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Zou H, Xu N, Xu H, Xing X, Chen Y, Wu S. Inflammatory cytokines may mediate the causal relationship between gut microbiota and male infertility: a bidirectional, mediating, multivariate Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1368334. [PMID: 38711980 PMCID: PMC11070575 DOI: 10.3389/fendo.2024.1368334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction Studies have shown that the gut microbiota is associated with male infertility (MI). However, their causal relationship and potential mediators need more evidence to prove. We aimed to investigate the causal relationship between the gut microbiome and MI and the potential mediating role of inflammatory cytokines from a genetic perspective through a Mendelian randomization approach. Methods This study used data from genome-wide association studies of gut microbes (Mibiogen, n = 18, 340), inflammatory cytokines (NFBC1966, FYPCRS, FINRISK 1997 and 2002, n=13, 365), and male infertility (Finngen, n=120, 706) to perform two-way Mendelian randomization (MR), mediated MR, and multivariate MR(MVMR) analyses. In this study, the inverse variance weighting method was used as the primary analysis method, and other methods were used as supplementary analysis methods. Results In the present study, two gut microbes and two inflammatory cytokines were found to have a potential causal relationship with MI. Of the two gut microorganisms causally associated with male infertility, Anaerotruncus increased the risk of male infertility (odds ratio = 1.81, 95% confidence interval = 1.18-2.77, P = 0.0062), and Bacteroides decreased the risk of male infertility (odds ratio = 0.57, 95% confidence interval = 0.33-0.96, P = 0.0363). In addition, of the two inflammatory cytokines identified, hepatocyte growth factor(HGF) reduced the risk of male infertility (odds ratio = 0.50, 95% confidence interval = 0.35-0.71, P = 0.0001), Monocyte chemotactic protein 3 (MCP-3) increased the risk of male infertility (odds ratio = 1.28, 95% confidence interval = 1.03-1.61, P = 0.0039). Mediated MR analysis showed that HGF mediated the causal effect of Bacteroides on MI (mediated percentage 38.9%). Multivariate MR analyses suggest that HGF may be one of the pathways through which Bacteroides affects MI, with other unexplored pathways. Conclusion The present study suggests a causal relationship between specific gut microbiota, inflammatory cytokines, and MI. In addition, HGF may mediate the relationship between Bacteroides and MI.
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Affiliation(s)
- Haoxi Zou
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
| | - Ningning Xu
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
| | - Huanying Xu
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
- TCM Gynecology Department, Foshan Fosun Chancheng Hospital, Chancheng District, Foshan, China
| | - Xiaoyan Xing
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yanfen Chen
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
| | - Suzhen Wu
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
- TCM Gynecology Department, Foshan Fosun Chancheng Hospital, Chancheng District, Foshan, China
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Xu YE, Ao DS, Sun X, Chen W, Luo X, Zhao C, Wang SY, Song H. A Novel Airway-Organoid Model Based on a Nano-Self-Assembling Peptide: Construction and Application in Adenovirus Infection Studies. Int J Nanomedicine 2023; 18:5225-5241. [PMID: 37727651 PMCID: PMC10505585 DOI: 10.2147/ijn.s413743] [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: 04/23/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Purpose Hydrogels containing the nano-self-assembling peptide RADA16-I (Nanogels) were utilized as scaffolds to establish airway organoids and an adenovirus-infected model. The results support in vitro adenovirus studies, including isolation and culture, pathogenesis research, and antiviral drug screening. Methods HSAEC1-KT, HuLEC-5a and HELF cells were cocultured in RADA16-I hydrogel scaffolds to construct an airway organoid model. Adenovirus was used to infect this model for adenovirus-related studies. The morphological characteristics and the proliferation and activity of airway organoids before and after adenovirus infection were evaluated. The expression of the airway organoid marker proteins CC10, KRT8, AQP5, SPC, VIM and CD31 was detected. TEM and qPCR were used to detect adenovirus proliferation in airway organoids. Results HSAEC1-KT, HuLEC-5a and HELF cells cocultured at 10:7:2 self-assembled into airway organoids and maintained long-term proliferation in a RADA16-I hydrogel 3D culture system. The organoids stably expressed the lumen-forming protein KRT8 and the terminal airway markers AQP5 and SPC. Adenoviruses maintained long-term proliferation in this model. Conclusion An airway-organoid model of adenovirus infection was constructed in vitro from three human lung-derived cell lines on RADA16-I hydrogels. The model has potential as a novel research tool for adenovirus isolation and culture, pathogenesis research, and antiviral drug screening.
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Affiliation(s)
- Yun-E Xu
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Di-Shu Ao
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Xin Sun
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Wei Chen
- Department of Hepatobiliary Surgery, Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi, 563000, People’s Republic of China
| | - Xue Luo
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Can Zhao
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Sheng-Yu Wang
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
| | - Hong Song
- Department of Microbiology, School of Basic Medical Sciences, Zunyi Medical University, Zunyi, 563000, People’s Republic of China
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McDuffie D, Barr D, Helm M, Baumert T, Agarwal A, Thomas E. Physiomimetic In Vitro Human Models for Viral Infection in the Liver. Semin Liver Dis 2023; 43:31-49. [PMID: 36402129 PMCID: PMC10005888 DOI: 10.1055/a-1981-5944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Viral hepatitis is a leading cause of liver morbidity and mortality globally. The mechanisms underlying acute infection and clearance, versus the development of chronic infection, are poorly understood. In vitro models of viral hepatitis circumvent the high costs and ethical considerations of animal models, which also translate poorly to studying the human-specific hepatitis viruses. However, significant challenges are associated with modeling long-term infection in vitro. Differentiated hepatocytes are best able to sustain chronic viral hepatitis infection, but standard two-dimensional models are limited because they fail to mimic the architecture and cellular microenvironment of the liver, and cannot maintain a differentiated hepatocyte phenotype over extended periods. Alternatively, physiomimetic models facilitate important interactions between hepatocytes and their microenvironment by incorporating liver-specific environmental factors such as three-dimensional ECM interactions and co-culture with non-parenchymal cells. These physiologically relevant interactions help maintain a functional hepatocyte phenotype that is critical for sustaining viral hepatitis infection. In this review, we provide an overview of distinct, novel, and innovative in vitro liver models and discuss their functionality and relevance in modeling viral hepatitis. These platforms may provide novel insight into mechanisms that regulate viral clearance versus progression to chronic infections that can drive subsequent liver disease.
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Affiliation(s)
- Dennis McDuffie
- Department of Biomedical Engineering, University of Miami, Coral Gables, Florida
| | - David Barr
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Madeline Helm
- Department of Biomedical Engineering, University of Miami, Coral Gables, Florida
| | - Thomas Baumert
- Inserm Research Institute for Viral and Liver Diseases, University of Strasbourg, Strasbourg, France
| | - Ashutosh Agarwal
- Department of Biomedical Engineering, University of Miami, Coral Gables, Florida
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Emmanuel Thomas
- Department of Biomedical Engineering, University of Miami, Coral Gables, Florida
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida
- Schiff Center for Liver Diseases, University of Miami Miller School of Medicine, Miami, Florida
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Address for correspondence Emmanuel Thomas, MD, PhD, FAASLD Department of Biomedical Engineering, University of MiamiCoral Gables, FL 33136-1015
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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [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: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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McDuffie D, Barr D, Agarwal A, Thomas E. Physiologically relevant microsystems to study viral infection in the human liver. Front Microbiol 2022; 13:999366. [PMID: 36246284 PMCID: PMC9555087 DOI: 10.3389/fmicb.2022.999366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Viral hepatitis is a leading cause of liver disease and mortality. Infection can occur acutely or chronically, but the mechanisms that govern the clearance of virus or lack thereof are poorly understood and merit further investigation. Though cures for viral hepatitis have been developed, they are expensive, not readily accessible in vulnerable populations and some patients may remain at an increased risk of developing hepatocellular carcinoma (HCC) even after viral clearance. To sustain infection in vitro, hepatocytes must be fully mature and remain in a differentiated state. However, primary hepatocytes rapidly dedifferentiate in conventional 2D in vitro platforms. Physiologically relevant or physiomimetic microsystems, are increasingly popular alternatives to traditional two-dimensional (2D) monocultures for in vitro studies. Physiomimetic systems reconstruct and incorporate elements of the native cellular microenvironment to improve biologic functionality in vitro. Multiple elements contribute to these models including ancillary tissue architecture, cell co-cultures, matrix proteins, chemical gradients and mechanical forces that contribute to increased viability, longevity and physiologic function for the tissue of interest. These microsystems are used in a wide variety of applications to study biological phenomena. Here, we explore the use of physiomimetic microsystems as tools for studying viral hepatitis infection in the liver and how the design of these platforms is tailored for enhanced investigation of the viral lifecycle when compared to conventional 2D cell culture models. Although liver-based physiomimetic microsystems are typically applied in the context of drug studies, the platforms developed for drug discovery purposes offer a solid foundation to support studies on viral hepatitis. Physiomimetic platforms may help prolong hepatocyte functionality in order to sustain chronic viral hepatitis infection in vitro for studying virus-host interactions for prolonged periods.
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Affiliation(s)
- Dennis McDuffie
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, United States
| | - David Barr
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ashutosh Agarwal
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, United States
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- *Correspondence: Ashutosh Agarwal,
| | - Emmanuel Thomas
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, United States
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Schiff Center for Liver Diseases, University of Miami Miller School of Medicine, Miami, FL, United States
- Emmanuel Thomas,
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Feige L, Sáenz-de-Santa-María I, Regnault B, Lavenir R, Lepelletier A, Halacu A, Rajerison R, Diop S, Nareth C, Reynes JM, Buchy P, Bourhy H, Dacheux L. Transcriptome Profile During Rabies Virus Infection: Identification of Human CXCL16 as a Potential New Viral Target. Front Cell Infect Microbiol 2021; 11:761074. [PMID: 34804996 PMCID: PMC8602097 DOI: 10.3389/fcimb.2021.761074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022] Open
Abstract
Rabies virus (RABV), the causative agent for rabies disease is still presenting a major public health concern causing approximately 60,000 deaths annually. This neurotropic virus (genus Lyssavirus, family Rhabdoviridae) induces an acute and almost always fatal form of encephalomyelitis in humans. Despite the lethal consequences associated with clinical symptoms of rabies, RABV limits neuro-inflammation without causing major histopathological lesions in humans. Nevertheless, information about the mechanisms of infection and cellular response in the central nervous system (CNS) remain scarce. Here, we investigated the expression of inflammatory genes involved in immune response to RABV (dog-adapted strain Tha) in mice, the most common animal model used to study rabies. To better elucidate the pathophysiological mechanisms during natural RABV infection, we compared the inflammatory transcriptome profile observed at the late stage of infection in the mouse brain (cortex and brain stem/cerebellum) with the ortholog gene expression in post-mortem brain biopsies of rabid patients. Our data indicate that the inflammatory response associated with rabies is more pronounced in the murine brain compared to the human brain. In contrast to murine transcription profiles, we identified CXC motif chemokine ligand 16 (CXCL16) as the only significant differentially expressed gene in post-mortem brains of rabid patients. This result was confirmed in vitro, in which Tha suppressed interferon alpha (IFN-α)-induced CXCL16 expression in human CNS cell lines but induced CXCL16 expression in IFN-α-stimulated murine astrocytes. We hypothesize that RABV-induced modulation of the CXCL16 pathway in the brain possibly affects neurotransmission, natural killer (NK) and T cell recruitment and activation. Overall, we show species-specific differences in the inflammatory response of the brain, highlighted the importance of understanding the potential limitations of extrapolating data from animal models to humans.
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Affiliation(s)
- Lena Feige
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Department of Global Health, Paris, France
| | | | | | - Rachel Lavenir
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Department of Global Health, Paris, France
| | - Anthony Lepelletier
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Department of Global Health, Paris, France
| | - Ala Halacu
- National Agency for Public Health, Chișinău, Moldova
| | | | - Sylvie Diop
- Infectious Diseases Department, National and University Hospital Center of Fann-Dakar, Dakar, Senegal
| | | | - Jean-Marc Reynes
- Virology Unit, Institut Pasteur de Madagascar, Tananarive, Madagascar
| | - Philippe Buchy
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Hervé Bourhy
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Department of Global Health, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Department of Global Health, Paris, France
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Hopkins HK, Traverse EM, Barr KL. Methodologies for Generating Brain Organoids to Model Viral Pathogenesis in the CNS. Pathogens 2021; 10:pathogens10111510. [PMID: 34832665 PMCID: PMC8625030 DOI: 10.3390/pathogens10111510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
(1) Background: The human brain is of interest in viral research because it is often the target of viruses. Neurological infections can result in consequences in the CNS, which can result in death or lifelong sequelae. Organoids modeling the CNS are notable because they are derived from stem cells that differentiate into specific brain cells such as neural progenitors, neurons, astrocytes, and glial cells. Numerous protocols have been developed for the generation of CNS organoids, and our goal was to describe the various CNS organoid models available for viral pathogenesis research to serve as a guide to determine which protocol might be appropriate based on research goal, timeframe, and budget. (2) Methods: Articles for this review were found in Pubmed, Scopus and EMBASE. The search terms used were "brain + organoid" and "CNS + organoid" (3) Results: There are two main methods for organoid generation, and the length of time for organoid generation varied from 28 days to over 2 months. The costs for generating a population of organoids ranged from USD 1000 to 5000. (4) Conclusions: There are numerous methods for generating organoids representing multiple regions of the brain, with several types of modifications for fine-tuning the model to a researcher's specifications. Organoid models of the CNS can serve as a platform for characterization and mechanistic studies that can reduce or eliminate the use of animals, especially for viruses that only cause disease in the human CNS.
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de Dios-Figueroa GT, Aguilera-Marquez JDR, Camacho-Villegas TA, Lugo-Fabres PH. 3D Cell Culture Models in COVID-19 Times: A Review of 3D Technologies to Understand and Accelerate Therapeutic Drug Discovery. Biomedicines 2021; 9:602. [PMID: 34073231 PMCID: PMC8226796 DOI: 10.3390/biomedicines9060602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
In the last decades, emerging viruses have become a worldwide concern. The fast and extensive spread of the disease caused by SARS-CoV-2 (COVID-19) has impacted the economy and human activity worldwide, highlighting the human vulnerability to infectious diseases and the need to develop and optimize technologies to tackle them. The three-dimensional (3D) cell culture models emulate major tissue characteristics such as the in vivo virus-host interactions. These systems may help to generate a quick response to confront new viruses, establish a reliable evaluation of the pathophysiology, and contribute to therapeutic drug evaluation in pandemic situations such as the one that humanity is living through today. This review describes different types of 3D cell culture models, such as spheroids, scaffolds, organoids, and organs-on-a-chip, that are used in virus research, including those used to understand the new severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Guadalupe Tonantzin de Dios-Figueroa
- Department of Medical and Pharmaceutical Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Av. Normalistas 800, Colinas de las Normal, Guadalajara, Jalisco 44270, Mexico; (G.T.d.D.-F.); (J.d.R.A.-M.)
| | - Janette del Rocío Aguilera-Marquez
- Department of Medical and Pharmaceutical Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Av. Normalistas 800, Colinas de las Normal, Guadalajara, Jalisco 44270, Mexico; (G.T.d.D.-F.); (J.d.R.A.-M.)
| | - Tanya A. Camacho-Villegas
- CONACYT-Department of Medical and Pharmaceutical Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Av. Normalistas 800, Colinas de las Normal, Guadalajara, Jalisco 44270, Mexico;
| | - Pavel H. Lugo-Fabres
- CONACYT-Department of Medical and Pharmaceutical Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Av. Normalistas 800, Colinas de las Normal, Guadalajara, Jalisco 44270, Mexico;
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Targeting the DEAD-Box RNA Helicase eIF4A with Rocaglates-A Pan-Antiviral Strategy for Minimizing the Impact of Future RNA Virus Pandemics. Microorganisms 2021; 9:microorganisms9030540. [PMID: 33807988 PMCID: PMC8001013 DOI: 10.3390/microorganisms9030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022] Open
Abstract
The increase in pandemics caused by RNA viruses of zoonotic origin highlights the urgent need for broad-spectrum antivirals against novel and re-emerging RNA viruses. Broad-spectrum antivirals could be deployed as first-line interventions during an outbreak while virus-specific drugs and vaccines are developed and rolled out. Viruses depend on the host’s protein synthesis machinery for replication. Several natural compounds that target the cellular DEAD-box RNA helicase eIF4A, a key component of the eukaryotic translation initiation complex eIF4F, have emerged as potential broad-spectrum antivirals. Rocaglates, a group of flavaglines of plant origin that clamp mRNAs with highly structured 5′ untranslated regions (5′UTRs) onto the surface of eIF4A through specific stacking interactions, exhibit the largest selectivity and potential therapeutic indices among all known eIF4A inhibitors. Their unique mechanism of action limits the inhibitory effect of rocaglates to the translation of eIF4A-dependent viral mRNAs and a minor fraction of host mRNAs exhibiting stable RNA secondary structures and/or polypurine sequence stretches in their 5′UTRs, resulting in minimal potential toxic side effects. Maintaining a favorable safety profile while inducing efficient inhibition of a broad spectrum of RNA viruses makes rocaglates into primary candidates for further development as pan-antiviral therapeutics.
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Sridhar A, Simmini S, Ribeiro CMS, Tapparel C, Evers MM, Pajkrt D, Wolthers K. A Perspective on Organoids for Virology Research. Viruses 2020; 12:v12111341. [PMID: 33238561 PMCID: PMC7700289 DOI: 10.3390/v12111341] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022] Open
Abstract
Animal models and cell lines are invaluable for virology research and host-pathogen interaction studies. However, it is increasingly evident that these models are not sufficient to fully understand human viral diseases. With the advent of three-dimensional organotypic cultures, it is now possible to study viral infections in the human context. This perspective explores the potential of these organotypic cultures, also known as organoids, for virology research, antiviral testing, and shaping the virology landscape.
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Affiliation(s)
- Adithya Sridhar
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands
| | - Salvatore Simmini
- Gastrointestinal Biology Group, STEMCELL Technologies UK Ltd., Cambridge CB28 9TL, UK;
| | - Carla M. S. Ribeiro
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands;
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland;
- Division of Infectious Diseases, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Melvin M. Evers
- Department of Research and Development, uniQure Biopharma B.V., 1105 BE Amsterdam, The Netherlands;
| | - Dasja Pajkrt
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands
| | - Katja Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Correspondence:
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11
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Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, King NP, Veesler D, Bloom JD. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell 2020; 182:1295-1310.e20. [PMID: 32841599 PMCID: PMC7418704 DOI: 10.1016/j.cell.2020.08.012] [Citation(s) in RCA: 1337] [Impact Index Per Article: 334.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Sarah K Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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12
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Starr TN, Greaney AJ, Hilton SK, Crawford KH, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, Veesler D, Bloom JD. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.157982. [PMID: 32587970 PMCID: PMC7310626 DOI: 10.1101/2020.06.17.157982] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
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Affiliation(s)
- Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Co-first authors
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
- Co-first authors
| | - Sarah K. Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead Contact
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13
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Discovery and development of safe-in-man broad-spectrum antiviral agents. Int J Infect Dis 2020; 93:268-276. [PMID: 32081774 PMCID: PMC7128205 DOI: 10.1016/j.ijid.2020.02.018] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
We reviewed the discovery and development process of broad-spectrum antiviral agents. We summarized the information on 120 safe-in-man agents in a freely accessible database. Further studies will increase the number of broad-spectrum antivirals, expand the spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections.
Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of the general population from emerging and re-emerging viral diseases, reinforcing the arsenal of available antiviral options. Here, we review discovery and development of BSAAs and summarize the information on 120 safe-in-man agents in a freely accessible database (https://drugvirus.info/). Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand the spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.
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14
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Honko AN, Johnson JC, Marchand JS, Huzella L, Adams RD, Oberlander N, Torzewski LM, Bennett RS, Hensley LE, Jahrling PB, Olinger GG. High dose sertraline monotherapy fails to protect rhesus macaques from lethal challenge with Ebola virus Makona. Sci Rep 2017; 7:5886. [PMID: 28725019 PMCID: PMC5517626 DOI: 10.1038/s41598-017-06179-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/07/2017] [Indexed: 11/09/2022] Open
Abstract
The recent epidemic of Ebola virus disease in West Africa resulted in an unprecedented number of cases and deaths. Due to the scope of the outbreak combined with the lack of available approved treatment options, there was strong motivation to investigate any potential drug which had existing data reporting anti-Ebola activity. Drugs with demonstrated antiviral activity in the nonhuman primate models already approved for another indication or for which there was existing safety data were considered to be priorities for evaluation by the World Health Organization. Sertraline hydrochloride was reported to have anti-Ebola activity in vitro alone and in combination with other approved drugs. Although the efficacy was less than 100% in the murine model, the established safety profile of this product, the potential benefit alone and in combination, as well as the lack of other available options prioritized this compound for testing in the Ebola virus intramuscular rhesus macaque challenge model. Using a blinded dosing strategy, we demonstrated that high dose sertraline monotherapy provided no benefit for the prevention of Ebola virus disease in rhesus macaques with regards to reduction of viral load, morbidity, or survival highlighting the challenges of translating results between in vitro and in vivo models.
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Affiliation(s)
- Anna N Honko
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA.
| | - Joshua C Johnson
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Jonathan S Marchand
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Louis Huzella
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Ricky D Adams
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Nicholas Oberlander
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
- BD Technologies/Charles River Labs, Research Triangle Park, 27709, North Carolina, USA
| | - Lisa M Torzewski
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Richard S Bennett
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Lisa E Hensley
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Peter B Jahrling
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
| | - Gene G Olinger
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, 21702, Maryland, USA
- MRIGlobal-Global Health Surveillance and Diagnostics, Gaithersburg, Maryland, 20878, USA
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15
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Three-dimensional cell culture models for investigating human viruses. Virol Sin 2016; 31:363-379. [PMID: 27822716 PMCID: PMC7090760 DOI: 10.1007/s12250-016-3889-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional (3D) culture models are physiologically relevant, as they provide reproducible results, experimental flexibility and can be adapted for high-throughput experiments. Moreover, these models bridge the gap between traditional two-dimensional (2D) monolayer cultures and animal models. 3D culture systems have significantly advanced basic cell science and tissue engineering, especially in the fields of cell biology and physiology, stem cell research, regenerative medicine, cancer research, drug discovery, and gene and protein expression studies. In addition, 3D models can provide unique insight into bacteriology, virology, parasitology and host-pathogen interactions. This review summarizes and analyzes recent progress in human virological research with 3D cell culture models. We discuss viral growth, replication, proliferation, infection, virus-host interactions and antiviral drugs in 3D culture models.
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Abstract
Full evaluation of the interactions between a virus and host during infection and clearance requires a living organism. A live animal is also necessary for development of vaccines requiring evaluation of immunogenicity and an immune response that protects from challenge. Study of the natural host for the virus is ideal, but often not possible. Mice have emerged over the last 60 years as the most popular animal model for studying viral pathogenesis due to extensive genetic and immunologic characterization, wide availability of reagents, inbred and transgenic strains, and small size. However, responses in mice are not always predictive of those in the natural host. Other species commonly used include guinea pigs, ferrets, chickens, and nonhuman primates. When choosing an animal model for a study, factors to be considered include host susceptibility to the infection, animal size, cost, availability of housing and reagents, potential confounding coinfections, and ethical restrictions.
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17
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Carey AJ, Tan CK, Ipe DS, Sullivan MJ, Cripps AW, Schembri MA, Ulett GC. Urinary tract infection of mice to model human disease: Practicalities, implications and limitations. Crit Rev Microbiol 2015; 42:780-99. [PMID: 26006172 DOI: 10.3109/1040841x.2015.1028885] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Murine models of human UTI are vital experimental tools that have helped to elucidate UTI pathogenesis and advance knowledge of potential treatment and infection prevention strategies. Fundamentally, several variables are inherent in different murine models, and understanding the limitations of these variables provides an opportunity to understand how models may be best applied to research aimed at mimicking human disease. In this review, we discuss variables inherent in murine UTI model studies and how these affect model usage, data analysis and data interpretation. We examine recent studies that have elucidated UTI host-pathogen interactions from the perspective of gene expression, and review new studies of biofilm and UTI preventative approaches. We also consider potential standards for variables inherent in murine UTI models and discuss how these might expand the utility of models for mimicking human disease and uncovering new aspects of pathogenesis.
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Affiliation(s)
- Alison J Carey
- a Menzies Health Institute Queensland & School of Medical Sciences, Griffith University , Gold Coast , Australia
| | - Chee K Tan
- a Menzies Health Institute Queensland & School of Medical Sciences, Griffith University , Gold Coast , Australia
| | - Deepak S Ipe
- a Menzies Health Institute Queensland & School of Medical Sciences, Griffith University , Gold Coast , Australia
| | - Matthew J Sullivan
- a Menzies Health Institute Queensland & School of Medical Sciences, Griffith University , Gold Coast , Australia
| | - Allan W Cripps
- b Menzies Health Institute Queensland, Griffith University , Gold Coast , Australia , and
| | - Mark A Schembri
- c School of Chemistry and Molecular Biosciences, University of Queensland , Brisbane , Australia
| | - Glen C Ulett
- a Menzies Health Institute Queensland & School of Medical Sciences, Griffith University , Gold Coast , Australia
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