1
|
Yin L, Yuan L, Li J, Jiang B. The liquid-liquid phase separation in programmed cell death. Cell Signal 2024; 120:111215. [PMID: 38740235 DOI: 10.1016/j.cellsig.2024.111215] [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: 03/25/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
In recent years, the physical phenomenon of liquid-liquid phase separation has been widely introduced into biological research. Membrane-free organelles have been found to exist in cells that were driven by liquid-liquid phase separation. Intermolecular multivalent interactions can drive liquid-liquid phase separation to form condensates that are independent of other substances in the environment and thus can play an effective role in regulating multiple biological processes in the cell. The way of cell death has also long been a focus in multiple research. In the face of various stresses, cell death-related mechanisms are crucial for maintaining cellular homeostasis and regulating cell fate. With the in-depth study of cell death pathways, it has been found that the process of cell death was also accompanied by the regulation of liquid-liquid phase separation and played a key role. Therefore, this review summarized the roles of liquid-liquid phase separation in various cell death pathways, and explored the regulation of cell fate by liquid-liquid phase separation, with the expectation that the exploration of the mechanism of liquid-liquid phase separation would provide new insights into the treatment of diseases caused by regulated cell death.
Collapse
Affiliation(s)
- Leijing Yin
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
| | - Ludong Yuan
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Jing Li
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
| |
Collapse
|
2
|
Wei X, Zhou Y, Shen X, Fan L, Liu D, Gao X, Zhou J, Wu Y, Li Y, Feng W, Zhang Z. Ciclopirox inhibits SARS-CoV-2 replication by promoting the degradation of the nucleocapsid protein. Acta Pharm Sin B 2024; 14:2505-2519. [PMID: 38828154 PMCID: PMC11143514 DOI: 10.1016/j.apsb.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/04/2024] [Accepted: 02/28/2024] [Indexed: 06/05/2024] Open
Abstract
The nucleocapsid protein (NP) plays a crucial role in SARS-CoV-2 replication and is the most abundant structural protein with a long half-life. Despite its vital role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assembly and host inflammatory response, it remains an unexplored target for drug development. In this study, we identified a small-molecule compound (ciclopirox) that promotes NP degradation using an FDA-approved library and a drug-screening cell model. Ciclopirox significantly inhibited SARS-CoV-2 replication both in vitro and in vivo by inducing NP degradation. Ciclopirox induced abnormal NP aggregation through indirect interaction, leading to the formation of condensates with higher viscosity and lower mobility. These condensates were subsequently degraded via the autophagy-lysosomal pathway, ultimately resulting in a shortened NP half-life and reduced NP expression. Our results suggest that NP is a potential drug target, and that ciclopirox holds substantial promise for further development to combat SARS-CoV-2 replication.
Collapse
Affiliation(s)
- Xiafei Wei
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Xiaotong Shen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Lujie Fan
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511495, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Xiang Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Jian Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yezi Wu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yunfei Li
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Wei Feng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| |
Collapse
|
3
|
Masood M, Singh P, Hariss D, Khan F, Yameen D, Siraj S, Islam A, Dohare R, Mahfuzul Haque M. Nitric oxide as a double-edged sword in pulmonary viral infections: Mechanistic insights and potential therapeutic implications. Gene 2024; 899:148148. [PMID: 38191100 DOI: 10.1016/j.gene.2024.148148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
In the face of the global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), researchers are tirelessly exploring novel therapeutic approaches to combat coronavirus disease 2019 (COVID-19) and its associated complications. Nitric oxide (NO) has appeared as a multifaceted signaling mediator with diverse and often contrasting biological activities. Its intricate biochemistry renders it a crucial regulator of cardiovascular and pulmonary functions, immunity, and neurotransmission. Perturbations in NO production, whether excessive or insufficient, contribute to the pathogenesis of various diseases, encompassing cardiovascular disease, pulmonary hypertension, asthma, diabetes, and cancer. Recent investigations have unveiled the potential of NO donors to impede SARS-CoV- 2 replication, while inhaled NO demonstrates promise as a therapeutic avenue for improving oxygenation in COVID-19-related hypoxic pulmonary conditions. Interestingly, NO's association with the inflammatory response in asthma suggests a potential protective role against SARS-CoV-2 infection. Furthermore, compelling evidence indicates the benefits of inhaled NO in optimizing ventilation-perfusion ratios and mitigating the need for mechanical ventilation in COVID-19 patients. In this review, we delve into the molecular targets of NO, its utility as a diagnostic marker, the mechanisms underlying its action in COVID-19, and the potential of inhaled NO as a therapeutic intervention against viral infections. The topmost significant pathway, gene ontology (GO)-biological process (BP), GO-molecular function (MF) and GO-cellular compartment (CC) terms associated with Nitric Oxide Synthase (NOS)1, NOS2, NOS3 were arginine biosynthesis (p-value = 1.15 x 10-9) regulation of guanylate cyclase activity (p-value = 7.5 x 10-12), arginine binding (p-value = 2.62 x 10-11), vesicle membrane (p-value = 3.93 x 10-8). Transcriptomics analysis further validates the significant presence of NOS1, NOS2, NOS3 in independent COVID-19 and pulmonary hypertension cohorts with respect to controls. This review investigates NO's molecular targets, diagnostic potentials, and therapeutic role in COVID-19, employing bioinformatics to identify key pathways and NOS isoforms' significance.
Collapse
Affiliation(s)
- Mohammad Masood
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Daaniyaal Hariss
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Faizya Khan
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Daraksha Yameen
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Seerat Siraj
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Mohammad Mahfuzul Haque
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| |
Collapse
|
4
|
Zhou J, Zhou Y, Wei XF, Fan L, Gao X, Li Y, Wu Y, Feng W, Shen X, Liu L, Xu G, Zhang Z. TRIM6 facilitates SARS-CoV-2 proliferation by catalyzing the K29-typed ubiquitination of NP to enhance the ability to bind viral genomes. J Med Virol 2024; 96:e29531. [PMID: 38515377 DOI: 10.1002/jmv.29531] [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: 11/20/2023] [Revised: 01/28/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
The Nucleocapsid Protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not only the core structural protein required for viral packaging, but also participates in the regulation of viral replication, and its post-translational modifications such as phosphorylation have been shown to be an important strategy for regulating virus proliferation. Our previous work identified NP could be ubiquitinated, as confirmed by two independent studies. But the function of NP ubiquitination is currently unknown. In this study, we first pinpointed TRIM6 as the E3 ubiquitin ligase responsible for NP ubiquitination, binding to NP's CTD via its RING and B-box-CCD domains. TRIM6 promotes the K29-typed polyubiquitination of NP at K102, K347, and K361 residues, increasing its binding to viral genomic RNA. Consistently, functional experiments such as the use of the reverse genetic tool trVLP model and gene knockout of TRIM6 further confirmed that blocking the ubiquitination of NP by TRIM6 significantly inhibited the proliferation of SARS-CoV-2. Notably, the NP of coronavirus is relatively conserved, and the NP of SARS-CoV can also be ubiquitinated by TRIM6, indicating that NP could be a broad-spectrum anti-coronavirus target. These findings shed light on the intricate interaction between SARS-CoV-2 and the host, potentially opening new opportunities for COVID-19 therapeutic development.
Collapse
Affiliation(s)
- Jian Zhou
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yuzheng Zhou
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xia-Fei Wei
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Lujie Fan
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Xiang Gao
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yunfei Li
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yezi Wu
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Wei Feng
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - XiaoTong Shen
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Lei Liu
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Gang Xu
- Department of Microbiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zheng Zhang
- The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| |
Collapse
|
5
|
Edalat F, Khakpour N, Heli H, Letafati A, Ramezani A, Hosseini SY, Moattari A. Immunological mechanisms of the nucleocapsid protein in COVID-19. Sci Rep 2024; 14:3711. [PMID: 38355695 PMCID: PMC10867304 DOI: 10.1038/s41598-024-53906-3] [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: 09/24/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
Collapse
Affiliation(s)
- Fahime Edalat
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Heli
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
6
|
Rosas-Murrieta NH, Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Santos-López G, Rivera-Benítez JF. Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses. Viruses 2024; 16:238. [PMID: 38400014 PMCID: PMC10892376 DOI: 10.3390/v16020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.
Collapse
Affiliation(s)
- Nora H. Rosas-Murrieta
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Alan Rodríguez-Enríquez
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Irma Herrera-Camacho
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Lourdes Millán-Pérez-Peña
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Gerardo Santos-López
- Centro de Investigación Biomédica de Oriente, Laboratorio de Biología Molecular y Virología, Instituto Mexicano del Seguro Social (IMSS), Metepec 74360, Mexico;
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad de México 38110, Mexico;
| |
Collapse
|
7
|
Zhou K, Chen D. Conventional Understanding of SARS-CoV-2 M pro and Common Strategies for Developing Its Inhibitors. Chembiochem 2023; 24:e202300301. [PMID: 37577869 DOI: 10.1002/cbic.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic has brought a widespread influence on the world, especially in the face of sudden coronavirus infections, and there is still an urgent need for specific small molecule therapies to cope with possible future pandemics. The pathogen responsible for this pandemic is Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and understanding its structure and lifecycle is beneficial for designing specific drugs of treatment for COVID-19. The main protease (Mpro ) which has conservative and specific advantages is essential for viral replication and transcription. It is regarded as one of the most potential targets for anti-SARS-CoV-2 drug development. This review introduces the popular knowledge of SARS-CoV-2 Mpro in drug development and lists a series of design principles and relevant activities of advanced Mpro inhibitors, hoping to provide some new directions and ideas for researchers.
Collapse
Affiliation(s)
- Kun Zhou
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
| | - Daquan Chen
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
| |
Collapse
|
8
|
Zhang Y, Li X, Zhang S, Chen W, Lu J, Xie Y, Wu S, Zhuang F, Bi X, Chu M, Wang F, Huang Y, Ding F, Hu C, Pan Y. Clinical Features and Predictive Nomogram of Acute Kidney Injury in Aging Population Infected with SARS-CoV-2 Omicron Variant. J Inflamm Res 2023; 16:2967-2978. [PMID: 37484995 PMCID: PMC10362882 DOI: 10.2147/jir.s413318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Background Since little is known about the acute kidney injury (AKI) in aging population infected with SARS-CoV-2 Omicron variant, we investigated the incidence, clinical features, risk factors and mid-term outcomes of AKI in hospitalized geriatric patients with and without COVID-19 and established a prediction model for mortality. Methods A real-time data from the Shanghai Ninth People's Hospital information system of inpatients with COVID-19 from 1 April 2022 to 30 June 2022 were extracted. Clinical spectrum, laboratory results, and clinical prognosis were included for the risk analyses. Moreover, Cox and Lasso regression analyses were applied to predict the 90-day death and a nomogram was established. Results A total of 1607 SARS-CoV-2 infected patients were enrolled; hypertension was the most common comorbidity, followed by chronic cardiovascular disease, diabetes mellitus, and lung disease. Most of the participants were non-vaccinated and the mean age of patients was 82.6 years old (range, 60-103 years). The AKI incidence was higher in relatively older patients (16.29% vs 3.63% in patients older than 80 years and 60 to 80 years, respectively). Linear regression models identified some variables associated with the incidence of AKI, such as older age, clinical spectrum, D-dimer level, number of comorbidities, baseline eGFR, and antibiotic or corticosteroid treatment. In this cohort, 11 patients died in-hospital and 21 patients died at 90-day follow-up. The predictive nomogram of 90-day death achieved a good C-index of 0.823 by using 5 predictor variables: ICU admission, D-dimer, peak of serum creatinine, rate of serum creatinine decline and white blood cell count (WBC). Conclusion Older age, clinical spectrum, D-dimer level, number of comorbidities, baseline eGFR, and antibiotic or corticosteroid treatment are clinical risk factors for the incidence of AKI in geriatric COVID-19 patients. The prediction nomogram achieved an excellent performance at the prediction of 90-day mortality.
Collapse
Affiliation(s)
- Yumei Zhang
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Xin Li
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Suning Zhang
- Division of Emergency, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Wei Chen
- Division of Neurology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Jianxin Lu
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yingxin Xie
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Shengbin Wu
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Feng Zhuang
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Xiao Bi
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Mingzi Chu
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Feng Wang
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yemin Huang
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Feng Ding
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Chun Hu
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yu Pan
- Division of Nephrology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| |
Collapse
|
9
|
Zhang X, Li H, Ma Y, Zhong D, Hou S. Study liquid-liquid phase separation with optical microscopy: A methodology review. APL Bioeng 2023; 7:021502. [PMID: 37180732 PMCID: PMC10171890 DOI: 10.1063/5.0137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Intracellular liquid-liquid phase separation (LLPS) is a critical process involving the dynamic association of biomolecules and the formation of non-membrane compartments, playing a vital role in regulating biomolecular interactions and organelle functions. A comprehensive understanding of cellular LLPS mechanisms at the molecular level is crucial, as many diseases are linked to LLPS, and insights gained can inform drug/gene delivery processes and aid in the diagnosis and treatment of associated diseases. Over the past few decades, numerous techniques have been employed to investigate the LLPS process. In this review, we concentrate on optical imaging methods applied to LLPS studies. We begin by introducing LLPS and its molecular mechanism, followed by a review of the optical imaging methods and fluorescent probes employed in LLPS research. Furthermore, we discuss potential future imaging tools applicable to the LLPS studies. This review aims to provide a reference for selecting appropriate optical imaging methods for LLPS investigations.
Collapse
Affiliation(s)
| | | | - Yue Ma
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | | | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
10
|
Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
Collapse
Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
11
|
Yang S, Shen W, Hu J, Cai S, Zhang C, Jin S, Guan X, Wu J, Wu Y, Cui J. Molecular mechanisms and cellular functions of liquid-liquid phase separation during antiviral immune responses. Front Immunol 2023; 14:1162211. [PMID: 37251408 PMCID: PMC10210139 DOI: 10.3389/fimmu.2023.1162211] [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: 02/09/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Spatiotemporal separation of cellular components is vital to ensure biochemical processes. Membrane-bound organelles such as mitochondria and nuclei play a major role in isolating intracellular components, while membraneless organelles (MLOs) are accumulatively uncovered via liquid-liquid phase separation (LLPS) to mediate cellular spatiotemporal organization. MLOs orchestrate various key cellular processes, including protein localization, supramolecular assembly, gene expression, and signal transduction. During viral infection, LLPS not only participates in viral replication but also contributes to host antiviral immune responses. Therefore, a more comprehensive understanding of the roles of LLPS in virus infection may open up new avenues for treating viral infectious diseases. In this review, we focus on the antiviral defense mechanisms of LLPS in innate immunity and discuss the involvement of LLPS during viral replication and immune evasion escape, as well as the strategy of targeting LLPS to treat viral infectious diseases.
Collapse
Affiliation(s)
- Shuai Yang
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Weishan Shen
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiajia Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Sihui Cai
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqiu Zhang
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shouheng Jin
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yaoxing Wu
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Cui
- The First Affiliated Hospital of Sun Yat-sen University, Ministry of Education MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
12
|
Cai S, Zhang C, Zhuang Z, Zhang S, Ma L, Yang S, Zhou T, Wang Z, Xie W, Jin S, Zhao J, Guan X, Wu J, Cui J, Wu Y. Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex. Signal Transduct Target Ther 2023; 8:170. [PMID: 37100798 PMCID: PMC10131525 DOI: 10.1038/s41392-023-01420-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/06/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023] Open
Abstract
Currently, the incidence and fatality rate of SARS-CoV-2 remain continually high worldwide. COVID-19 patients infected with SARS-CoV-2 exhibited decreased type I interferon (IFN-I) signal, along with limited activation of antiviral immune responses as well as enhanced viral infectivity. Dramatic progresses have been made in revealing the multiple strategies employed by SARS-CoV-2 in impairing canonical RNA sensing pathways. However, it remains to be determined about the SARS-CoV-2 antagonism of cGAS-mediated activation of IFN responses during infection. In the current study, we figure out that SARS-CoV-2 infection leads to the accumulation of released mitochondria DNA (mtDNA), which in turn triggers cGAS to activate IFN-I signaling. As countermeasures, SARS-CoV-2 nucleocapsid (N) protein restricts the DNA recognition capacity of cGAS to impair cGAS-induced IFN-I signaling. Mechanically, N protein disrupts the assembly of cGAS with its co-factor G3BP1 by undergoing DNA-induced liquid-liquid phase separation (LLPS), subsequently impairs the double-strand DNA (dsDNA) detection ability of cGAS. Taken together, our findings unravel a novel antagonistic strategy by which SARS-CoV-2 reduces DNA-triggered IFN-I pathway through interfering with cGAS-DNA phase separation.
Collapse
Affiliation(s)
- Sihui Cai
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, The First Affiliated Hospital of Sun Yat-sen University, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chenqiu Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, The First Affiliated Hospital of Sun Yat-sen University, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ling Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuai Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tao Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zheyu Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weihong Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shouheng Jin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Jun Cui
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, The First Affiliated Hospital of Sun Yat-sen University, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Yaoxing Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, The First Affiliated Hospital of Sun Yat-sen University, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| |
Collapse
|
13
|
Yang G, Zhang S, Song W, Bai X, Li L, Luo F, Cheng Y, Wang D, Wang Y, Chen J, Zhao J, Zhao Y. Efficient Targeted Delivery of Bifunctional Circular Aptamer-ASO Chimera to Suppress the SARS-CoV-2 Proliferation and Inflammation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207066. [PMID: 36683236 DOI: 10.1002/smll.202207066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and excessive inflammation is the current task in the prevention and treatment of corona vireus disease 2019 (COVID-19). Here, a dual-function circular aptamer-ASO chimera (circSApt-NASO) is designed to suppress SARS-CoV-2 replication and inflammation. The chemically unmodified circSApt-NASO exhibits high serum stability by artificial cyclization. It is also demonstrated that the SApt binding to spike protein enables the chimera to be efficiently delivered into the host cells expressing ACE2 along with the infection of SARS-CoV-2. Among them, the SApt potently inhibits spike-induced inflammation. The NASO targeting to silence N genes not only display robust anti-N-induced inflammatory activity, but also achieve efficient inhibition of SARS-CoV-2 replication. Overall, benefiting from the high stability of the cyclization, antispike aptamer-dependent, and viral infection-mediate targeted delivery, the circSApt-NASO displays robust potential against authentic SARS-CoV-2 and Omicron, providing a promising specific anti-inflammatory and antiproliferative reagent for therapeutic COVID-19.
Collapse
Affiliation(s)
- Gang Yang
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | | | - Xia Bai
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Ling Li
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Fatao Luo
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Yiran Cheng
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Diyue Wang
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jiantao Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yongyun Zhao
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| |
Collapse
|
14
|
Lodola C, Secchi M, Sinigiani V, De Palma A, Rossi R, Perico D, Mauri PL, Maga G. Interaction of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicases DDX1 and DDX3X Modulates Their Activities on Double-Stranded RNA. Int J Mol Sci 2023; 24:ijms24065784. [PMID: 36982856 PMCID: PMC10058294 DOI: 10.3390/ijms24065784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The nucleocapsid protein Np of SARS-CoV-2 is involved in the replication, transcription, and packaging of the viral genome, but it also plays a role in the modulation of the host cell innate immunity and inflammation response. Ectopic expression of Np alone was able to induce significant changes in the proteome of human cells. The cellular RNA helicase DDX1 was among the proteins whose levels were increased by Np expression. DDX1 and its related helicase DDX3X were found to physically interact with Np and to increase 2- to 4-fold its affinity for double-stranded RNA in a helicase-independent manner. Conversely, Np inhibited the RNA helicase activity of both proteins. These functional interactions among Np and DDX1 and DDX3X highlight novel possible roles played by these host RNA helicases in the viral life cycle.
Collapse
Affiliation(s)
- Camilla Lodola
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Massimiliano Secchi
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Virginia Sinigiani
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Antonella De Palma
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Rossana Rossi
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Davide Perico
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Pier Luigi Mauri
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| |
Collapse
|
15
|
Treatment with quercetin inhibits SARS-CoV-2 N protein-induced acute kidney injury by blocking Smad3-dependent G1 cell-cycle arrest. Mol Ther 2023; 31:344-361. [PMID: 36514292 PMCID: PMC9743779 DOI: 10.1016/j.ymthe.2022.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence shows that SARS-CoV-2 can infect kidneys and cause acute kidney injury (AKI) in critically ill COVID-19 patients. However, mechanisms through which COVID-19 induces AKI are largely unknown, and treatment remains ineffective. Here, we report that kidney-specific overexpressing SARS-CoV-2 N gene can cause AKI, including tubular necrosis and elevated levels of serum creatinine and BUN in 8-week-old diabetic db/db mice, which become worse in those with older age (16 weeks) and underlying diabetic kidney disease (DKD). Treatment with quercetin, a purified product from traditional Chinese medicine (TCM) that shows effective treatment of COVID-19 patients, can significantly inhibit SARS-CoV-2 N protein-induced AKI in diabetic mice with or without underlying DKD. Mechanistically, quercetin can block the binding of SARS-CoV-2 N protein to Smad3, thereby inhibiting Smad3 signaling and Smad3-mediated cell death via the p16-dependent G1 cell-cycle arrest mechanism in vivo and in vitro. In conclusion, SARS-CoV-2 N protein is pathogenic and can cause severe AKI in diabetic mice, particularly in those with older age and pre-existing DKD, via the Smad3-dependent G1 cell-cycle arrest mechanism. Importantly, we identify that quercetin may be an effective TCM compound capable of inhibiting COVID-19 AKI by blocking SARS-CoV-2 N-Smad3-mediated cell death pathway.
Collapse
|
16
|
Dang M, Li T, Song J. ATP and nucleic acids competitively modulate LLPS of the SARS-CoV2 nucleocapsid protein. Commun Biol 2023; 6:80. [PMID: 36681763 PMCID: PMC9862227 DOI: 10.1038/s42003-023-04480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
SARS-CoV-2 nucleocapsid (N) protein with very low mutation rates is the only structural protein which not only functions to package viral genomic RNA, but also manipulates host-cell machineries, thus representing a key target for drug development. Recent discovery of its liquid-liquid phase separation (LLPS) opens up a new direction for developing anti-SARS-CoV-2 strategies/drugs. However, so far the high-resolution mechanism of its LLPS still remains unknown. Here by DIC and NMR characterization, we have demonstrated: 1) nucleic acids modulate LLPS by dynamic and multivalent interactions over both folded NTD/CTD and Arg/Lys residues within IDRs; 2) ATP with concentrations > mM in all living cells but absent in viruses not only binds NTD/CTD, but also Arg residues within IDRs with a Kd of 2.8 mM; and 3) ATP dissolves nucleic-acid-induced LLPS by competitively displacing nucleic acid from binding the protein. Our study deciphers that the essential binding of N protein with nucleic acid and its LLPS are targetable by small molecules including ATP, which is emerging as a cellular factor controlling the host-SARS-CoV-2 interaction. Fundamentally, our results imply that the mechanisms of LLPS of IDR-containing proteins mediated by ATP and nucleic acids appear to be highly conserved from human to virus.
Collapse
Affiliation(s)
- Mei Dang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore
| | - Tongyang Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore.
| |
Collapse
|
17
|
Chen Y, Sun T, Liu K, Yuan P, Liu C. Exploration of the common genetic landscape of COVID-19 and male infertility. Front Immunol 2023; 14:1123913. [PMID: 37020555 PMCID: PMC10067640 DOI: 10.3389/fimmu.2023.1123913] [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: 12/14/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Background COVID-19 has spread widely across continents since 2019, causing serious damage to human health. Accumulative research uncovered that SARS-CoV-2 poses a great threat to male fertility, and male infertility (MI) is a common comorbidity for the COVID-19 pandemic. The aim of the study was to explore the cross-talk molecular mechanisms between COVID-19 and MI. Materials and methods A total of four transcriptome data regarding COVID-19 and MI were downloaded from the Gene Expression Omnibus (GEO) repository, and were divided for two purposes (initial analysis and external validation). Differentially expressed genes (DEGs) analysis, GO and pathway annotation, protein-protein interaction (PPI) network, connectivity ranking, ROC analysis, immune infiltration, and translational and post-translational interaction were performed to gain hub COVID-19-related DEGs (CORGs). Moreover, we recorded medical information of COVID-19 patients with MI and matched healthy controls, and harvested their sperm samples in the university hospital. Expressions of hub CORGs were detected through the qRT-PCR technique. Results We identified 460 overlapped CORGs in both the COVID-19 DEGs and MI DEGs. CORGs were significantly enriched in DNA damage and repair-associated, cell cycle-associated, ubiquitination-associated, and coronavirus-associated signaling. Module assessment of PPI network revealed that enriched GO functions were closely related to cell cycle and DNA metabolism processes. Pharmacologic agent prediction displayed protein-drug interactions of ascorbic acid, biotin, caffeine, and L-cysteine with CORGs. After connectivity ranking and external validation, three hub CORGs (ENTPD6, CIB1, and EIF3B) showed good diagnostic performance (area under the curve > 0.75). Subsequently, three types of immune cells (CD8+ T cells, monocytes, and macrophages M0) were dominantly enriched, and 24 transcription factor-CORGs interactions and 13 miRNA-CORGs interactions were constructed in the network. Finally, qRT-PCR analysis confirmed that there were significant differences in the expression of hub CORGs (CIB1 and EIF3B) between the patient and control groups. Conclusion The present study identified and validated hub CORGs in COVID-19 and MI, and systematically explored molecular interactions and regulatory features in various biological processes. Our data provide new insights into the novel biomarkers and potential therapeutic targets of COVID-19-associated MI.
Collapse
Affiliation(s)
- Yinwei Chen
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Taotao Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Penghui Yuan
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Penghui Yuan, ; Chang Liu,
| | - Chang Liu
- Reproductive Medicine Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- *Correspondence: Penghui Yuan, ; Chang Liu,
| |
Collapse
|
18
|
Guan Y, Wang Y, Fu X, Bai G, Li X, Mao J, Yan Y, Hu L. Multiple functions of stress granules in viral infection at a glance. Front Microbiol 2023; 14:1138864. [PMID: 36937261 PMCID: PMC10014870 DOI: 10.3389/fmicb.2023.1138864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Stress granules (SGs) are distinct RNA granules induced by various stresses, which are evolutionarily conserved across species. In general, SGs act as a conservative and essential self-protection mechanism during stress responses. Viruses have a long evolutionary history and viral infections can trigger a series of cellular stress responses, which may interact with SG formation. Targeting SGs is believed as one of the critical and conservative measures for viruses to tackle the inhibition of host cells. In this systematic review, we have summarized the role of SGs in viral infection and categorized their relationships into three tables, with a particular focus on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Moreover, we have outlined several kinds of drugs targeting SGs according to different pathways, most of which are potentially effective against SARS-CoV-2. We believe this review would offer a new view for the researchers and clinicians to attempt to develop more efficacious treatments for virus infection, particularly for the treatment of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Yuelin Guan
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yan Wang
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xudong Fu
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Guannan Bai
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xue Li
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhua Mao
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yongbin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
- *Correspondence: Yongbin Yan,
| | - Lidan Hu
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Lidan Hu,
| |
Collapse
|
19
|
Ma H, Liu M, Fu R, Feng J, Ren H, Cao J, Shi M. Phase separation in innate immune response and inflammation-related diseases. Front Immunol 2023; 14:1086192. [PMID: 36860877 PMCID: PMC9970293 DOI: 10.3389/fimmu.2023.1086192] [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: 11/02/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Inflammation induced by nonspecific pathogenic or endogenous danger signals is an essential mechanism of innate immune response. The innate immune responses are rapidly triggered by conserved germline-encoded receptors that recognize broad patterns indicative of danger, with subsequent signal amplification by modular effectors, which have been the subject of intense investigation for many years. Until recently, however, the critical role of intrinsic disorder-driven phase separation in facilitating innate immune responses went largely unappreciated. In this review, we discuss emerging evidences that many innate immune receptors, effectors, and/or interactors function as "all-or-nothing" switch-like hubs to stimulate acute and chronic inflammation. By concentrating or relegating modular signaling components to phase-separated compartments, cells construct flexible and spatiotemporal distributions of key signaling events to ensure rapid and effective immune responses to a myriad of potentially harmful stimuli.
Collapse
Affiliation(s)
- Huihui Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Mingxi Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Rao Fu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jia Feng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Haoran Ren
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jingyan Cao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| |
Collapse
|
20
|
Meng ZH, Ma WY, Wang Y, Li YR, Zhang J, Liu YF, Zhao XK, Da CH. An Exploration of the Safety of “Pneumonia Prevention No. 1” in Healthy Populations. Infect Drug Resist 2022; 15:6695-6701. [DOI: 10.2147/idr.s377974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
|