally, by employing interference and overexpression experiments, we found that LEF-2 influences host cell DNA replication and blocks the cell cycle in the G2/M phase by regulating the expression of CyclinB and CDK1. Finally, we found that BmNPV lef-2 triggered a DNA damage response in the host cell, and inhibiting this response removed the cell cycle block caused by BmNPV LEF-2. Thus, our findings indicate that the BmNPV lef-2 gene plays a crucial role in viral DNA replication and can regulate host cell cycle processes. This study furthers our understanding of baculovirus-host cell interactions and provides new insight into the molecular mechanisms of antiviral research.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Miao Xiao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Zhigang Hu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Yu Lin
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Kejie Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Peng Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Cheng Lu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Zhanqi Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Minhui Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
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28
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Xu D, Guo M, Xu X, Luo G, Liu Y, Bush SJ, Wang C, Xu T, Zeng W, Liao C, Wang Q, Zhao W, Zhao W, Liu Y, Li S, Zhao S, Jiu Y, Sauvonnet N, Lu W, Sansonetti PJ, Ye K. Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11. Nat Microbiol 2025; 10:509-526. [PMID: 39901059 DOI: 10.1038/s41564-024-01901-9] [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: 02/28/2024] [Accepted: 12/02/2024] [Indexed: 02/05/2025]
Abstract
Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant filopodial extensions in epithelial cells that capture Shigella, a major human enteroinvasive pathogen that is able to exploit these filopodia for invasion, revealing a mechanism for HD5-augmented bacterial invasion. Using multi-omics screening and in vitro, organoid, dynamic gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of the human colonic epithelium. Inhibitor screening identified cAMP-PKA signalling as the main pathway mediating the cytoskeleton-regulating activity of HD5. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of alternative intervention strategies against HD5-augmented infections.
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Affiliation(s)
- Dan Xu
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Mengyao Guo
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Xu
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Gan Luo
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Yaxin Liu
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Chengyao Wang
- The First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Tun Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Wenxin Zeng
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Chongbing Liao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Qingxia Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Wei Zhao
- The First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Wenying Zhao
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yuezhuangnan Liu
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Shanshan Li
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Shuangshuang Zhao
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Yaming Jiu
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Nathalie Sauvonnet
- Tissue Homeostasis group, Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Philippe J Sansonetti
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- Institut Pasteur, Paris, France.
| | - Kai Ye
- Key Laboratory of Biomedical Information Engineering (MOE), School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- The First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, China.
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29
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Zeng Q, Chen Z, Huang Y, Fu Q, Chen Z, Wu H. SRPK1 facilitates IBDV replication by phosphorylating VP1 at S48. Int J Biol Macromol 2025; 291:139002. [PMID: 39716705 DOI: 10.1016/j.ijbiomac.2024.139002] [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: 08/11/2024] [Revised: 12/15/2024] [Accepted: 12/17/2024] [Indexed: 12/25/2024]
Abstract
Infectious Bursal Disease Virus (IBDV), a double-stranded RNA virus of the Avibirnavirus genus, causes significant vaccine failures in immunocompromised young poultry. The VP1 protein of IBDV undergoes post-translational modifications that are critical for viral RNA transcription, genome replication, and overall viral proliferation. Phosphorylation enhances the ability of the IBDV polymerase VP1 and facilitates viral replication, while the specific mechanisms underlying VP1 phosphorylation and its role in the IBDV life cycle remain largely unexplored. This study shows that SRPK1 phosphorylates VP1 at the serine 48 (S48) residue in the N-terminal 46SPSR49 motif, enhancing polymerase activity and promoting replication. During IBDV infection, VP1 recruits SRPK1 and co-localizes with it. Inhibiting or deleting SRPK1 greatly reduced VP1 polymerase activity, a leading to a decrease in viral replication. Mutant strains S48A and S48E displayed impaired replication, highlighting the crucial role of SRPK1-mediated phosphorylation in VP1 function. These findings emphasize the key role of SRPK1-mediated VP1 phosphorylation in IBDV replication, providing new insights into viral-host interactions and potential therapeutic targets.
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Affiliation(s)
- Qinghua Zeng
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Zheng Chen
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Qiuling Fu
- Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Zhen Chen
- Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Huansheng Wu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, PR China.
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30
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Zodda E, Pons M, DeMoya-Valenzuela N, Calvo-González C, Benítez-Rodríguez C, López-Ayllón BD, Hibot A, Zuin A, Crosas B, Cascante M, Montoya M, Pujol MD, Rubio-Martínez J, Thomson TM. Induction of the Inflammasome by the SARS-CoV-2 Accessory Protein ORF9b, Abrogated by Small-Molecule ORF9b Homodimerization Inhibitors. J Med Virol 2025; 97:e70145. [PMID: 39902616 DOI: 10.1002/jmv.70145] [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: 06/11/2024] [Revised: 10/07/2024] [Accepted: 11/07/2024] [Indexed: 02/05/2025]
Abstract
Viral accessory proteins play critical roles in viral escape from host innate immune responses and in viral inflammatory pathogenesis. Here we show that the SARS-CoV-2 accessory protein, ORF9b, but not other SARS-CoV-2 accessory proteins (ORF3a, ORF3b, ORF6, ORF7, ORF8, ORF9c, and ORF10), strongly activates inflammasome-dependent caspase-1 in A549 lung carcinoma cells and THP-1 monocyte-macrophage cells. Exposure to lipopolysaccharide (LPS) and ATP additively enhanced the activation of caspase-1 by ORF9b, suggesting that ORF9b and LPS follow parallel pathways in the activation of the inflammasome and caspase-1. Following rational in silico approaches, we have designed small molecules capable of inhibiting the homodimerization of ORF9b, which experimentally inhibited ORF9b-ORF9b homotypic interactions, caused mitochondrial eviction of ORF9b, inhibited ORF9b-induced activation of caspase-1 in A549 and THP-1 cells, cytokine release in THP-1 cells, and restored type I interferon (IFN-I) signaling suppressed by ORF9b in both cell models. These small molecules are first-in-class compounds targeting a viral accessory protein critical for viral-induced exacerbated inflammation and escape from innate immune responses, with the potential of mitigating the severe immunopathogenic damage induced by highly pathogenic coronaviruses and restoring antiviral innate immune responses curtailed by viral infection.
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Grants
- This work was funded by the Spanish National Research Council (CSIC, project numbers CSIC-COV19-006, CSIC-COV-19-201, CSIC-COV-19-117, SGL2103019, SGL2103015, 202020E079 and 202320E187 and LINCGLOBAL INCGL20009), the Catalan Agency for Management of University and Research Grants (AGAUR, 2020PANDE00048, 2021SGR1490, 2021SGR00350), the Spanish Ministry of Science (PID2021-123399OB-I00), the CSIC's Global Health Platform (PTI Salud Global), The Networked Center for Biomedical Research in Liver and Digestive Diseases (CIBER-EHD), the Spanish Structures and Excellence María de Maeztu program (CEX2021-001202-M), the European Commission-Next Generation EU (Regulation EU 2020/2094), and INDICASAT-AIP.
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Affiliation(s)
- Erika Zodda
- Laboratory of Cell Signaling and Cancer, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Mònica Pons
- Laboratory of Cell Signaling and Cancer, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Natàlia DeMoya-Valenzuela
- Department of Materials Science and Physical Chemistry, University of Barcelona, Barcelona, Spain
- Theoretical and Computational Chemistry Research Institute (IQTCUB), Barcelona, Spain
| | - Cristina Calvo-González
- Laboratory of Cell Signaling and Cancer, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Cristina Benítez-Rodríguez
- Laboratory of Cell Signaling and Cancer, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Blanca D López-Ayllón
- Viral immunology Lab, Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Achraf Hibot
- Laboratory of Pharmaceutical Chemistry, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Alice Zuin
- Regulation of the Proteasome Laboratory, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Bernat Crosas
- Regulation of the Proteasome Laboratory, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBER-EHD), Madrid, Spain
| | - María Montoya
- Viral immunology Lab, Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - María D Pujol
- Laboratory of Pharmaceutical Chemistry, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Jaime Rubio-Martínez
- Department of Materials Science and Physical Chemistry, University of Barcelona, Barcelona, Spain
- Theoretical and Computational Chemistry Research Institute (IQTCUB), Barcelona, Spain
| | - Timothy M Thomson
- Laboratory of Cell Signaling and Cancer, Barcelona Institute for Molecular Biology, Spanish National Scientific Research Council (IBMB-CSIC), Barcelona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBER-EHD), Madrid, Spain
- High-Altitude Research Institute (IIA), Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Investigaciones Científicas y Servicio de Alta Tecnología (INDICASAT AIP), Panama City, Panama
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31
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Kokot T, Zimmermann JP, Chand Y, Krier F, Reimann L, Scheinost L, Höfflin N, Esch A, Höhfeld J, Warscheid B, Köhn M. Identification of phosphatases that dephosphorylate the co-chaperone BAG3. Life Sci Alliance 2025; 8:e202402734. [PMID: 39562141 PMCID: PMC11576475 DOI: 10.26508/lsa.202402734] [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: 03/25/2024] [Revised: 11/06/2024] [Accepted: 11/07/2024] [Indexed: 11/21/2024] Open
Abstract
The co-chaperone BAG3 plays critical roles in maintaining cellular proteostasis. It associates with 14-3-3 proteins during the trafficking of aggregation-prone proteins and facilitates their degradation through chaperone-assisted selective autophagy in cooperation with small heat shock proteins. Although reversible phosphorylation regulates BAG3 function, the involved phosphatases remain unknown. Here, we used affinity purification mass spectrometry to identify phosphatases that target BAG3. Of the hits, we evaluated the involvement of protein phosphatase-1 (PP1) using chemical inhibitors and activators in in vitro and cellular approaches. Our results demonstrate that PP1 can dephosphorylate BAG3-pS136 in cells and counteract 14-3-3γ association with BAG3 at this motif. Furthermore, protein phosphatase-5 (PP5) co-enriched with proteostasis-related proteins, and it has the capacity to dephosphorylate a BAG3 phosphorylation-site cluster regulating the interaction of BAG3 with small heat shock proteins and BAG3-mediated protein degradation. Our findings provide new insights into the regulation of BAG3 by phosphatases. This paves the way for future research focused on the precise control of BAG3 function through its regulatory proteins, potentially holding therapeutic promise for diseases characterized by disrupted proteostasis.
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Affiliation(s)
- Thomas Kokot
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Johannes P Zimmermann
- Biochemistry II, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Yamini Chand
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Fabrice Krier
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Lena Reimann
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Scheinost
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Nico Höfflin
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Alessandra Esch
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Jörg Höhfeld
- Institute for Cell Biology, University of Bonn, Bonn, Germany
| | - Bettina Warscheid
- Biochemistry II, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maja Köhn
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
- Institute for Cell Biology, University of Bonn, Bonn, Germany
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32
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Ruhoff VT, Leijnse N, Doostmohammadi A, Bendix PM. Filopodia: integrating cellular functions with theoretical models. Trends Cell Biol 2025; 35:129-140. [PMID: 38969554 DOI: 10.1016/j.tcb.2024.05.005] [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: 02/29/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 07/07/2024]
Abstract
Filopodia, widely distributed on cell surfaces, are distinguished by their dynamic extensions, playing pivotal roles in a myriad of biological processes. Their functions span from mechanosensing and guidance to cell-cell communication during cellular organization in the early embryo. Filopodia have significant roles in pathogenic processes, such as cancer invasion and viral dissemination. Molecular mapping of the filopodome has revealed generic components essential for filopodia functions. In parallel, recent insights into biophysical mechanisms governing filopodia dynamics have provided the foundation for broader investigations of filopodia's biological functions. We highlight recent discoveries of engagement of filopodia in various stages of development and pathogenesis and present an overview of intricate molecular and physical features of these cellular structures across a spectrum of cellular activities.
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Affiliation(s)
| | - Natascha Leijnse
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
| | - Poul Martin Bendix
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark.
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33
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Hickey TE, Mudunuri U, Hempel HA, Kemp TJ, Roche NV, Talsania K, Sellers BA, Cherry JM, Pinto LA. Proteomic and serologic assessments of responses to mRNA-1273 and BNT162b2 vaccines in human recipient sera. Front Immunol 2025; 15:1502458. [PMID: 39931577 PMCID: PMC11808009 DOI: 10.3389/fimmu.2024.1502458] [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: 09/26/2024] [Accepted: 11/25/2024] [Indexed: 02/13/2025] Open
Abstract
Introduction The first vaccines approved against SARS-CoV-2, mRNA-1273 and BNT162b2, utilized mRNA platforms. However, little is known about the proteomic markers and pathways associated with host immune responses to mRNA vaccination. In this proof-of-concept study, sera from male and female vaccine recipients were evaluated for proteomic and immunologic responses 1-month and 6-months following homologous third vaccination. Methods An aptamer-based (7,289 marker) proteomic assay coupled with traditional serology was leveraged to generate a comprehensive evaluation of systemic responsiveness in 64 and 68 healthy recipients of mRNA-1273 and BNT162b2 vaccines, respectively. Results Sera from female recipients of mRNA-1273 showed upregulated indicators of inflammatory and immunological responses at 1-month post-third vaccination, and sera from female recipients of BNT162b2 demonstrated upregulated negative regulators of RNA sensors at 1-month. Sera from male recipients of mRNA-1273 showed no significant upregulation of pathways at 1-month post-third vaccination, though there were multiple significantly upregulated proteomic markers. Sera from male recipients of BNT162b2 demonstrated upregulated markers of immune response to doublestranded RNA and cell-cycle G(2)/M transition at 1-month. Random Forest analysis of proteomic data from pre-third-dose sera identified 85 markers used to develop a model predictive of robust or weaker IgG responses and antibody levels to SARS-CoV-2 spike protein at 6-months following boost; no specific markers were individually predictive of 6-month IgG response. Thirty markers that contributed most to the model were associated with complement cascade and activation; IL-17, TNFR pro-apoptotic, and PI3K signaling; and cell cycle progression. Discussion These results demonstrate the utility of proteomics to evaluate correlates or predictors of serological responses to SARS-CoV-2 vaccination.
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Affiliation(s)
- Thomas E. Hickey
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Uma Mudunuri
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Heidi A. Hempel
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Troy J. Kemp
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Nancy V. Roche
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Keyur Talsania
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Brian A. Sellers
- Center for Human Immunology, Inflammation and Autoimmunity, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - James M. Cherry
- Center for Human Immunology, Inflammation and Autoimmunity, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ligia A. Pinto
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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Liu Y, Rao S, Hoskins I, Geng M, Zhao Q, Chacko J, Ghatpande V, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vighnesh Ghatpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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35
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Sekine R, Takeda K, Suenaga T, Tsuno S, Kaiya T, Kiso M, Yamayoshi S, Takaku Y, Ohno S, Yamaguchi Y, Nishizawa S, Sumitomo K, Ikuta K, Kanda T, Kawaoka Y, Nishimura H, Kuge S. G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication. Commun Biol 2025; 8:27. [PMID: 39815031 PMCID: PMC11735773 DOI: 10.1038/s42003-024-07351-7] [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: 02/27/2024] [Accepted: 12/03/2024] [Indexed: 01/18/2025] Open
Abstract
Future pandemic threats may be caused by novel coronaviruses and influenza A viruses. Here we show that when directly added to a cell culture, 12mer guanine RNA (G12) and its phosphorothioate-linked derivatives (G12(S)), rapidly entered cytoplasm and suppressed the propagation of human coronaviruses and influenza A viruses to between 1/100 and nearly 1/1000 of normal virus infectivity without cellular toxicity and induction of innate immunity. Moreover, G12(S) alleviated the weight loss caused by coronavirus infection in mice. G12(S) might exhibit a stable G-tetrad with left-handed parallel-stranded G-quadruplex, and inhibit the replication process by impeding interaction between viral nucleoproteins and viral RNA in the cytoplasm. Unlike previous antiviral strategies that target the G-quadruplexes of the viral genome, we now show that excess exogenous G-quadruplex-forming small RNA displaces genomic RNA from ribonucleoprotein, effectively inhibiting viral replication. The approach has the potential to facilitate the creation of versatile middle-molecule antivirals featuring lipid nanoparticle-free delivery.
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Affiliation(s)
- Ryoya Sekine
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Kouki Takeda
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Tsukasa Suenaga
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Satsuki Tsuno
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Takumi Kaiya
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Maki Kiso
- Division of Virology, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan
- The University of Tokyo, Pandemic Preparedness, Infection, and Advanced Research Center, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan
- The University of Tokyo, Pandemic Preparedness, Infection, and Advanced Research Center, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Yoshihide Takaku
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Azaaoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Azaaoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Kazuhiro Sumitomo
- Division of Geriatric and Community Medicine, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi, 983-8536, Japan
| | - Kazufumi Ikuta
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi, 983-8536, Japan
| | - Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi, 983-8536, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan
- The University of Tokyo, Pandemic Preparedness, Infection, and Advanced Research Center, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, National Hospital Organization Sendai Medical Center, 2-1-12, Miyagino, Miyagino-ku, Sendai, Miyagi, 983-8520, Japan
| | - Shusuke Kuge
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan.
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Rawal O, Turhan B, Peradejordi IF, Chandrasekar S, Kalayci S, Gnjatic S, Johnson J, Bouhaddou M, Gümüş ZH. PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data. PATTERNS (NEW YORK, N.Y.) 2025; 6:101148. [PMID: 39896259 PMCID: PMC11783894 DOI: 10.1016/j.patter.2024.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 11/12/2024] [Accepted: 12/11/2024] [Indexed: 02/04/2025]
Abstract
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets across multiple conditions. Researchers then must infer kinases responsible for changes in phosphosites of each substrate. However, tools that infer kinase-substrate interactions (KSIs) are not optimized to interactively explore the resulting large and complex networks, significant phosphosites, and states. There is thus an unmet need for a tool that facilitates user-friendly analysis, interactive exploration, visualization, and communication of phosphoproteomics datasets. We present PhosNetVis, a web-based tool for researchers of all computational skill levels to easily infer, generate, and interactively explore KSI networks in 2D or 3D by streamlining phosphoproteomics data analysis steps within a single tool. PhostNetVis lowers barriers for researchers by rapidly generating high-quality visualizations to gain biological insights from their phosphoproteomics datasets. It is available at https://gumuslab.github.io/PhosNetVis/.
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Affiliation(s)
- Osho Rawal
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Berk Turhan
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Türkiye
| | - Irene Font Peradejordi
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Cornell Tech, Cornell University, New York, NY 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Cornell Tech, Cornell University, New York, NY 10044, USA
| | - Selim Kalayci
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zeynep H. Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Xu F, Shang D, Zhu C, Du G, Shi J, Dong X, Li X, Liang X. In Situ MXene-Controlled Synthesis of Polycrystalline TiO 2 for Highly Efficient Enrichment of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2025; 17:260-268. [PMID: 39714392 DOI: 10.1021/acsami.4c14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Phosphopeptide enrichment methods based on commercial TiO2 suffer from difficulties in regulating intermolecular interactions, resulting in low coverage rate and the loss of information on multiphosphorylation sites, thereby limiting comprehensive phosphoproteomic analysis. In this work, MXene Ti3C2Tx was incorporated into the design of enrichment materials, with its surface structure functionalized and regulated to address the low elution efficiency of TiO2 for multiphosphorylated peptides. Upon oxidation treatment, the Ti3C2Tx material formed numerous uniformly distributed TiO2 nanoparticles on the surface of Ti3C2Tx-O, providing abundant affinity sites (Ti-O) for selective phosphopeptide enrichment. The polycrystalline structure and rich oxygen vacancies of the material effectively regulated its binding affinity with phosphate groups, achieving simultaneous high-efficiency enrichment of both monophosphorylated and multiphosphorylated peptides. Its performance was significantly superior to that of commercial TiO2 and IMAC materials. This study presents great promise for the practical application of comprehensive phosphoproteomic analysis in the future and broadens the application of MXene in the biological field.
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Affiliation(s)
- Feifei Xu
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P.R. China
| | - Danyi Shang
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
| | - Congcong Zhu
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P.R. China
| | - Guangzhu Du
- Department of Materials Science and Engineering, Dalian Maritime University, Dalian 116026, P.R. China
| | - Jingchen Shi
- School of Pharmacy, Dalian Medical University, Dalian 116044, P.R. China
| | - Xuefang Dong
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P.R. China
| | - Xiuling Li
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P.R. China
| | - Xinmiao Liang
- Key Laboratory of Phytochemistry and Natural Medicines, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P.R. China
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38
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dos Santos F, Vindel-Alfageme J, Ciordia S, Castro V, Orera I, Garaigorta U, Gastaminza P, Corrales F. Dynamic Cellular Proteome Remodeling during SARS-CoV-2 Infection. Identification of Plasma Protein Readouts. J Proteome Res 2025; 24:171-188. [PMID: 39593238 PMCID: PMC11705369 DOI: 10.1021/acs.jproteome.4c00566] [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: 07/03/2024] [Revised: 11/06/2024] [Accepted: 11/19/2024] [Indexed: 11/28/2024]
Abstract
The outbreak of COVID-19, led to an ongoing pandemic with devastating consequences for the global economy and human health. With the global spread of SARS-CoV-2, multidisciplinary initiatives were launched to explore new diagnostic, therapeutic, and vaccination strategies. From this perspective, proteomics could help to understand the mechanisms associated with SARS-CoV-2 infection and to identify new therapeutic options. A TMT-based quantitative proteomics and phosphoproteomics analysis was performed to study the proteome remodeling of human lung alveolar cells expressing human ACE2 (A549-ACE2) after infection with SARS-CoV-2. Detectability and the prognostic value of selected proteins was analyzed by targeted PRM. A total of 6802 proteins and 6428 phospho-sites were identified in A549-ACE2 cells after infection with SARS-CoV-2. The differential proteins here identified revealed that A549-ACE2 cells undergo a time-dependent regulation of essential processes, delineating the precise intervention of the cellular machinery by the viral proteins. From this mechanistic background and by applying machine learning modeling, 29 differential proteins were selected and detected in the serum of COVID-19 patients, 14 of which showed promising prognostic capacity. Targeting these proteins and the protein kinases responsible for the reported phosphorylation changes may provide efficient alternative strategies for the clinical management of COVID-19.
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Affiliation(s)
- Fátima
Milhano dos Santos
- Functional
Proteomics Laboratory, National Center for
Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Jorge Vindel-Alfageme
- Functional
Proteomics Laboratory, National Center for
Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Sergio Ciordia
- Functional
Proteomics Laboratory, National Center for
Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Victoria Castro
- Department
of Molecular and Cell Biology, National
Center for Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Irene Orera
- Proteomics
Research Core Facility, Instituto Aragonés
de Ciencias de la Salud (IACS), Zaragoza 50009, Spain
| | - Urtzi Garaigorta
- Department
of Molecular and Cell Biology, National
Center for Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Pablo Gastaminza
- Department
of Molecular and Cell Biology, National
Center for Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
| | - Fernando Corrales
- Functional
Proteomics Laboratory, National Center for
Biotechnology (CNB-CSIC), Darwin 3, Madrid 28049, Spain
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Liu M, Peng W, Ji X. Repurposing of CDK Inhibitors as Host Targeting Antivirals: A Mini- Review. Mini Rev Med Chem 2025; 25:178-189. [PMID: 39185650 DOI: 10.2174/0113895575311618240820103549] [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: 02/20/2024] [Revised: 04/30/2024] [Accepted: 07/09/2024] [Indexed: 08/27/2024]
Abstract
Most of the antiviral drugs in the market are designed to target viral proteins directly. They are generally considered safe for human use. However, they also suffer from several inherent limitations, in particular, narrow-spectrum antiviral profiles and liability to drug resistance. The other strategy for antiviral drug development is targeting host factors, which are highly involved at different stages in the viral life cycle. In contrast to direct-acting antiviral agents, host-targeting antiviral ones normally exhibit broad-spectrum antiviral properties along with a much higher genetic barrier to drug resistance. Cyclin-dependent kinases (CDKs) represent one such host factor. In this review, we summarized a number of CDK inhibitors (CDKIs) of varied chemical scaffolds with demonstrated antiviral activity. Challenges and issues associated with the repurposing of CDKIs as antiviral agents were also discussed.
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Affiliation(s)
- Miao Liu
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 215021, China
| | - Wei Peng
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, China
| | - Xingyue Ji
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 215021, China
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Song Z, Jiang M, Wang M, Zou J, Chen Z, Zheng F, Wang Q. MAPK pathways regulated apoptosis and pyroptosis in respiratory epithelial cells of a primitive vertebrate model during bacterial infection. Int J Biol Macromol 2025; 286:138587. [PMID: 39662566 DOI: 10.1016/j.ijbiomac.2024.138587] [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: 07/03/2024] [Revised: 12/07/2024] [Accepted: 12/07/2024] [Indexed: 12/13/2024]
Abstract
Respiratory diseases caused by bacterial and viral infection have seriously affected human health. The invaginated lung structure in mammals caused difficulties in relevant research, here we evaluated the regulatory roles of MAPK pathways in apoptosis and pyroptosis during bacterial infection in an evaginated respiratory organ model for the first time. F. columnare was adopted for bacterial infection in rainbow trout in vivo and RTgill-W1 cells in vitro. Infected trout gills were separated for histological analysis, transcriptomic sequencing, TUNEL, RT-qPCR and enzyme activity assay. RTgill-W1 cells were treated with different inhibitors of MAPK pathway for evaluating apoptosis and pyroptosis. Bacterial infection induced serious histological changes and apoptosis in trout gill, accompanied with p38MAPK/ JNK pathway activation, while pyroptosis were induced after secondary infection along with ERK pathway activation. In vitro study confirmed pro-apoptotic roles of bacterial infection, accompanied with the increased phosphorylation of p38 MAPK and JNK. Moreover, p38 MAPK inhibition significantly decreased the F. columnare infection-induced apoptosis of RTgill-W1 cell via affecting Bcl2 protein expression and mitochondrial membrane potential. Therefore, our study indicated that MAPK pathways regulated apoptosis and pyroptosis in teleost respiratory organ during bacterial infection, which will benefit developing strategies in fighting against bacterial disease in aquaculture practice.
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Affiliation(s)
- Zixi Song
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Mingxu Jiang
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Mengya Wang
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jiahong Zou
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhenwei Chen
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Feifei Zheng
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qingchao Wang
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, 430070 Wuhan, China.
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Lai H, Zhu T, Xie S, Luo X, Hong F, Luo D, Dao F, Lin H, Shu K, Lv H. Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection. Int J Mol Sci 2024; 25:13674. [PMID: 39769436 PMCID: PMC11678915 DOI: 10.3390/ijms252413674] [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: 12/05/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the large coronavirus family with high infectivity and pathogenicity and is the primary pathogen causing the global pandemic of coronavirus disease 2019 (COVID-19). Phosphorylation is a major type of protein post-translational modification that plays an essential role in the process of SARS-CoV-2-host interactions. The precise identification of phosphorylation sites in host cells infected with SARS-CoV-2 will be of great importance to investigate potential antiviral responses and mechanisms and exploit novel targets for therapeutic development. Numerous computational tools have been developed on the basis of phosphoproteomic data generated by mass spectrometry-based experimental techniques, with which phosphorylation sites can be accurately ascertained across the whole SARS-CoV-2-infected proteomes. In this work, we have comprehensively reviewed several major aspects of the construction strategies and availability of these predictors, including benchmark dataset preparation, feature extraction and refinement methods, machine learning algorithms and deep learning architectures, model evaluation approaches and metrics, and publicly available web servers and packages. We have highlighted and compared the prediction performance of each tool on the independent serine/threonine (S/T) and tyrosine (Y) phosphorylation datasets and discussed the overall limitations of current existing predictors. In summary, this review would provide pertinent insights into the exploitation of new powerful phosphorylation site identification tools, facilitate the localization of more suitable target molecules for experimental verification, and contribute to the development of antiviral therapies.
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Affiliation(s)
- Hongyan Lai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (H.L.); (T.Z.); (D.L.)
| | - Tao Zhu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (H.L.); (T.Z.); (D.L.)
| | - Sijia Xie
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; (S.X.); (X.L.); (F.H.); (H.L.)
| | - Xinwei Luo
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; (S.X.); (X.L.); (F.H.); (H.L.)
| | - Feitong Hong
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; (S.X.); (X.L.); (F.H.); (H.L.)
| | - Diyu Luo
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (H.L.); (T.Z.); (D.L.)
| | - Fuying Dao
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore;
| | - Hao Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; (S.X.); (X.L.); (F.H.); (H.L.)
| | - Kunxian Shu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (H.L.); (T.Z.); (D.L.)
| | - Hao Lv
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; (S.X.); (X.L.); (F.H.); (H.L.)
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Rawal O, Turhan B, Peradejordi IF, Chandrasekar S, Kalayci S, Gnjatic S, Johnson J, Bouhaddou M, Gümüş ZH. PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data. ARXIV 2024:arXiv:2402.05016v4. [PMID: 39010877 PMCID: PMC11247916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets across multiple conditions. Researchers then must infer kinases responsible for changes in phosphosites of each substrate. However, tools that infer kinase-substrate interactions (KSIs) are not optimized to interactively explore the resulting large and complex networks, significant phosphosites, and states. There is thus an unmet need for a tool that facilitates user-friendly analysis, interactive exploration, visualization, and communication of phosphoproteomics datasets. We present PhosNetVis, a web-based tool for researchers of all computational skill levels to easily infer, generate and interactively explore KSI networks in 2D or 3D by streamlining phosphoproteomics data analysis steps within a single tool. PhostNetVis lowers barriers for researchers in rapidly generating high-quality visualizations to gain biological insights from their phosphoproteomics datasets. It is available at: https://gumuslab.github.io/PhosNetVis/.
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Affiliation(s)
- Osho Rawal
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- These authors contributed equally
| | - Berk Turhan
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Türkiye
- These authors contributed equally
| | - Irene Font Peradejordi
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Cornell Tech, Cornell University, New York, NY 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Cornell Tech, Cornell University, New York, NY 10044, USA
| | - Selim Kalayci
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Zeynep H. Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Lead contact
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Thakur N, Chakraborty P, Tufariello JM, Basler CF. SARS-CoV-2 Nsp14 binds Tollip and activates pro-inflammatory pathways while downregulating interferon-α and interferon-γ receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.12.628214. [PMID: 39713296 PMCID: PMC11661139 DOI: 10.1101/2024.12.12.628214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
SARS coronavirus 2 (SARS-CoV-2) non-structural protein 14 (Nsp14) possesses an N-terminal exonuclease (ExoN) domain that provides a proofreading function for the viral RNA-dependent RNA polymerase and a C-terminal N7-methyltransferase (N7-MTase) domain that methylates viral mRNA caps. Nsp14 also modulates host functions. This includes the activation of NF-κB and downregulation of interferon alpha/beta receptor 1 (IFNAR1). Here we demonstrate that Nsp14 exerts broader effects, activating not only NF-κB responses but also ERK, p38 and JNK MAP kinase (MAPK) signaling, promoting cytokine production. Further, Nsp14 downregulates not only IFNAR1 but also IFN-γ receptor 1 (IFNGR1), impairing cellular responses to both IFNα and IFNγ. IFNAR1 and IFNGR1 downregulation is via a lysosomal pathway and also occurs in SARS-CoV-2 infected cells. Analysis of a panel of Nsp14 mutants reveals a consistent pattern. Mutants that disable ExoN function remain active, whereas N7-MTase mutations impair both pro-inflammatory pathway activation and IFN receptor downregulation. Innate immune modulating functions also require the presence of both the ExoN and N7-MTase domains likely reflecting the need for the ExoN domain for N7-MTase activity. We further identify multi-functional host protein Tollip as an Nsp14 interactor. Interaction requires the phosphoinositide-binding C2 domain of Tollip and sequences C-terminal to the C2 domain. Full length Tollip or regions encompassing the Nsp14 interaction domain are sufficient to counteract both Nsp14-mediated and Nsp14-independent activation of NF-κB. Knockdown of Tollip partially reverses IFNAR1 and IFNGR1 downregulation in SARS-CoV-2 infected cells, suggesting relevance of Nsp14-Tollip interaction for Nsp14 innate immune evasion functions.
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Affiliation(s)
- Naveen Thakur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Poushali Chakraborty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - JoAnn M. Tufariello
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Huuskonen S, Liu X, Pöhner I, Redchuk T, Salokas K, Lundberg R, Maljanen S, Belik M, Reinholm A, Kolehmainen P, Tuhkala A, Tripathi G, Laine P, Belanov S, Auvinen P, Vartiainen M, Keskitalo S, Österlund P, Laine L, Poso A, Julkunen I, Kakkola L, Varjosalo M. The comprehensive SARS-CoV-2 'hijackome' knowledge base. Cell Discov 2024; 10:125. [PMID: 39653747 PMCID: PMC11628605 DOI: 10.1038/s41421-024-00748-y] [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: 04/30/2024] [Accepted: 10/29/2024] [Indexed: 12/12/2024] Open
Abstract
The continuous evolution of SARS-CoV-2 has led to the emergence of several variants of concern (VOCs) that significantly affect global health. This study aims to investigate how these VOCs affect host cells at proteome level to better understand the mechanisms of disease. To achieve this, we first analyzed the (phospho)proteome changes of host cells infected with Alpha, Beta, Delta, and Omicron BA.1 and BA.5 variants over time frames extending from 1 to 36 h post infection. Our results revealed distinct temporal patterns of protein expression across the VOCs, with notable differences in the (phospho)proteome dynamics that suggest variant-specific adaptations. Specifically, we observed enhanced expression and activation of key components within crucial cellular pathways such as the RHO GTPase cycle, RNA splicing, and endoplasmic reticulum-associated degradation (ERAD)-related processes. We further utilized proximity biotinylation mass spectrometry (BioID-MS) to investigate how specific mutation of these VOCs influence viral-host protein interactions. Our comprehensive interactomics dataset uncovers distinct interaction profiles for each variant, illustrating how specific mutations can change viral protein functionality. Overall, our extensive analysis provides a detailed proteomic profile of host cells for each variant, offering valuable insights into how specific mutations may influence viral protein functionality and impact therapeutic target identification. These insights are crucial for the potential use and design of new antiviral substances, aiming to enhance the efficacy of treatments against evolving SARS-CoV-2 variants.
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Affiliation(s)
- Sini Huuskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ina Pöhner
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Taras Redchuk
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kari Salokas
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Sari Maljanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Milja Belik
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Arttu Reinholm
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Antti Tuhkala
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Garima Tripathi
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sergei Belanov
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Vartiainen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pamela Österlund
- Finnish Institute for Health and Welfare, THL, Helsinki, Finland
| | - Larissa Laine
- Finnish Institute for Health and Welfare, THL, Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
- InFlames Research Flagship Center, University of Turku, Turku, Finland
| | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
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Zhou Z, Jin Z, Tian Y, Huangfu C, Fan Z, Liu D. CDK14 is regulated by IGF2BP2 and involved in osteogenic differentiation via Wnt/β-catenin signaling pathway in vitro. Life Sci 2024; 358:123148. [PMID: 39447733 DOI: 10.1016/j.lfs.2024.123148] [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: 06/18/2024] [Revised: 10/07/2024] [Accepted: 10/14/2024] [Indexed: 10/26/2024]
Abstract
AIMS Cyclin-dependent kinase (CDK) family proteins involve in various cellular processes via regulating the cell cycle; however, their expression during osteogenic differentiation and postmenopausal osteoporosis remains poorly understood. MAIN METHODS Using bioinformatics, we screened for CDK14 bound to Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and explored its expression in vitro with time-gradient model and in a mouse model of postmenopausal osteoporosis, building on prior research. Subsequently, we investigated its effect on osteoblast proliferation, cell cycle dynamics, and osteogenic differentiation by administering CDK14 siRNA and the covalent inhibitor FMF-04-159-2. Furthermore, we examined the interaction between IGF2BP2 and CDK14. Finally, we validated the regulatory role of CDK14 on the Wnt/β-catenin pathway. KEY FINDINGS Our findings demonstrate a time-dependent CDK14 expression patterns during osteogenic differentiation of MC3T3-E1 cell line, with an initial increase followed by gradual decline over time. Notably, CDK14 expression exhibited significant reduction in bone tissue of postmenopausal osteoporosis mouse model. CDK14 inhibition altered osteoblast cell cycle dynamics, significantly reduced cellular proliferation capacity, and impaired osteogenic differentiation ability. IGF2BP2 interacted with CDK14 mRNA, and stabilizing mRNA's structure and inhibiting its degradation. Additionally, CDK14 facilitated Low-density lipoprotein receptor-related protein 6 (LRP6) and Glycogen synthase kinase 3β (GSK3β) phosphorylation, thus regulating β-catenin levels. SIGNIFICANCE These findings provide further insight into the molecular mechanisms governing osteoblast proliferation, differentiation and osteoporosis.
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Affiliation(s)
- Zimo Zhou
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Zhuoru Jin
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Yicheng Tian
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Chenghao Huangfu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Zheng Fan
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| | - Da Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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46
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Aboulache BL, Hoitsma NM, Luger K. Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange. J Biol Chem 2024; 300:107893. [PMID: 39424143 PMCID: PMC11742319 DOI: 10.1016/j.jbc.2024.107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/13/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024] Open
Abstract
Maintaining the dynamic structure of chromatin is critical for regulating the cellular processes that require access to the DNA template, such as DNA damage repair, transcription, and replication. Histone chaperones and ATP-dependent chromatin remodeling factors facilitate transitions in chromatin structure by assembling and positioning nucleosomes through a variety of enzymatic activities. SMARCAD1 is a unique chromatin remodeler that combines the ATP-dependent ability to exchange histones, with the chaperone-like activity of nucleosome deposition. We have shown previously that phosphorylated SMARCAD1 exhibits reduced binding to nucleosomes. However, it is unknown how phosphorylation affects SMARCAD1's ability to perform its various enzymatic activities. Here we use mutational analysis, activity assays, and mass spectrometry, to probe SMARCAD1 regulation and to investigate the role of its flexible N-terminal region. We show that phosphorylation affects SMARCAD1 binding to nucleosomes, DNA, and histones H2A-H2B, as well as ATP hydrolysis and histone exchange. Conversely, we report only a marginal effect of phosphorylation for histone H3-H4 binding and nucleosome assembly. In addition, the SMARCAD1 N-terminal region is revealed to be critical for nucleosome assembly and histone exchange. Together, this work examines the intricacies of how phosphorylation governs SMARCAD1 activity and provides insight into its complex regulation and diverse activities.
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Affiliation(s)
- Briana L Aboulache
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Nicole M Hoitsma
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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47
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Sui L, Wang W, Guo X, Zhao Y, Tian T, Zhang J, Wang H, Xu Y, Chi H, Xie H, Xu W, Liu N, Zhao L, Song G, Wang Z, Zhang K, Che L, Zhao Y, Wang G, Liu Q. Multi-protomics analysis identified host cellular pathways perturbed by tick-borne encephalitis virus infection. Nat Commun 2024; 15:10435. [PMID: 39616195 PMCID: PMC11608235 DOI: 10.1038/s41467-024-54628-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 11/15/2024] [Indexed: 05/17/2025] Open
Abstract
Tick-borne encephalitis virus (TBEV) represents a pivotal tick-transmitted flavivirus responsible for severe neurological consequences in Europe and Asia. The emergence of TBEV genetic mutations and vaccine-breakthrough infections, along with the absence of effective vaccines and specific drugs for other tick-borne flaviviruses associated with severe encephalitis or hemorrhagic fever, underscores the urgent need for progress in understanding the pathogenesis and intervention strategies for TBEV and related flaviviruses. Here we elucidate cellular alterations in the proteome, phosphoproteome, and acetylproteome upon TBEV infection. Our findings reveal a substantial impact of TBEV infection on the innate immune response, ribosomal biogenesis, autophagy, and DNA damage response (DDR). Mechanically, the non-structural protein NS5 of TBEV impedes DNA damage repair by interacting with SIRT1 to suppress the deacetylation of KAP1 and Ku70. Additionally, the precursor membrane protein prM induces autophagy via associating with AKT1 while constrains autolysosome formation through binding to VPS11. Inhibitors targeting DDR, as well as specific kinases, exhibit potent antiviral activity, suggesting the dysregulated pathways and kinases as potential targets for antiviral intervention. These results from our study contribute to elucidating the pathogenesis and offers insights for developing effective antiviral drugs against TBEV and other tick-borne flaviviruses.
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Affiliation(s)
- Liyan Sui
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wenfang Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Basic Medical Science, Jilin University, Changchun, China
| | - Xuerui Guo
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Yinghua Zhao
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Tian Tian
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jinlong Zhang
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Heming Wang
- Biomaterials and Translational Medicine, Puheng Technology Co., Ltd, Suzhou, China
| | - Yueshan Xu
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China
| | - Hongmiao Chi
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Hanxi Xie
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Basic Medical Science, Jilin University, Changchun, China
| | - Wenbo Xu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Nan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Li Zhao
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Guangqi Song
- Biomaterials and Translational Medicine, Puheng Technology Co., Ltd, Suzhou, China
| | - Zedong Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Kaiyu Zhang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Lihe Che
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Yicheng Zhao
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China.
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China.
- China-Japan Union Hospital of Jilin University, Changchun, China.
| | - Guoqing Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Basic Medical Science, Jilin University, Changchun, China.
| | - Quan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China.
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
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48
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Sui L, Guo X, Wang W, Xu Y, Zhao Y, Liu Q. Multi-proteomics and interactome dataset of tick-borne encephalitis virus infected host cells. Sci Data 2024; 11:1280. [PMID: 39587125 PMCID: PMC11589117 DOI: 10.1038/s41597-024-04036-y] [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: 05/23/2024] [Accepted: 10/23/2024] [Indexed: 11/27/2024] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a significant viral pathogen transmitted by ticks, causing severe neurological complications in humans across Europe and Asia, highlighting the urgent need for an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Multi-omics analysis of how TBEV hijack cellular processes provides information about their replication and pathogenic mechanisms. Here, we focused on the proteome, phosphoproteome, and acetylproteome of Vero cells infected by TBEV, revealing the host perturbations triggered by TBEV infection. Additionally, we performed protein-protein interactome analysis to examine the interactions between TBEV and the host. We have provided technical validation, demonstrating the high quality and correlation of samples across all datasets, and evidence of biological consistency of virus-infected cells at the proteomic, phosphoproteomics and acetylomic levels. This comprehensive multi-omics dataset serves as a valuable resource for studying TBEV pathogenesis and identifying potential drug targets for TBEV therapy.
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Affiliation(s)
- Liyan Sui
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, 130012, China.
| | - Xuerui Guo
- China-Japan Union Hospital of Jilin University, Changchun, 130031, China
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130061, China
| | - Wenfang Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, 130012, China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Basic Medical Science, Jilin University, Changchun, 130061, China
| | - Yueshan Xu
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yicheng Zhao
- China-Japan Union Hospital of Jilin University, Changchun, 130031, China.
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, 130117, China.
| | - Quan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, 130012, China
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49
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Yu J, Ge S, Li J, Zhang Y, Xu J, Wang Y, Liu S, Yu X, Wang Z. Interaction between coronaviruses and the autophagic response. Front Cell Infect Microbiol 2024; 14:1457617. [PMID: 39650836 PMCID: PMC11621220 DOI: 10.3389/fcimb.2024.1457617] [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: 07/01/2024] [Accepted: 10/18/2024] [Indexed: 12/11/2024] Open
Abstract
In recent years, the emergence and widespread dissemination of the coronavirus SARS-CoV-2 has posed a significant threat to global public health and social development. In order to safely and effectively prevent and control the spread of coronavirus diseases, a profound understanding of virus-host interactions is paramount. Cellular autophagy, a process that safeguards cells by maintaining cellular homeostasis under diverse stress conditions. Xenophagy, specifically, can selectively degrade intracellular pathogens, such as bacteria, fungi, viruses, and parasites, thus establishing a robust defense mechanism against such intruders. Coronaviruses have the ability to induce autophagy, and they manipulate this pathway to ensure their efficient replication. While progress has been made in elucidating the intricate relationship between coronaviruses and autophagy, a comprehensive summary of how autophagy either benefits or hinders viral replication remains elusive. In this review, we delve into the mechanisms that govern how different coronaviruses regulate autophagy. We also provide an in-depth analysis of virus-host interactions, particularly focusing on the latest data pertaining to SARS-CoV-2. Our aim is to lay a theoretical foundation for the development of novel coronavirus vaccines and the screening of potential drug targets.
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Affiliation(s)
- Jiarong Yu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shengqiang Ge
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | | | - Jiao Xu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shan Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaojing Yu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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50
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Bonet-Aleta J, Maehara T, Craig BA, Bernardes GJL. Small Molecule RNA Degraders. Angew Chem Int Ed Engl 2024; 63:e202412925. [PMID: 39162084 DOI: 10.1002/anie.202412925] [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: 07/09/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/21/2024]
Abstract
RNA is a central molecule in life, involved in a plethora of biological processes and playing a key role in many diseases. Targeting RNA emerges as a significant endeavor in drug discovery, diverging from conventional protein-centric approaches to tackle various pathologies. Whilst identifying small molecules that bind to specific RNA regions is the first step, the abundance of non-functional RNA segments renders many interactions biologically inert. Consequently, small molecule binding does not necessarily meet stringent criteria for clinical translation, calling for solutions to push the field forward. Converting RNA-binders into RNA-degraders presents a promising avenue to enhance RNA-targeting. This mini-review outlines strategies and exemplars wherein simple small molecule RNA binders are reprogrammed into active degraders through the linkage of functional groups. These approaches encompass mechanisms that induce degradation via endogenous enzymes, termed RIBOTACs, as well as those with functional moieties acting autonomously to degrade RNA. Through this exploration, we aim to offer insights into advancing RNA-targeted therapeutic strategies.
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Affiliation(s)
- Javier Bonet-Aleta
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, United Kingdom
| | - Tomoaki Maehara
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, United Kingdom
| | - Benjamin A Craig
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, United Kingdom
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, United Kingdom
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