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Biondi MJ, Addo M, Zahoor MA, Salvant E, Yip P, Barber B, Smookler D, Wasif S, Gaete K, Kandel C, Feld JJ, Tsui H, Kozak RA. Differential Gene Expression in the Upper Respiratory Tract following Acute COVID-19 Infection in Ambulatory Patients That Develop Long COVID. Pathogens 2024; 13:510. [PMID: 38921807 PMCID: PMC11206334 DOI: 10.3390/pathogens13060510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Background: Post-acute sequelae of COVID-19, or long COVID, is a condition characterized by persistent COVID-19 symptoms. As long COVID is defined by clinical criteria after an elapsed period, an opportunity for early intervention may aid in future prophylactic approaches; however, at present, the pathobiological mechanisms are multifactorial. By analyzing early virally infected upper respiratory tract tissue prior to eventual clinical diagnosis, it may be possible to identify biomarkers of altered immune response to facilitate future studies and interventions. Methods: This is a sub-group analysis of samples collected from those with confirmed COVID-19. RNA extraction from nasopharyngeal/mid-turbinate samples, sequencing, and bioinformatic analysis were performed to analyze long COVID and non-long COVID cohorts at day 14 post infection. Differences in mean viral load at various timepoints were analyzed as well as serological data. Results: We identified 26 upregulated genes in patients experiencing long COVID. Dysregulated pathways including complement and fibrinolysis pathways and IL-7 upregulation. Additionally, genes involved in neurotransmission were dysregulated, and the long COVID group had a significantly higher viral load and slower viral clearance. Conclusions: Uncovering early gene pathway abnormalities associated with eventual long COVID diagnosis may aid in early identification. We show that, post acute infection, in situ pathogenic deviations in viral response are associated with patients destined to meet consensus long COVID diagnosis that is entirely dependent on clinical factors. These results identify an important biological temporal window in the natural history of COVID-19 infection and long COVID pathogenesis amenable to testing from standard-of-care upper respiratory tract specimens.
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Affiliation(s)
- Mia J. Biondi
- School of Nursing, York University, Toronto, ON M3J 1P3, Canada
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada; (M.A.Z.); (B.B.); (D.S.); (J.J.F.)
| | - Mary Addo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (M.A.); (P.Y.); (H.T.)
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
| | - Muhammad Atif Zahoor
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada; (M.A.Z.); (B.B.); (D.S.); (J.J.F.)
| | - Elsa Salvant
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
| | - Paul Yip
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (M.A.); (P.Y.); (H.T.)
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
- Precision Diagnostics and Therapeutics Program, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Bethany Barber
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada; (M.A.Z.); (B.B.); (D.S.); (J.J.F.)
| | - David Smookler
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada; (M.A.Z.); (B.B.); (D.S.); (J.J.F.)
| | - Sumaiyah Wasif
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
| | - Kayla Gaete
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
| | | | - Jordan J. Feld
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada; (M.A.Z.); (B.B.); (D.S.); (J.J.F.)
| | - Hubert Tsui
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (M.A.); (P.Y.); (H.T.)
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
- Precision Diagnostics and Therapeutics Program, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert A. Kozak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (M.A.); (P.Y.); (H.T.)
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; (E.S.); (K.G.)
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Bhat AA, Gupta G, Goyal A, Thapa R, Almalki WH, Kazmi I, Alzarea SI, Kukreti N, Sekar M, Meenakshi DU, Singh SK, MacLoughlin R, Dua K. Unwinding circular RNA's role in inflammatory pulmonary diseases. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2567-2588. [PMID: 37917370 DOI: 10.1007/s00210-023-02809-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression and cellular processes in various physiological and pathological conditions. In recent years, there has been a growing interest in investigating the role of circRNAs in inflammatory lung diseases, owing to their potential to modulate inflammation-associated pathways and contribute to disease pathogenesis. Inflammatory lung diseases, like asthma, chronic obstructive pulmonary disease (COPD), and COVID-19, pose significant global health challenges. The dysregulation of inflammatory responses demonstrates a pivotal function in advancing these diseases. CircRNAs have been identified as important players in regulating inflammation by functioning as miRNA sponges, engaging with RNA-binding proteins, and participating in intricate ceRNA networks. These interactions enable circRNAs to regulate the manifestation of key inflammatory genes and signaling pathways. Furthermore, emerging evidence suggests that specific circRNAs are differentially expressed in response to inflammatory stimuli and exhibit distinct patterns in various lung diseases. Their involvement in immune cell activation, cytokine production, and tissue remodeling processes underscores their possible capabilities as therapeutic targets and diagnostic biomarkers. Harnessing the knowledge of circRNA-mediated regulation in inflammatory lung diseases could lead to the development of innovative strategies for disease management and intervention. This review summarizes the current understanding of the role of circRNAs in inflammatory lung diseases, focusing on their regulatory mechanisms and functional implications.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 602105, India.
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72388, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun, 248007, India
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | | | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ronan MacLoughlin
- Research and Development, Aerogen Limited, IDA Business Park, Galway, Connacht, H91 HE94, Ireland
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster, D02 YN77, Ireland
- School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster, D02 PN40, Ireland
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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Marzoog BA. Transcription Factors in Brain Regeneration: A Potential Novel Therapeutic Target. Curr Drug Targets 2024; 25:46-61. [PMID: 38444255 DOI: 10.2174/0113894501279977231210170231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/07/2024]
Abstract
Transcription factors play a crucial role in providing identity to each cell population. To maintain cell identity, it is essential to balance the expression of activator and inhibitor transcription factors. Cell plasticity and reprogramming offer great potential for future therapeutic applications, as they can regenerate damaged tissue. Specific niche factors can modify gene expression and differentiate or transdifferentiate the target cell to the required fate. Ongoing research is being carried out on the possibilities of transcription factors in regenerating neurons, with neural stem cells (NSCs) being considered the preferred cells for generating new neurons due to their epigenomic and transcriptome memory. NEUROD1/ASCL1, BRN2, MYTL1, and other transcription factors can induce direct reprogramming of somatic cells, such as fibroblasts, into neurons. However, the molecular biology of transcription factors in reprogramming and differentiation still needs to be fully understood.
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Affiliation(s)
- Basheer Abdullah Marzoog
- World-Class Research Center, Digital Biodesign and Personalized Healthcare», I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
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Chen ZJ, Xiao J, Chen HH. Identification of Key Genes Related to Immune Cells in Patients with COVID-19 Via Integrated Bioinformatics-Based Analysis. Biochem Genet 2023; 61:2650-2671. [PMID: 37222960 PMCID: PMC10206360 DOI: 10.1007/s10528-023-10400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
COVID-19 has spread all over the world which poses a serious threat to social economic development and public health. Despite enormous progress has been made in the prevention and treatment of COVID-19, the specific mechanism and biomarker related to disease severity or prognosis have not been clarified yet. Our study intended to further explore the diagnostic markers of COVID-19 and their relationship with serum immunology by bioinformatics analysis. The datasets about COVID-19 were downloaded from the Gene Expression Omnibus (GEO) dataset. The differentially expressed genes (DEGs) were selected via the limma package. Then, weighted gene co-expression network analysis (WGCNA) was conducted to identify the critical module associated with the clinic status. The intersection DEGs were processed for further enrichment analysis. The final diagnostic genes for COVID-19 were selected and verified through special bioinformatics algorithms. There were significant DEGs between the normal and COVID-19 patients. These genes were mainly enriched in cell cycle, complement and coagulation cascade, extracellular matrix (ECM) receptor interaction, and the P53 signaling pathway. As much as 357 common intersected DEGs were selected in the end. These DEGs were enriched in organelle fission, mitotic cell cycle phase transition, DNA helicase activity, cell cycle, cellular senescence, and P53 signaling pathway. Our study also identified CDC25A, PDCD6, and YWAHE were potential diagnostic markers of COVID-19 with the AUC (area under curve), 0.958 (95% CI 0.920-0.988), 0.941(95% CI 0.892-0.980), and 0.929 (95% CI 0.880-0.971). Moreover, CDC25A, PDCD6, and YWAHE were correlated with plasma cells, macrophages M0, T cells CD4 memory resting, T cells CD8, dendritic cells, and NK cells. Our study discovered that CDC25A, PDCD6, and YWAHE can be used as diagnostic markers for COVID-19. Moreover, these biomarkers were also closely associated with immune cell infiltration, which plays a pivotal role in the diagnosis and progression of COVID-19.
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Affiliation(s)
- Zhao-Jun Chen
- Department of Infectious Disease, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Xiao
- Department of Cardiology, Wuhan Asia Heart General Hospital, Wuhan, China
| | - Hai-Hua Chen
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Chetta M, Cammarota AL, De Marco M, Bukvic N, Marzullo L, Rosati A. The Continuous Adaptive Challenge Played by Arboviruses: An In Silico Approach to Identify a Possible Interplay between Conserved Viral RNA Sequences and Host RNA Binding Proteins (RBPs). Int J Mol Sci 2023; 24:11051. [PMID: 37446229 DOI: 10.3390/ijms241311051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Climate change and globalization have raised the risk of vector-borne disease (VBD) introduction and spread in various European nations in recent years. In Italy, viruses carried by tropical vectors have been shown to cause viral encephalitis, one of the symptoms of arboviruses, a spectrum of viral disorders spread by arthropods such as mosquitoes and ticks. Arboviruses are currently causing alarm and attention, and the World Health Organization (WHO) has released recommendations to adopt essential measures, particularly during the hot season, to restrict the spreading of the infectious agents among breeding stocks. In this scenario, rapid analysis systems are required, because they can quickly provide information on potential virus-host interactions, the evolution of the infection, and the onset of disabling clinical symptoms, or serious illnesses. Such systems include bioinformatics approaches integrated with molecular evaluation. Viruses have co-evolved different strategies to transcribe their own genetic material, by changing the host's transcriptional machinery, even in short periods of time. The introduction of genetic alterations, particularly in RNA viruses, results in a continuous adaptive fight against the host's immune system. We propose an in silico pipeline method for performing a comprehensive motif analysis (including motif discovery) on entire genome sequences to uncover viral sequences that may interact with host RNA binding proteins (RBPs) by interrogating the database of known RNA binding proteins, which play important roles in RNA metabolism and biological processes. Indeed, viral RNA sequences, able to bind host RBPs, may compete with cellular RNAs, altering important metabolic processes. Our findings suggest that the proposed in silico approach could be a useful and promising tool to investigate the complex and multiform clinical manifestations of viral encephalitis, and possibly identify altered metabolic pathways as targets of pharmacological treatments and innovative therapeutic protocols.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy
| | - Anna Lisa Cammarota
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Nenad Bukvic
- Medical Genetics Section, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Liberato Marzullo
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Alessandra Rosati
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
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6
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Chaumont H, Kaczorowski F, San-Galli A, Michel PP, Tressières B, Roze E, Quadrio I, Lannuzel A. Cerebrospinal fluid biomarkers in SARS-CoV-2 patients with acute neurological syndromes. Rev Neurol (Paris) 2023; 179:208-217. [PMID: 36610823 PMCID: PMC9708608 DOI: 10.1016/j.neurol.2022.11.002] [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: 09/19/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND AND PURPOSE Mechanisms underlying acute brain injury in SARS-CoV-2 patients remain poorly understood. A better characterization of such mechanisms remains essential to preventing long-term neurological sequelae. Our present aim was to study a panel of biomarkers of neuroinflammation and neurodegeneration in the cerebrospinal fluid (CSF) of NeuroCOVID patients. METHODS We retrospectively collected clinical and CSF biomarkers data from 24 NeuroCOVID adults seen at the University Hospital of Guadeloupe between March and June 2021. RESULTS Among 24 NeuroCOVID patients, 71% had encephalopathy and 29% meningoencephalitis. A number of these patients also experienced de novo movement disorder (33%) or stroke (21%). The CSF analysis revealed intrathecal immunoglobulin synthesis in 54% of NeuroCOVID patients (two with a type 2 pattern and 11 with a type 3) and elevated neopterin levels in 75% of them (median 9.1nM, IQR 5.6-22.1). CSF neurofilament light chain (NfL) was also increased compared to a control group of non-COVID-19 patients with psychiatric illnesses (2905ng/L, IQR 1428-7124 versus 1222ng/L, IQR 1049-1566). Total-tau was elevated in the CSF of 24% of patients, whereas protein 14-3-3, generally undetectable, reached intermediate levels in two patients. Finally, CSF Aß1-42 was reduced in 52.4% of patients (median 536ng/L, IQR 432-904) with no change in the Aß1-42/Aß1-40 ratio (0.082, IQR 0.060-0.096). CONCLUSIONS We showed an elevation of CSF biomarkers of neuroinflammation in NeuroCOVID patients and a rise of CSF NfL, evocative of neuronal damage. However, longitudinal studies are needed to determine whether NeuroCOVID could evolve into a chronic neurodegenerative condition.
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Affiliation(s)
- H Chaumont
- Service de neurologie, centre hospitalier universitaire de la Guadeloupe, Pointe-à-Pitre/Abymes, French West Indies, France; Faculté de médecine de l'université des Antilles, French West Indies, Pointe-à-Pitre, France; U 1127, CNRS, unité mixte de recherche (UMR) 7225, faculté de médecine de Sorbonne université, Institut national de la santé et de la recherche médicale, Institut du Cerveau, ICM, Paris, France.
| | - F Kaczorowski
- Laboratory of neurobiology and neurogenetics, department of biochemistry and molecular biology, Lyon university hospital, Bron, France; CNRS UMR 5292, Inserm U1028, BIORAN team, Lyon neuroscience research center, Lyon 1 university, Bron, France
| | - A San-Galli
- Service de neurologie, centre hospitalier universitaire de la Guadeloupe, Pointe-à-Pitre/Abymes, French West Indies, France
| | - P P Michel
- U 1127, CNRS, unité mixte de recherche (UMR) 7225, faculté de médecine de Sorbonne université, Institut national de la santé et de la recherche médicale, Institut du Cerveau, ICM, Paris, France
| | - B Tressières
- Inserm CIC 1424, centre d'investigation Clinique Antilles Guyane, CHU de la Guadeloupe, Pointe-à-Pitre, France
| | - E Roze
- U 1127, CNRS, unité mixte de recherche (UMR) 7225, faculté de médecine de Sorbonne université, Institut national de la santé et de la recherche médicale, Institut du Cerveau, ICM, Paris, France; Département de neurologie, hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | - I Quadrio
- Laboratory of neurobiology and neurogenetics, department of biochemistry and molecular biology, Lyon university hospital, Bron, France; CNRS UMR 5292, Inserm U1028, BIORAN team, Lyon neuroscience research center, Lyon 1 university, Bron, France
| | - A Lannuzel
- Service de neurologie, centre hospitalier universitaire de la Guadeloupe, Pointe-à-Pitre/Abymes, French West Indies, France; Faculté de médecine de l'université des Antilles, French West Indies, Pointe-à-Pitre, France; U 1127, CNRS, unité mixte de recherche (UMR) 7225, faculté de médecine de Sorbonne université, Institut national de la santé et de la recherche médicale, Institut du Cerveau, ICM, Paris, France; Inserm CIC 1424, centre d'investigation Clinique Antilles Guyane, CHU de la Guadeloupe, Pointe-à-Pitre, France
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Westcott CE, Isom CM, Karki D, Sokoloski KJ. Dancing with the Devil: A Review of the Importance of Host RNA-Binding Proteins to Alphaviral RNAs during Infection. Viruses 2023; 15:164. [PMID: 36680204 PMCID: PMC9865062 DOI: 10.3390/v15010164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/02/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Alphaviruses are arthropod-borne, single-stranded positive sense RNA viruses that rely on the engagement of host RNA-binding proteins to efficiently complete the viral lifecycle. Because of this reliance on host proteins, the identification of host/pathogen interactions and the subsequent characterization of their importance to viral infection has been an intensive area of study for several decades. Many of these host protein interaction studies have evaluated the Protein:Protein interactions of viral proteins during infection and a significant number of host proteins identified by these discovery efforts have been RNA Binding Proteins (RBPs). Considering this recognition, the field has shifted towards discovery efforts involving the direct identification of host factors that engage viral RNAs during infection using innovative discovery approaches. Collectively, these efforts have led to significant advancements in the understanding of alphaviral molecular biology; however, the precise extent and means by which many RBPs influence viral infection is unclear as their specific contributions to infection, as per any RNA:Protein interaction, have often been overlooked. The purpose of this review is to summarize the discovery of host/pathogen interactions during alphaviral infection with a specific emphasis on RBPs, to use new ontological analyses to reveal potential functional commonalities across alphaviral RBP interactants, and to identify host RBPs that have, and have yet to be, evaluated in their native context as RNA:Protein interactors.
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Affiliation(s)
- Claire E. Westcott
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Cierra M. Isom
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Deepa Karki
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Kevin J. Sokoloski
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
- Center for Predictive Medicine for Biodefense and Emerging Infectious Disease (CPM), University of Louisville, Louisville, KY 40202, USA
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Hamdy NM, Shaker FH, Zhan X, Basalious EB. Tangled quest of post-COVID-19 infection-caused neuropathology and what 3P nano-bio-medicine can solve? EPMA J 2022; 13:261-284. [PMID: 35668839 PMCID: PMC9160520 DOI: 10.1007/s13167-022-00285-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022]
Abstract
COVID-19-caused neurological problems are the important post-CoV-2 infection complications, which are recorded in ~ 40% of critically ill COVID-19 patients. Neurodegeneration (ND) is one of the most serious complications. It is necessary to understand its molecular mechanism(s), define research gaps to direct research to, hopefully, design new treatment modalities, for predictive diagnosis, patient stratification, targeted prevention, prognostic assessment, and personalized medical services for this type of complication. Individualized nano-bio-medicine combines nano-medicine (NM) with clinical and molecular biomarkers based on omics data to improve during- and post-illness management or post-infection prognosis, in addition to personalized dosage profiling and drug selection for maximum treatment efficacy, safety with least side-effects. This review will enumerate proteins, receptors, and enzymes involved in CoV-2 entrance into the central nervous system (CNS) via the blood–brain barrier (BBB), and list the repercussions after that entry, ranging from neuroinflammation to neurological symptoms disruption mechanism. Moreover, molecular mechanisms that mediate the host effect or viral detrimental effect on the host are discussed here, including autophagy, non-coding RNAs, inflammasome, and other molecular mechanisms of CoV-2 infection neuro-affection that are defined here as hallmarks of neuropathology related to COVID-19 infection. Thus, a couple of questions are raised; for example, “What are the hallmarks of neurodegeneration during COVID-19 infection?” and “Are epigenetics promising solution against post-COVID-19 neurodegeneration?” In addition, nano-formulas might be a better novel treatment for COVID-19 neurological complications, which raises one more question, “What are the challenges of nano-bio-based nanocarriers pre- or post-COVID-19 infection?” especially in the light of omics-based changes/challenges, research, and clinical practice in the framework of predictive preventive personalized medicine (PPPM / 3P medicine).
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Affiliation(s)
- Nadia M Hamdy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Ain Shams University, Abassia, 11566 Cairo Egypt
| | - Fatma H Shaker
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Ain Shams University, Abassia, 11566 Cairo Egypt
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China.,Medical Science and Technology Innovation Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117 People's Republic of China.,Gastroenterology Research Institute and Clinical Center, Shandong First Medical University, 38 Wuying Shan Road, Jinan, Shandong 250031 People's Republic of China
| | - Emad B Basalious
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Al Kasr AlAiny, Cairo, 11562 Egypt
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Mukund K, Nayak P, Ashokkumar C, Rao S, Almeda J, Betancourt-Garcia MM, Sindhi R, Subramaniam S. Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. Front Immunol 2021; 12:738073. [PMID: 34721400 PMCID: PMC8548832 DOI: 10.3389/fimmu.2021.738073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 12/18/2022] Open
Abstract
The mechanisms underlying the immune remodeling and severity response in coronavirus disease 2019 (COVID-19) are yet to be fully elucidated. Our comprehensive integrative analyses of single-cell RNA sequencing (scRNAseq) data from four published studies, in patients with mild/moderate and severe infections, indicate a robust expansion and mobilization of the innate immune response and highlight mechanisms by which low-density neutrophils and megakaryocytes play a crucial role in the cross talk between lymphoid and myeloid lineages. We also document a marked reduction of several lymphoid cell types, particularly natural killer cells, mucosal-associated invariant T (MAIT) cells, and gamma-delta T (γδT) cells, and a robust expansion and extensive heterogeneity within plasmablasts, especially in severe COVID-19 patients. We confirm the changes in cellular abundances for certain immune cell types within a new patient cohort. While the cellular heterogeneity in COVID-19 extends across cells in both lineages, we consistently observe certain subsets respond more potently to interferon type I (IFN-I) and display increased cellular abundances across the spectrum of severity, as compared with healthy subjects. However, we identify these expanded subsets to have a more muted response to IFN-I within severe disease compared to non-severe disease. Our analyses further highlight an increased aggregation potential of the myeloid subsets, particularly monocytes, in COVID-19. Finally, we provide detailed mechanistic insights into the interaction between lymphoid and myeloid lineages, which contributes to the multisystemic phenotype of COVID-19, distinguishing severe from non-severe responses.
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Affiliation(s)
- Kavitha Mukund
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Priya Nayak
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Chethan Ashokkumar
- Plexision Inc., Pittsburgh, PA, United States
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sohail Rao
- DHR Health and DHR Health Institute for Research and Development, Edinburg, TX, United States
| | - Jose Almeda
- DHR Health and DHR Health Institute for Research and Development, Edinburg, TX, United States
| | | | - Rakesh Sindhi
- Plexision Inc., Pittsburgh, PA, United States
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, Pittsburgh, PA, United States
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
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10
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Zaffina S, Lanteri P, Gilardi F, Garbarino S, Santoro A, Vinci MR, Carsetti R, Scorpecci A, Raponi M, Magnavita N, Camisa V. Recurrence, Reactivation, or Inflammatory Rebound of SARS-CoV-2 Infection With Acute Vestibular Symptoms: A Case Report and Revision of Literature. Front Hum Neurosci 2021; 15:666468. [PMID: 34456694 PMCID: PMC8385757 DOI: 10.3389/fnhum.2021.666468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023] Open
Abstract
A case of recurrent coronavirus disease 2019 (COVID-19) with neurovestibular symptoms was reported. In March 2020, a physician working in an Italian pediatric hospital had flu-like symptoms with anosmia and dysgeusia, and following a reverse transcription PCR (RT/PCR) test with a nasopharyngeal swab tested positive for SARS-CoV-2. After home quarantine, 21 days from the beginning of the symptoms, the patient tested negative in two subsequent swabs and was declared healed and readmitted to work. Serological testing showed a low level of immunoglobulin G (IgG) antibody title and absence of immunoglobulin M (IgM). However, 2 weeks later, before resuming work, the patient complained of acute vestibular syndrome, and the RT/PCR test with mucosal swab turned positive. On the basis of the literature examined and reviewed for recurrence cases and vestibular symptoms during COVID-19, to our knowledge this case is the first case of recurrence with vestibular impairment as a neurological symptom, and we defined it as probably a viral reactivation. The PCR retest positivity cannot differentiate re-infectivity, relapse, and dead-viral RNA detection. Serological antibody testing and viral genome sequencing could be always performed in recurrence cases.
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Affiliation(s)
- Salvatore Zaffina
- Health Directorate, Occupational Medicine Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Post-graduate School of Occupational Health, Section of Occupational Medicine and Labor Law, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paola Lanteri
- Department of Diagnostics and Applied Technology, Neurophysiopathology Centre, Fondazione IRCCS, Istituto Neurologico “Carlo Besta”, Milan, Italy
| | | | - Sergio Garbarino
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal/Child Sciences, University of Genoa, Genoa, Italy
| | - Annapaola Santoro
- Health Directorate, Occupational Medicine Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Rosaria Vinci
- Health Directorate, Occupational Medicine Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Post-graduate School of Occupational Health, Section of Occupational Medicine and Labor Law, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rita Carsetti
- Department of Laboratories, Unit of Diagnostic Immunology and Immunology Research Area, Unit of B-Cell Pathophysiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandro Scorpecci
- Audiology and Otosurgery Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Nicola Magnavita
- Post-graduate School of Occupational Health, Section of Occupational Medicine and Labor Law, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman, Child and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Vincenzo Camisa
- Health Directorate, Occupational Medicine Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Post-graduate School of Occupational Health, Section of Occupational Medicine and Labor Law, Università Cattolica del Sacro Cuore, Rome, Italy
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11
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Liu J, Cao S, Ding G, Wang B, Li Y, Zhao Y, Shao Q, Feng J, Liu S, Qin L, Xiao Y. The role of 14-3-3 proteins in cell signalling pathways and virus infection. J Cell Mol Med 2021; 25:4173-4182. [PMID: 33793048 PMCID: PMC8093981 DOI: 10.1111/jcmm.16490] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/06/2021] [Accepted: 03/13/2021] [Indexed: 12/14/2022] Open
Abstract
14-3-3 proteins are highly conserved in species ranging from yeast to mammals and regulate numerous signalling pathways via direct interactions with proteins carrying phosphorylated 14-3-3-binding motifs. Recent studies have shown that 14-3-3 proteins can also play a role in viral infections. This review summarizes the biological functions of 14-3-3 proteins in protein trafficking, cell-cycle control, apoptosis, autophagy and other cell signal transduction pathways, as well as the associated mechanisms. Recent findings regarding the role of 14-3-3 proteins in viral infection and innate immunity are also reviewed.
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Affiliation(s)
- Jiaqi Liu
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Shengliang Cao
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Guofei Ding
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Bin Wang
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Yingchao Li
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Yuzhong Zhao
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Qingyuan Shao
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Jian Feng
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Sidang Liu
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
| | - Liting Qin
- Shandong New Hope Liuhe Group Co., Ltd.QingdaoChina
- Qingdao Jiazhi Biotechnology Co., Ltd.QingdaoChina
| | - Yihong Xiao
- Department of Fundamental Veterinary MedicineCollege of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai'anChina
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai’anChina
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