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Galanti M, Patiño-Galindo JA, Filip I, Morita H, Galianese A, Youssef M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Tagne E, Shittu A, Elliott O, Perea-Chamblee T, Natesan S, Rosenbloom DS, Shaman J, Rabadan R. Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people. PLoS Biol 2024; 22:e3002089. [PMID: 38236818 PMCID: PMC10796020 DOI: 10.1371/journal.pbio.3002089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024] Open
Abstract
Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.
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Affiliation(s)
- Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Juan Angel Patiño-Galindo
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ioan Filip
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Angelica Galianese
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mariam Youssef
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Nelsa Matienzo
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sadiat Ibrahim
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Eudosie Tagne
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Atinuke Shittu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Oliver Elliott
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomin Perea-Chamblee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sanjay Natesan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Daniel Scholes Rosenbloom
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
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Pal A, Tripathi SK, Rani P, Rastogi M, Das S. p53 and RNA viruses: The tug of war. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1826. [PMID: 37985142 DOI: 10.1002/wrna.1826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Host factors play essential roles in viral infection, and their interactions with viral proteins are necessary for establishing effective pathogenesis. p53 is a host factor that maintains genomic integrity by controlling cell-cycle progression and cell survival. It is a well-known tumor suppressor protein that gets activated by various stress signals, thereby regulating cellular pathways. The cellular outcomes from different stresses are tightly related to p53 dynamics, including its alterations at gene, mRNA, or protein levels. p53 also contributes to immune responses leading to the abolition of viral pathogens. In turn, the viruses have evolved strategies to subvert p53-mediated host responses to improve their life cycle and pathogenesis. Some viruses attenuate wild-type p53 (WT-p53) function for successful pathogenesis, including degradation and sequestration of p53. In contrast, some others exploit the WT-p53 function through regulation at the transcriptional/translational level to spread infection. One area in which the importance of such host factors is increasingly emerging is the positive-strand RNA viruses that cause fatal viral infections. In this review, we provide insight into all the possible mechanisms of p53 modulation exploited by the positive-strand RNA viruses to establish infection. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Regulation RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Apala Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sachin Kumar Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Priya Rani
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Meghana Rastogi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India, Kalyani, West Bengal, India
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Chen S, Xin Y, Tang K, Wu Y, Guo Y. Nardosinone and aurantio-obtusin, two medicine food homology natural compounds, are anti-influenza agents as indicated by transcriptome signature reversion. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 108:154515. [PMID: 36347176 DOI: 10.1016/j.phymed.2022.154515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Medicine food homology (MFH) refers to food that can be used as medicine, and compounds isolated from MFH materials are valuable in novel drug discovery due to their good safety. Transcriptome signature reversion (TSR) is an attractive method for discovering drugs through transcriptional reverse matching; namely, the changes in transcriptional signatures induced by compounds are matched to a certain disease. This strategy can be used to discover anti-influenza agents among MFH natural compounds. PURPOSE MFH natural compounds with anti-influenza activities were identified through analyses of the reversal in the expression of multiple informative genes followed by in vitro evaluation of the cytopathic effect (CPE) caused by influenza infection and relative quantification of the nucleoprotein (NP) gene in viral RNA (vRNA). The combined effect of active compounds was determined through network-based separation score prediction followed by quantification of the viral hemagglutinin (HA) level. METHODS The transcriptome profiles of 4 lung or airway cell lines infected with 7 influenza virus strains were analyzed by robust rank aggregation (RRA) to identify informative genes in the signature of influenza virus infection. The identified informative genes were then matched to a transcriptomic profile library of MFH natural compounds. The anti-influenza activities of MFH natural compounds with negative enrichment scores (ESs) were evaluated in vitro using a CPE assay and relative quantification of the NP gene in the vRNA in the supernatant and cytoplasm to identify anti-influenza agents. The effects of combinations of active compounds were analyzed using network-based calculations followed by confirmation through bioassays for quantifying the viral HA levels. RESULTS Among the 159 MFH natural compounds, 54 compounds had negative ESs, as determined through TSR, and the anti-influenza activities of nardosinone and aurantio-obtusin were confirmed by bioassays. The half-maximal effective concentrations (EC50) of nardosinone and aurantio-obtusin were 4.3-84.4 μM and 31.9-113.6 μM, respectively. The separation score between the informative genes with expression that was negatively regulated by nardosinone and aurantio-obtusin in the human protein-protein interaction (PPI) network was calculated to be 0.10, which indicated that the two compounds potentially exert a synergistic effect, and this effect was confirmed by the finding that the combination indexes (CIs) were calculated to equal 0.86 at inhibition level of 50% and 0.44 at inhibition level of 90%. CONCLUSION The TSR analysis and in vitro evaluation identified nardosinone and aurantio-obtusin as anti-influenza agents. Their antiviral activities were exerted by reversing the expression of multiple informative genes of the host cells. The separation analysis between the informative genes that were reversely regulated by nardosinone and aurantio-obtusin indicated that their combination may exert a synergistic effect, which was confirmed in vitro.
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Affiliation(s)
- Shubing Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yijing Xin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ke Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - You Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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Esteves P, Allard B, Celle A, Dupin I, Maurat E, Ousova O, Thumerel M, Dupuy JW, Leste-Lasserre T, Marthan R, Girodet PO, Trian T, Berger P. Asthmatic bronchial smooth muscle increases rhinovirus replication within the bronchial epithelium. Cell Rep 2022; 38:110571. [PMID: 35354045 DOI: 10.1016/j.celrep.2022.110571] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 12/13/2021] [Accepted: 03/04/2022] [Indexed: 11/27/2022] Open
Abstract
Rhinovirus (RV) infection of the bronchial epithelium is implicated in the vast majority of severe asthma exacerbations. Interestingly, the susceptibility of bronchial epithelium to RV infection is increased in persons with asthma. Bronchial smooth muscle (BSM) remodeling is an important feature of severe asthma pathophysiology, and its reduction using bronchial thermoplasty has been associated with a significant decrease in the exacerbation rate. We hypothesized that asthmatic BSM can play a role in RV infection of the bronchial epithelium. Using an original co-culture model between bronchial epithelium and BSM cells, we show that asthmatic BSM cells increase RV replication in bronchial epithelium following RV infection. These findings are related to the increased production of CCL20 by asthmatic BSM cells. Moreover, we demonstrate an original downregulation of the activity of the epithelial protein kinase RNA-activated (PKR) antiviral pathway. Finally, we identify a direct bottom-up effect of asthmatic BSM cells on bronchial epithelium susceptibility to RV infection.
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Affiliation(s)
- Pauline Esteves
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Benoit Allard
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Alexis Celle
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Isabelle Dupin
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Elise Maurat
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Olga Ousova
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Matthieu Thumerel
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France; CHU de Bordeaux, Service d'exploration fonctionnelle respiratoire, Service de pharmacologie, CIC 1401, Service de chirurgie thoracique, 33604 Pessac, France
| | - Jean-William Dupuy
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Thierry Leste-Lasserre
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France
| | - Roger Marthan
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France; CHU de Bordeaux, Service d'exploration fonctionnelle respiratoire, Service de pharmacologie, CIC 1401, Service de chirurgie thoracique, 33604 Pessac, France
| | - Pierre-Olivier Girodet
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France; CHU de Bordeaux, Service d'exploration fonctionnelle respiratoire, Service de pharmacologie, CIC 1401, Service de chirurgie thoracique, 33604 Pessac, France
| | - Thomas Trian
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France.
| | - Patrick Berger
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, Département de Pharmacologie, CIC 1401, 33000 Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux U1045, Plateforme Transcriptome Neurocentre Magendie U1215, Functionnal Genomics Center (CGFB) Proteomics Facility, CIC 1401, PTIB - Hôpital Xavier Arnozan, Avenue du Haut Lévêque, 33600 PESSAC, 33000 Bordeaux, France; CHU de Bordeaux, Service d'exploration fonctionnelle respiratoire, Service de pharmacologie, CIC 1401, Service de chirurgie thoracique, 33604 Pessac, France
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Chandrashekar DS, Athar M, Manne U, Varambally S. Comparative transcriptome analyses reveal genes associated with SARS-CoV-2 infection of human lung epithelial cells. Sci Rep 2021; 11:16212. [PMID: 34376762 PMCID: PMC8355180 DOI: 10.1038/s41598-021-95733-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
During 2020, understanding the molecular mechanism of SARS-CoV-2 infection (the cause of COVID-19) became a scientific priority due to the devastating effects of the COVID-19. Many researchers have studied the effect of this viral infection on lung epithelial transcriptomes and deposited data in public repositories. Comprehensive analysis of such data could pave the way for development of efficient vaccines and effective drugs. In the current study, we obtained high-throughput gene expression data associated with human lung epithelial cells infected with respiratory viruses such as SARS-CoV-2, SARS, H1N1, avian influenza, rhinovirus and Dhori, then performed comparative transcriptome analysis to identify SARS-CoV-2 exclusive genes. The analysis yielded seven SARS-CoV-2 specific genes including CSF2 [GM-CSF] (colony-stimulating factor 2) and calcium-binding proteins (such as S100A8 and S100A9), which are known to be involved in respiratory diseases. The analyses showed that genes involved in inflammation are commonly altered by infection of SARS-CoV-2 and influenza viruses. Furthermore, results of protein–protein interaction analyses were consistent with a functional role of CSF2 and S100A9 in COVID-19 disease. In conclusion, our analysis revealed cellular genes associated with SARS-CoV-2 infection of the human lung epithelium; these are potential therapeutic targets.
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Affiliation(s)
- Darshan S Chandrashekar
- Molecular and Cellular Pathology, Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, 4th Floor, 20B, Birmingham, AL, 35233, USA.
| | - Mohammad Athar
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Upender Manne
- Molecular and Cellular Pathology, Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, 4th Floor, 20B, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sooryanarayana Varambally
- Molecular and Cellular Pathology, Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, 4th Floor, 20B, Birmingham, AL, 35233, USA. .,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA. .,Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA.
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Impact of human rhinoviruses on gene expression in pediatric patients with severe acute respiratory infection. Virus Res 2021; 300:198408. [PMID: 33878402 DOI: 10.1016/j.virusres.2021.198408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 11/22/2022]
Abstract
Human rhinovirus (HRV) is one of the most common viruses, causing mild to severe respiratory tract infections in children and adults. Moreover, it can lead to patients' hospitalization. Nowadays, evaluation of gene expression alterations in host cells due to viral respiratory infections considered essential to understand the viral effects on cells. OBJECTIVE In this study, we aimed to find important differentially expressed genes (DEGs) related to rhinitis and asthma exacerbation stimulated with Poly (I: C) and then to validate their expression in clinical samples of children how were less than 5 years old, hospitalized with severe acute respiratory infection (SARI) due to HRV infection in comparison with healthy cases. METHODS Eight candidate genes involved in immunity, viral defense, inflammation, P53 pathway, and viral release processes were selected based on the analysis of a gene expression data set (GSE51392) and gene enrichment analysis. Then quantitative real-time PCR on cDNAs was performed for selected genes. The results were analyzed by Livak method and visualized by GraphPad prism software (8.4.3). RESULT CXCL10, CMPK2, RSAD2, SERPINA3, TNFAIP6, CXCL14, IVNS1AB, and ZMAT3 were selected based on the enrichment and topological analysis of the constructed protein-protein interaction (PPI) network. Laboratory validation by real-time PCR showed CXCL10, CMPK2, RSAD2, SERPINA3, and TNFAIP6 (belonged to immunity, inflammatory responses and viral defense) were up-regulated, whereas CXCL14 (related to immunity) and IVNS1AB, ZMAT3 (associated to Influenza and P53 pathway) were down-regulated. CONCLUSION Our results showed, that in children less than 5 years old affected by HRV and hospitalized with SARI, the inflammatory responses, antiviral defense, and type 1 interferon-signaling pathway have significantly affected by viral infection.
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7
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Guo J, Yu H, Yang J, Li Y, Zhang X, Mei K, Chi S, Yuan S, Liu H, El-Ashram S, Huang S, Wen F. Weighted gene co-expression network analysis revealed host transcriptional response to H1N1 influenza A virus infection. J Infect 2020; 82:e4-e7. [PMID: 33359050 DOI: 10.1016/j.jinf.2020.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Jinyue Guo
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jing Yang
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Yong Li
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Xuelian Zhang
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Kun Mei
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Shihong Chi
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Sheng Yuan
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Hao Liu
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Saeed El-Ashram
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China
| | - Feng Wen
- College of Life Science and Engineering, Foshan University, No33 Guangyun road, Shishan town, Nanhai District, Foshan 528231, Guangdong, China.
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Fujiogi M, Camargo CA, Raita Y, Bochkov YA, Gern JE, Mansbach JM, Piedra PA, Hasegawa K. Association of rhinovirus species with nasopharyngeal metabolome in bronchiolitis infants: A multicenter study. Allergy 2020; 75:2379-2383. [PMID: 32306415 DOI: 10.1111/all.14326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/11/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Michimasa Fujiogi
- Department of Emergency Medicine Massachusetts General Hospital Harvard Medical School Boston MA USA
| | - Carlos A. Camargo
- Department of Emergency Medicine Massachusetts General Hospital Harvard Medical School Boston MA USA
| | - Yoshihiko Raita
- Department of Emergency Medicine Massachusetts General Hospital Harvard Medical School Boston MA USA
| | - Yury A. Bochkov
- Department of Pediatrics University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - James E. Gern
- Department of Pediatrics University of Wisconsin School of Medicine and Public Health Madison WI USA
- Department of Medicine University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Jonathan M. Mansbach
- Department of Pediatrics Boston Children's Hospital Harvard Medical School Boston MA USA
| | - Pedro A. Piedra
- Departments of Molecular Virology and Microbiology and Pediatrics Baylor College of Medicine Houston TX USA
| | - Kohei Hasegawa
- Department of Emergency Medicine Massachusetts General Hospital Harvard Medical School Boston MA USA
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9
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Dissanayake TK, Schäuble S, Mirhakkak MH, Wu WL, Ng ACK, Yip CCY, López AG, Wolf T, Yeung ML, Chan KH, Yuen KY, Panagiotou G, To KKW. Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection. Front Microbiol 2020; 11:1580. [PMID: 32849329 PMCID: PMC7396524 DOI: 10.3389/fmicb.2020.01580] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Rhinovirus (RV) and influenza virus are the most frequently detected respiratory viruses among adult patients with community acquired pneumonia. Previous clinical studies have identified major differences in the clinical presentations and inflammatory or immune response during these infections. A systematic transcriptomic analysis directly comparing influenza and RV is lacking. Here, we sought to compare the transcriptomic response to these viral infections. Human airway epithelial Calu-3 cells were infected with contemporary clinical isolates of RV, influenza A virus (IAV), or influenza B virus (IBV). Host gene expression was determined using RNA-seq. Differentially expressed genes (DEGs) with respect to mock-infected cells were identified using the overlapping gene-set of four different statistical models. Transcriptomic analysis showed that RV-infected cells have a more blunted host response with fewer DEGs than IAV or IBV-infected cells. IFNL1 and CXCL10 were among the most upregulated DEGs during RV, IAV, and IBV infection. Other DEGs that were highly expressed for all 3 viruses were mainly genes related to type I or type III interferons (RSAD2, IDO1) and chemokines (CXCL11). Notably, ICAM5, a known receptor for enterovirus D68, was highly expressed during RV infection only. Gene Set Enrichment Analysis (GSEA) confirmed that pathways associated with interferon response, innate immunity, or regulation of inflammatory response, were most perturbed for all three viruses. Network analysis showed that steroid-related pathways were enriched. Taken together, our data using contemporary virus strains suggests that genes related to interferon and chemokine predominated the host response associated with RV, IAV, and IBV infection. Several highly expressed genes, especially ICAM5 which is preferentially-induced during RV infection, deserve further investigation.
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Affiliation(s)
| | - Sascha Schäuble
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Mohammad Hassan Mirhakkak
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Wai-Lan Wu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anthony Chin-Ki Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Albert García López
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Man-Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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10
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Jones AC, Anderson D, Galbraith S, Fantino E, Gutierrez Cardenas D, Read JF, Serralha M, Holt BJ, Strickland DH, Sly PD, Bosco A, Holt PG. Personalized Transcriptomics Reveals Heterogeneous Immunophenotypes in Children with Viral Bronchiolitis. Am J Respir Crit Care Med 2020; 199:1537-1549. [PMID: 30562046 DOI: 10.1164/rccm.201804-0715oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rationale: A subset of infants are hypersusceptible to severe/acute viral bronchiolitis (AVB), for reasons incompletely understood. Objectives: To characterize the cellular/molecular mechanisms underlying infant AVB in circulating cells/local airway tissues. Methods: Peripheral blood mononuclear cells and nasal scrapings were obtained from infants (<18 mo) and children (≥18 mo to 5 yr) during AVB and after convalescence. Immune response patterns were profiled by multiplex analysis of plasma cytokines, flow cytometry, and transcriptomics (RNA-Seq). Molecular profiling of group-level data used a combination of upstream regulator and coexpression network analysis, followed by individual subject-level data analysis using personalized N-of-1-pathways methodology. Measurements and Main Results: Group-level analyses demonstrated that infant peripheral blood mononuclear cell responses were dominated by monocyte-associated hyperupregulated type 1 IFN signaling/proinflammatory pathways (drivers: TNF [tumor necrosis factor], IL-6, TREM1 [triggering receptor expressed on myeloid cells 1], and IL-1B), versus a combination of inflammation (PTGER2 [prostaglandin E receptor 2] and IL-6) plus growth/repair/remodeling pathways (ERBB2 [erbb-b2 receptor tyrosine kinase 2], TGFB1 [transforming growth factor-β1], AREG [amphiregulin], and HGF [hepatocyte growth factor]) coupled with T-helper cell type 2 and natural killer cell signaling in children. Age-related differences were not attributable to differential steroid usage or variations in underlying viral pathogens. Nasal mucosal responses were comparable qualitatively in infants/children, dominated by IFN types 1-3, but the magnitude of upregulation was higher in infants (range, 6- to 48-fold) than children (5- to 17-fold). N-of-1-pathways analysis confirmed differential upregulation of innate immunity in infants and natural killer cell networks in children, and additionally demonstrated covert AVB response subphenotypes that were independent of chronologic age. Conclusions: Dysregulated expression of IFN-dependent pathways after respiratory viral infections is a defining immunophenotypic feature of AVB-susceptible infants and a subset of children. Susceptible subjects seem to represent a discrete subgroup who cluster based on (slow) kinetics of postnatal maturation of innate immune competence.
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Affiliation(s)
- Anya C Jones
- 1 Telethon Kids Institute and.,2 School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia; and
| | | | - Sally Galbraith
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Emmanuelle Fantino
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | | | - James F Read
- 1 Telethon Kids Institute and.,2 School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia; and
| | | | | | | | - Peter D Sly
- 3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Patrick G Holt
- 1 Telethon Kids Institute and.,3 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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11
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Mukund K, Mathee K, Subramaniam S. Plasmin Cascade Mediates Thrombotic Events in SARS-CoV-2 Infection via Complement and Platelet-Activating Systems. IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY 2020; 1:220-227. [PMID: 34786557 PMCID: PMC8527892 DOI: 10.1109/ojemb.2020.3014798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/11/2022] Open
Abstract
Objective: Recently emerged beta-coronavirus SARS-CoV-2, has resulted in the current pandemic designated COVID-19. COVID-19 manifests as severe illness exhibiting systemic inflammatory response syndrome, acute respiratory distress syndrome (ARDS), thrombotic events, and shock, exacerbated further by co-morbidities and age. Recent clinical evidence suggests that the development of ARDS and subsequent pulmonary failure result from a complex interplay between cell types (endothelial, epithelial and immune) within the lung promoting inflammatory infiltration and a pro-coagulative state. How the complex molecular events mediated by SARS-CoV-2 in infected lung epithelial cells lead to thrombosis and pulmonary failure, is yet to be fully understood. Methods: We address these questions here, using publicly available transcriptomic data in the context of lung epithelia affected by SARS-CoV-2 and other respiratory infections, in vitro. We then extend our results to the understanding of in vivo lung, using a publicly available COVID-19 lung transcriptomic study. Results and Conclusions: Our analysis indicates that there exists a complex interplay between the fibrinolytic system particularly plasmin, and the complement and platelet-activating systems upon SARS-CoV-2 infection, with a potential for therapeutic intervention.
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Affiliation(s)
- Kavitha Mukund
- 1 Department of BioengineeringUniversity of California San Diego La Jolla CA 92093 USA
| | - Kalai Mathee
- 2 Department of Human and Molecular GeneticsHerbert Wertheim College of Medicine Miami FL 33199 USA
- 3 Biomolecular Sciences InstituteFlorida International University Miami FL 33199 USA
| | - Shankar Subramaniam
- 1 Department of BioengineeringUniversity of California San Diego La Jolla CA 92093 USA
- 4 Department of Cellular and Molecular MedicineUniversity of California San Diego La Jolla CA 92093 USA
- 5 Department of Computer Science and EngineeringUniversity of California San Diego La Jolla CA 92093 USA
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12
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Sun S, Yu X, Sun F, Tang Y, Zhao J, Zeng T. Dynamically characterizing individual clinical change by the steady state of disease-associated pathway. BMC Bioinformatics 2019; 20:697. [PMID: 31874621 PMCID: PMC6929545 DOI: 10.1186/s12859-019-3271-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Along with the development of precision medicine, individual heterogeneity is attracting more and more attentions in clinical research and application. Although the biomolecular reaction seems to be some various when different individuals suffer a same disease (e.g. virus infection), the final pathogen outcomes of individuals always can be mainly described by two categories in clinics, i.e. symptomatic and asymptomatic. Thus, it is still a great challenge to characterize the individual specific intrinsic regulatory convergence during dynamic gene regulation and expression. Except for individual heterogeneity, the sampling time also increase the expression diversity, so that, the capture of similar steady biological state is a key to characterize individual dynamic biological processes. Results Assuming the similar biological functions (e.g. pathways) should be suitable to detect consistent functions rather than chaotic genes, we design and implement a new computational framework (ABP: Attractor analysis of Boolean network of Pathway). ABP aims to identify the dynamic phenotype associated pathways in a state-transition manner, using the network attractor to model and quantify the steady pathway states characterizing the final steady biological sate of individuals (e.g. normal or disease). By analyzing multiple temporal gene expression datasets of virus infections, ABP has shown its effectiveness on identifying key pathways associated with phenotype change; inferring the consensus functional cascade among key pathways; and grouping pathway activity states corresponding to disease states. Conclusions Collectively, ABP can detect key pathways and infer their consensus functional cascade during dynamical process (e.g. virus infection), and can also categorize individuals with disease state well, which is helpful for disease classification and prediction.
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Affiliation(s)
- Shaoyan Sun
- School of Mathematics and Statistics Science, Ludong University, Yantai, 264025, China.
| | - Xiangtian Yu
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.,Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy Science, Shanghai, 200031, China
| | - Fengnan Sun
- Medical Laboratory, Yantaishan Hospital, Yantai, 264001, China
| | - Ying Tang
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy Science, Shanghai, 200031, China
| | - Juan Zhao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy Science, Shanghai, 200031, China
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy Science, Shanghai, 200031, China. .,Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210, China.
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13
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Millette G, Langlois JP, Brouillette E, Frost EH, Cantin AM, Malouin F. Despite Antagonism in vitro, Pseudomonas aeruginosa Enhances Staphylococcus aureus Colonization in a Murine Lung Infection Model. Front Microbiol 2019; 10:2880. [PMID: 31921058 PMCID: PMC6923662 DOI: 10.3389/fmicb.2019.02880] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/29/2019] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus and Pseudomonas aeruginosa are prevalent lung pathogens in cystic fibrosis (CF). Whereas co-infection worsens the clinical outcome, prototypical strains are usually antagonistic in vitro. We sought to resolve the discrepancy between these in vitro and in vivo observations. In vitro, growth kinetics for co-cultures of co-isolates from CF patients showed that not all P. aeruginosa strains affected S. aureus viability. On solid media, S. aureus slow-growing colonies were visualized around some P. aeruginosa strains whether or not S. aureus viability was reduced in liquid co-cultures. The S. aureus-P. aeruginosa interactions were then characterized in a mouse lung infection model. Lung homogenates were plated on selective media allowing colony counts of either bacterium. Overall, 35 P. aeruginosa and 10 S. aureus strains (clinical, reference, and mutant strains), for a total of 200 co-infections, were evaluated. We observed that S. aureus colonization of lung tissues was promoted by P. aeruginosa and even by strains showing antagonism in vitro. Promotion was proportional to the extent of P. aeruginosa colonization, but no correlation was found with the degree of myeloperoxidase quantification (as marker of inflammation) or with specific virulence-associated factors using known mutant strains of S. aureus and P. aeruginosa. On the other hand, P. aeruginosa significantly increased the expression of two possible cell receptors for S. aureus, i.e., ICAM-1 and ITGA-5 (marker for integrin α5β1) in lung tissue, while mono-infections by S. aureus did not. This study provides insights on polymicrobial interactions that may influence the progression of CF-associated pulmonary infections.
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Affiliation(s)
- Guillaume Millette
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Philippe Langlois
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Brouillette
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric H Frost
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et de Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - André M Cantin
- Service de Pneumologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François Malouin
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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14
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Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J. Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets. SYSTEMS MEDICINE 2019; 2:1-9. [PMID: 31119214 PMCID: PMC6524659 DOI: 10.1089/sysm.2018.0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introduction: Drug-resistant infections are becoming increasingly frequent worldwide, causing hundreds of thousands of deaths annually. This is partly due to the very limited set of protein drug targets known for human-infecting viral genomes. The eleven influenza virus proteins, for instance, exploit host cell factors for replication and suppression of the antiviral immune responses. A systems medicine approach to identify relevant and druggable host factors would dramatically expand therapeutic options. Therapeutic target identification, however, has hitherto relied on static molecular networks, whereas in reality the interactome, in particular during an infection, is subject to constant change. Methods: We developed time-course network enrichment (TiCoNE), an expert-centered approach for discovering temporal response pathways. In the first stage of TiCoNE, time-series expression data is clustered in a human-augmented manner to identify groups of biological entities with coherent temporal responses. Throughout this process, the expert can add, remove, merge, or split temporal patterns. The resulting groups can then be mapped to an interaction network to identify enriched pathways and to analyze cross-talk enrichments and depletions between groups. Finally, temporal response groups of two experiments can be intersected, to identify condition-variant response patterns that represent promising drug-target candidates. Results: We applied TiCoNE to human gene expression data for influenza A virus infection and rhino virus infection, respectively. We then identified coherent temporal response patterns and employed our cross-talk analysis to establish two potential timelines of systems-level host responses for either infection. Next, we compared the two phenotypes and unraveled condition-variant temporal groups interacting on a networks level. The highest-ranking ones we then validated via literature search and wet-lab experiments. This not only confirmed many of our candidates as previously known, but we also identified phospholipid scramblase 1 (encoded by PLSCR1) as a previously not recognized host factor that is essential for influenza A virus infection. Conclusion: With TiCoNE we developed a novel approach for conjointly analyzing molecular networks with time-series expression data and demonstrated its power by identifying temporal drug-targets. We provide proof-of-concept that not only novel targets can be identified using our approach, but also that anti-infective drug target discovery can be enhanced by investigating temporal molecular networks of the host in response to viral infection.
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Affiliation(s)
- Christian Wiwie
- Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Irina Kuznetsova
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Ahmed Mostafa
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.,Center of Scientific Excellence for Influenza Viruses, National Research Centre, Cairo, Egypt
| | - Alexander Rauch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anders Haakonsson
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Inigo Barrio-Hernandez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalized Medicine, Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Richard Röttger
- Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Department of Experimental Bioinformatics, Technical University of Munich, Freising, Germany
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15
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Miura TA. Respiratory epithelial cells as master communicators during viral infections. CURRENT CLINICAL MICROBIOLOGY REPORTS 2019; 6:10-17. [PMID: 31592409 PMCID: PMC6779166 DOI: 10.1007/s40588-019-0111-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Communication by epithelial cells during respiratory viral infections is critical in orchestrating effective anti-viral responses but also can lead to excessive inflammation. This review will evaluate studies that investigate how respiratory epithelial cells influence the behavior of immune cells and how epithelial cell/immune cell interactions contribute to antiviral responses and immunopathology outcomes. RECENT FINDINGS Previous studies have characterized cytokine responses of virus-infected epithelial cells. More recent studies have carefully demonstrated the effects of these cytokines on cellular behaviors within the infected lung. Infected epithelial cells release exosomes that specifically regulate responses of monocytes and neighboring epithelial cells without promoting spread of virus. In contrast, rhinovirus-infected cells induce monocytes to upregulate expression of the viral receptor, promoting spread of the virus to alternate cell types. The precise alteration of PDL expression on infected epithelial cells has been shown to switch between inhibition and activation of antiviral responses. SUMMARY These studies have more precisely defined the interactions between epithelial and immune cells during viral infections. This level of understanding is critical for the development of novel therapeutic strategies that promote effective antiviral responses or epithelial repair, or inhibit damaging inflammatory responses during severe respiratory viral infections.
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Affiliation(s)
- Tanya A Miura
- Department of Biological Sciences and Center for Modeling Complex Interactions, University of Idaho, Moscow, ID 83844, USA,
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16
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Chung M, Cho SY, Lee YS. Construction of a Transcriptome-Driven Network at the Early Stage of Infection with Influenza A H1N1 in Human Lung Alveolar Epithelial Cells. Biomol Ther (Seoul) 2018; 26:290-297. [PMID: 29401570 PMCID: PMC5933896 DOI: 10.4062/biomolther.2017.240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022] Open
Abstract
We aimed to understand the molecular changes in host cells that accompany infection by the seasonal influenza A H1N1 virus because the initial response rapidly changes owing to the fact that the virus has a robust initial propagation phase. Human epithelial alveolar A549 cells were infected and total RNA was extracted at 30 min, 1 h, 2 h, 4 h, 8 h, 24 h, and 48 h post infection (h.p.i.). The differentially expressed host genes were clustered into two distinct sets of genes as the infection progressed over time. The patterns of expression were significantly different at the early stages of infection. One of the responses showed roles similar to those associated with the enrichment gene sets to known 'gp120 pathway in HIV.' This gene set contains genes known to play roles in preventing the progress of apoptosis, which infected cells undergo as a response to viral infection. The other gene set showed enrichment of 'Drug Metabolism Enzymes (DMEs).' The identification of two distinct gene sets indicates that the virus regulates the cell's mechanisms to create a favorable environment for its stable replication and protection of gene metabolites within 8 h.
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Affiliation(s)
- Myungguen Chung
- Division of Molecular and Life Sciences, Hanyang University, Ansan 15588, Republic of Korea
| | - Soo Young Cho
- National Cancer Center, Goyang 10408, Republic of Korea
| | - Young Seek Lee
- Division of Molecular and Life Sciences, Hanyang University, Ansan 15588, Republic of Korea
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17
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Yang Y, Jing Y, Yang J, Yang Q. Effects of intranasal administration with Bacillus subtilis on immune cells in the nasal mucosa and tonsils of piglets. Exp Ther Med 2018; 15:5189-5198. [PMID: 29805543 PMCID: PMC5958783 DOI: 10.3892/etm.2018.6093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
The nasal mucosa is the body's first barrier against pathogens entering through the respiratory tract. The respiratory immune system of pigs has more similarities with humans than the mouse respiratory system does, and so was selected as the animal model in the present study. To evaluate the effects of Bacillus subtilis as a potential probiotic to stimulate local immune responses, piglets were intranasally administered with Dylight 488-labeled B. subtilis (WB800-green fluorescent protein). The results revealed that B. subtilis was able to reach the lamina propria of the nasal mucosa, nasopharyngeal tonsils and soft palate tonsils. Piglets were subsequently administered intranasally with B. subtilis (WB800) at 3, 12 and 28 days. The results revealed that, following administration with B. subtilis, the number of dendritic cells, immunoglobulin A+ B cells and T cells in the nasal mucosa and tonsils significantly increased (P<0.05). No obvious differences were observed in the morphological structure following B. subtilis administration. There were no statistical differences were observed in the expression of interleukin (IL)-1β, tumor necrosis factor-α and IL-8 mRNA between the B. subtilis treated group and the control group in the nasal mucosa, nasopharyngeal tonsil or soft palate tonsil. Toll-like receptor (TLR)-2 and TLR-9 mRNA expression in the tonsils was significantly increased following B. subtilis administration compared with the control group (P<0.05). The results demonstrate that B. subtilis administration increases the number of immune cells in the nasal mucosa and tonsils of piglets and stimulates nasal mucosal and tonsillar immunity. The present study lays the foundation for further study into the intranasal administration of B. subtilis in humans to enhance the immunity of human nasal mucosa to respiratory diseases.
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Affiliation(s)
- Yunhan Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Yuchao Jing
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Jingjing Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qian Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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18
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VanLeuven JT, Ridenhour BJ, Gonzalez AJ, Miller CR, Miura TA. Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PLoS One 2017; 12:e0178408. [PMID: 28575086 PMCID: PMC5456070 DOI: 10.1371/journal.pone.0178408] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 05/13/2017] [Indexed: 12/28/2022] Open
Abstract
The severity of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to viruses from different families while controlling other experimental parameters. Murine models are commonly used to study the pathogenesis of respiratory viral infections, and in vitro studies using murine cells provide mechanistic insight into the pathogenesis observed in vivo. We used microarray analysis to compare changes in gene expression of murine lung epithelial cells infected individually by three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to change through 24 hours. MHV-1 had comparatively few effects on host gene expression. The viruses elicited highly overlapping responses in antiviral genes, though MHV-1 induced a lower type I interferon response than the other two viruses. Signature genes were identified for each virus and included host defense genes for PR8, tissue remodeling genes for RV1B, and transcription factors for MHV-1. Our comparative approach identified universal and specific transcriptional signatures of virus infection that can be used to distinguish shared and virus-specific mechanisms of pathogenesis in the respiratory tract.
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Affiliation(s)
- James T. VanLeuven
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
| | - Benjamin J. Ridenhour
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Andres J. Gonzalez
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Craig R. Miller
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
| | - Tanya A. Miura
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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19
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Troy NM, Bosco A. Respiratory viral infections and host responses; insights from genomics. Respir Res 2016; 17:156. [PMID: 27871304 PMCID: PMC5117516 DOI: 10.1186/s12931-016-0474-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/10/2016] [Indexed: 01/23/2023] Open
Abstract
Respiratory viral infections are a leading cause of disease and mortality. The severity of these illnesses can vary markedly from mild or asymptomatic upper airway infections to severe wheezing, bronchiolitis or pneumonia. In this article, we review the viral sensing pathways and organizing principles that govern the innate immune response to infection. Then, we reconstruct the molecular networks that differentiate symptomatic from asymptomatic respiratory viral infections, and identify the underlying molecular drivers of these networks. Finally, we discuss unique aspects of the biology and pathogenesis of infections with respiratory syncytial virus, rhinovirus and influenza, drawing on insights from genomics.
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Affiliation(s)
- Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Subiaco, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Subiaco, Australia.
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Chandler JD, Hu X, Ko EJ, Park S, Lee YT, Orr M, Fernandes J, Uppal K, Kang SM, Jones DP, Go YM. Metabolic pathways of lung inflammation revealed by high-resolution metabolomics (HRM) of H1N1 influenza virus infection in mice. Am J Physiol Regul Integr Comp Physiol 2016; 311:R906-R916. [PMID: 27558316 DOI: 10.1152/ajpregu.00298.2016] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/19/2016] [Indexed: 12/21/2022]
Abstract
Influenza is a significant health concern worldwide. Viral infection induces local and systemic activation of the immune system causing attendant changes in metabolism. High-resolution metabolomics (HRM) uses advanced mass spectrometry and computational methods to measure thousands of metabolites inclusive of most metabolic pathways. We used HRM to identify metabolic pathways and clusters of association related to inflammatory cytokines in lungs of mice with H1N1 influenza virus infection. Infected mice showed progressive weight loss, decreased lung function, and severe lung inflammation with elevated cytokines [interleukin (IL)-1β, IL-6, IL-10, tumor necrosis factor (TNF)-α, and interferon (IFN)-γ] and increased oxidative stress via cysteine oxidation. HRM showed prominent effects of influenza virus infection on tryptophan and other amino acids, and widespread effects on pathways including purines, pyrimidines, fatty acids, and glycerophospholipids. A metabolome-wide association study (MWAS) of the aforementioned inflammatory cytokines was used to determine the relationship of metabolic responses to inflammation during infection. This cytokine-MWAS (cMWAS) showed that metabolic associations consisted of distinct and shared clusters of 396 metabolites highly correlated with inflammatory cytokines. Strong negative associations of selected glycosphingolipid, linoleate, and tryptophan metabolites with IFN-γ contrasted strong positive associations of glycosphingolipid and bile acid metabolites with IL-1β, TNF-α, and IL-10. Anti-inflammatory cytokine IL-10 had strong positive associations with vitamin D, purine, and vitamin E metabolism. The detailed metabolic interactions with cytokines indicate that targeted metabolic interventions may be useful during life-threatening crises related to severe acute infection and inflammation.
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Affiliation(s)
- Joshua D Chandler
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | - Xin Hu
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | - Eun-Ju Ko
- Georgia State University, Atlanta, Georgia
| | | | | | - Michael Orr
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | - Jolyn Fernandes
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | - Karan Uppal
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | | | - Dean P Jones
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
| | - Young-Mi Go
- Division of Pulmonary Medicine, Department of Medicine, Emory University, Atlanta, Georgia; and
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