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Feng K, Cen J, Zou X, Zhang T. Novel insight into MDA-7/IL-24: A potent therapeutic target for autoimmune and inflammatory diseases. Clin Immunol 2024; 266:110322. [PMID: 39033900 DOI: 10.1016/j.clim.2024.110322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Melanoma differentiation-associated gene-7 (MDA-7)/interleukin-24 (IL-24) is a pleiotropic member of the IL-10 family of cytokines, and is involved in multiple biological processes, including cell proliferation, cell differentiation, tissue fibrosis, the inflammatory response, and antitumor activity. MDA-7/IL-24 can regulate epithelial integrity, homeostasis, mucosal immunity and host resistance to various pathogens by enhancing immune and inflammatory responses. Our recent study revealed the mechanism of MDA-7/IL-24 in promoting airway inflammation and airway remodeling through activating the JAK/STAT3 and ERK signaling pathways in bronchial epithelial cells. Herein, we summarize the cellular sources, inducers, target cells, signaling pathways, and biological effects of MDA-7/IL-24 in several allergic and autoimmune diseases. This review also synopsizes recent advances in clinical research targeting MDA-7/IL-24 or its receptors. Based on these advancements, we emphasize its potential as a target for immunotherapy and discuss the challenges of developing immunotherapeutic drugs targeting MDA-7/IL-24 or its receptors in autoimmune and inflammatory disorders.
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Affiliation(s)
- Kangni Feng
- Department of Pulmonary and Critical Care Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Disease of Sun Yat-sen University, Guangzhou, Guangdong Province 510630, China
| | - Jiemei Cen
- Department of Pulmonary and Critical Care Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Disease of Sun Yat-sen University, Guangzhou, Guangdong Province 510630, China
| | - Xiaoling Zou
- Department of Pulmonary and Critical Care Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Disease of Sun Yat-sen University, Guangzhou, Guangdong Province 510630, China
| | - Tiantuo Zhang
- Department of Pulmonary and Critical Care Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Disease of Sun Yat-sen University, Guangzhou, Guangdong Province 510630, China.
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Oh SJ, Kumari P, Auroni TT, Stone S, Pathak H, Elsharkawy A, Natekar JP, Shin OS, Kumar M. Upregulation of Neuroinflammation-Associated Genes in the Brain of SARS-CoV-2-Infected Mice. Pathogens 2024; 13:528. [PMID: 39057755 PMCID: PMC11280415 DOI: 10.3390/pathogens13070528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Neurological manifestations are a significant complication of coronavirus disease 2019 (COVID-19), but the underlying mechanisms are yet to be understood. Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced neuroinvasion and encephalitis were observed in K18-hACE2 mice, leading to mortality. Our goal in this study was to gain insights into the molecular pathogenesis of neurological manifestations in this mouse model. To analyze differentially expressed genes (DEGs) in the brains of mice following SARS-CoV-2 infection, we performed NanoString gene expression analysis using three individual animal samples at 1, 3, and 6 days post-infection. We identified the DEGs by comparing them to animals that were not infected with the virus. We found that genes upregulated at day 6 post-infection were mainly associated with Toll-like receptor (TLR) signaling, RIG-I-like receptor (RLR) signaling, and cell death pathways. However, downregulated genes were associated with neurodegeneration and synaptic signaling pathways. In correlation with gene expression profiles, a multiplexed immunoassay showed the upregulation of multiple cytokines and chemokines involved in inflammation and cell death in SARS-CoV-2-infected brains. Furthermore, the pathway analysis of DEGs indicated a possible link between TLR2-mediated signaling pathways and neuroinflammation, as well as pyroptosis and necroptosis in the brain. In conclusion, our work demonstrates neuroinflammation-associated gene expression profiles, which can provide key insight into the severe disease observed in COVID-19 patients.
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Affiliation(s)
- Soo-Jin Oh
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea;
| | - Pratima Kumari
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Tabassum Tasnim Auroni
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Shannon Stone
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Heather Pathak
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Amany Elsharkawy
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Janhavi Prasad Natekar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
| | - Ok Sarah Shin
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea;
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 30303, USA; (P.K.); (T.T.A.); (S.S.); (H.P.); (A.E.); (J.P.N.)
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Li X, Ye Z, Plant EP. 5' copyback defective viral genomes are major component in clinical and non-clinical influenza samples. Virus Res 2024; 339:199274. [PMID: 37981214 PMCID: PMC10701078 DOI: 10.1016/j.virusres.2023.199274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Clinical samples from people with influenza disease have been analyzed to assess the presence and abundance of Defective Viral Genomes (DVGs), but these have not been assessed using the same bioinformatic pipeline. The type of DVG most described for influenza infections (deletion DVGs) differs from the most commonly described DVGs from non-segmented negative stranded viruses (5' copyback). This could be attributed to either differences between viruses or the tools used to detect and characterize DVGs. Here we analyze several NGS datasets from people infected with different types of influenza virus using the same bioinformatic pipeline. We observe that 5' copyback DVGs are prevalent in all human clinical samples but not in the cultured samples. To address this discrepancy between clinical and laboratory cultures, we infected cell culture and ferrets with an H5N8 influenza A virus (FLUAV) and analyzed the DVG composition. The results demonstrate that the DVG population is skewed toward 5' copyback DVGs in the in vivo infections and deletion DVGs in the in vitro infections. This demonstrates that there are differences in vivo genome production and in vitro genome production, and this has implications for how the role of DVGs in clinical disease is studied. We also investigate the role the host cofactor ANP32B has in DVG production.
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Affiliation(s)
- Xing Li
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Ewan P Plant
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA.
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Small RNA sequencing of small extracellular vesicles secreted by umbilical cord mesenchymal stem cells following replicative senescence. Genes Genomics 2023; 45:347-358. [PMID: 35917089 DOI: 10.1007/s13258-022-01297-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/20/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Umbilical cord mesenchymal stem cells (UCMSC) are subsets of multipotent stem cells involved in immune modulation, tissue regeneration, and antimicrobial defense. Cellular senescence is associated with the onset of aging-related diseases and small extracellular vesicles (sEVs) are important mediators of senescence and aging. OBJECTIVE However, little is known about the role and function of microRNAs (miRNAs) carried by UCMSC-derived sEVs. To analyze the expression profiles of miRNAs secreted by senescent UCMSC, small RNA sequencing of the miRNAs within the sEVs was performed in this study. METHODS UCMSC cultures underwent serial passaging beyond passage number 20 to achieve replicative senescence, which was confirmed by various methods, including increased senescence-associated β-gal staining and cytokine secretion levels. sEVs derived from non-senescent and senescent UCMSC were isolated and characterized by nanoparticle tracking analysis, transmission electron microscopy, and immunoblot analysis. RESULTS Small RNA sequencing of the miRNAs within the sEVs revealed senescence-associated differences in the miRNA composition, as shown by the upregulation of miR-122-5p and miR-146a-5p, and downregulation of miR-125b-5p and miR-29-3p. In addition, total RNA sequencing analysis showed that PENK, ITGA8, and TSIX were upregulated, whereas AKR1B10, UNC13D, and IL21R were downregulated by replicative senescence in UCMSC. In sEVs, upregulated genes were linked to downregulated miRNAs, and vice versa. In the gene-concept network analysis, five gynecologic terms were retrieved. CONCLUSIONS The study provides an insight into the cellular characteristics of UCMSC following replicative senescence and emphasizes the importance of monitoring passage numbers of UCMSC for further therapeutic use.
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Hsieh TH, Lin YJ, Hsioa MJ, Wang HJ, Chen LT, Yang SL, Huang CG. Transcriptome Differences in Normal Human Bronchial Epithelial Cells in Response to Influenza A pdmH1N1 or H7N9 Virus Infection. Cells 2022; 11:cells11050781. [PMID: 35269402 PMCID: PMC8909308 DOI: 10.3390/cells11050781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/25/2023] Open
Abstract
Avian influenza A (H7N9) virus infections frequently lead to acute respiratory distress syndrome and death in humans. The emergence of H7N9 virus infections is a serious public health threat. To identify virus–host interaction differences between the highly virulent H7N9 and pandemic influenza H1N1 (pdmH1N1), RNA sequencing was performed of normal human bronchial epithelial (NHBE) cells infected with either virus. The transcriptomic analysis of host cellular responses to viral infection enables the identification of potential cellular factors related to infection. Significantly different gene expression patterns were found between pdmH1N1- and H7N9-infected NHBE cells. In addition, the H7N9 virus infection induced strong immune responses, while cellular repair mechanisms were inhibited. The differential expression of specific factors observed between avian H7N9 and pdmH1N1 influenza virus strains can account for variations in disease pathogenicity. These findings provide a framework for future studies examining the molecular mechanisms underlying the pathogenicity of avian H7N9 virus.
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Affiliation(s)
- Tzu-Hsuan Hsieh
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Ya-Jhu Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Mei-Jen Hsioa
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Hsin-Ju Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Lu-Ting Chen
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; (T.-H.H.); (Y.-J.L.); (M.-J.H.); (H.-J.W.); (L.-T.C.); (S.-L.Y.)
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence:
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Wang Y, Wang L, Fu C, Wang X, Zuo S, Shu C, Shan Y, He J, Zhou Q, Li W, Yang YG, Hu Z, Hua S. Exploration of Human Lung-Resident Immunity and Response to Respiratory Viral Immunization in a Humanized Mouse Model. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:420-428. [PMID: 34903640 DOI: 10.4049/jimmunol.2100122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
There are urgent needs for humanized mouse models of viral respiratory diseases to study immunopathogenesis and therapeutic interventions. Although human immune system (HIS) mice permit analysis in real time of human immune responses in vivo, evolutionary divergences preclude their usefulness for the respiratory viruses that do not infect mouse lungs. In this study, we sought to use HIS mice with human lung (HL) tissue xenografts (HISL mice) to address this issue. The grafted HL tissue maintained histologically normal structure, and populated with human tissue-resident immune cells, including CD11c+ dendritic cells and CD4+ and CD8+ tissue-resident memory T cells. HISL mice showed a marked expansion of tissue-resident memory T cells and generation of viral Ag-specific T cells in the HL xenografts, and production of antiviral IgM and IgG Abs upon immunization of the HL xenograft by H1N1 influenza viruses. RNA-seq analysis on H1N1-infected and control HL xenografts identified a total of 5089 differentially expressed genes with enrichments for genes involved in respiratory diseases, viral infections, and associated immune responses. Furthermore, prophylactic viral exposures resulted in protection against subsequent lethal challenge by intranasal viral inoculation. This study supports the usefulness of this preclinical model in exploring the immunopathology and therapies of respiratory viral diseases.
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Affiliation(s)
- Yixin Wang
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Lei Wang
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Cong Fu
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Xue Wang
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Siyao Zuo
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Chang Shu
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Yanhong Shan
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Jin He
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China; and
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China; and
| | - Yong-Guang Yang
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China;
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Zheng Hu
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China;
- National-Local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Shucheng Hua
- Department of Respiration, Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, China;
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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Transcriptomic Characterization Reveals Attributes of High Influenza Virus Productivity in MDCK Cells. Viruses 2021; 13:v13112200. [PMID: 34835006 PMCID: PMC8620111 DOI: 10.3390/v13112200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/24/2022] Open
Abstract
The Madin–Darby Canine Kidney (MDCK) cell line is among the most commonly used cell lines for the production of influenza virus vaccines. As cell culture-based manufacturing is poised to replace egg-based processes, increasing virus production is of paramount importance. To shed light on factors affecting virus productivity, we isolated a subline, H1, which had twice the influenza virus A (IAV) productivity of the parent (P) through cell cloning, and characterized H1 and P in detail on both physical and molecular levels. Transcriptome analysis revealed that within a few hours after IAV infection, viral mRNAs constituted over one fifth of total mRNA, with several viral genes more highly expressed in H1 than P. Functional analysis of the transcriptome dynamics showed that H1 and P responded similarly to IAV infection, and were both subjected to host shutoff and inflammatory responses. Importantly, H1 was more active in translation and RNA processing intrinsically and after infection. Furthermore, H1 had more subdued inflammatory and antiviral responses. Taken together, we postulate that the high productivity of IAV hinges on the balance between suppression of host functions to divert cellular resources and the sustaining of sufficient activities for virus replication. Mechanistic insights into virus productivity can facilitate the process optimization and cell line engineering for advancing influenza vaccine manufacturing.
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Azli B, Ravi S, Hair-Bejo M, Omar AR, Ideris A, Mat Isa N. Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection. BMC Genomics 2021; 22:461. [PMID: 34147086 PMCID: PMC8214787 DOI: 10.1186/s12864-021-07690-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation's food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens. RESULTS A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value < 0.05. Yet, only 9 upregulated and 13 downregulated uni-genes had BLAST hits against the Non-redundant and Swiss-Prot databases. The genome ontology enrichment keywords of these DEGs were associated with immune response, cell signalling and apoptosis. Consequently, the Weighted Gene Correlation Network Analysis R tool was used to predict the functional annotation of the remaining unknown uni-genes with no significant BLAST hits. Interestingly, the functions of the three upregulated uni-genes were predicted to be related to innate immune response, while the five downregulated uni-genes were predicted to be related to cell surface functions. These results further elucidated and supported the current molecular knowledge regarding the pathophysiology of chicken's bursal infected with IBDV. CONCLUSION Our data revealed the commonly up- and downregulated novel uni-genes identified to be immune- and extracellular binding-related, respectively. Besides, these novel findings are valuable contributions in improving the current existing integrative chicken transcriptomics annotation and may pave a path towards the control of viral particles especially towards the suppression of IBD and other infectious diseases in chickens.
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Affiliation(s)
- Bahiyah Azli
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Sharanya Ravi
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Mohd Hair-Bejo
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Aini Ideris
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
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Seong RK, Lee JK, Cho GJ, Kumar M, Shin OS. mRNA and miRNA profiling of Zika virus-infected human umbilical cord mesenchymal stem cells identifies miR-142-5p as an antiviral factor. Emerg Microbes Infect 2021; 9:2061-2075. [PMID: 32902370 PMCID: PMC7534337 DOI: 10.1080/22221751.2020.1821581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy is associated with congenital brain abnormalities, a finding that highlights the urgent need to understand mother-to-fetus transmission mechanisms. Human umbilical cord mesenchymal stem cells (hUCMSCs) are susceptible to ZIKV infection but the underlying mechanisms of viral susceptibility remain largely unexplored. In this study, we have characterized and compared host mRNA and miRNA expression profiles in hUCMSCs after infection with two lineages of ZIKV, African (MR766) and Asian (PRVABC59). RNA sequencing analysis identified differentially expressed genes involved in anti-viral immunity and mitochondrial dynamics following ZIKV infection. In particular, ZIKV-infected hUCMSCs displayed mitochondrial elongation and the treatment of hUCMSCs with mitochondrial fission inhibitor led to a dose-dependent increase in ZIKV gene expression and decrease in anti-viral signalling pathways. Moreover, small RNA sequencing analysis identified several significantly up- or down-regulated microRNAs. Interestingly, miR-142-5p was significantly downregulated upon ZIKV infection, whereas cellular targets of miR-142-5p, IL6ST and ITGAV, were upregulated. Overexpression of miR-142-5p resulted in the suppression of ZIKV replication. Furthermore, blocking ITGAV expression resulted in a significant suppression of ZIKV binding to cells, suggesting a potential role of ITGAV in ZIKV entry. In conclusion, these results demonstrate both common and specific host responses to African and Asian ZIKV lineages and indicate miR-142-5p as a key regulator of ZIKV replication in the umbilical cords.
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Affiliation(s)
- Rak-Kyun Seong
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jae Kyung Lee
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Geum Joon Cho
- Department of Obstetrics and Gynaecology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Mukesh Kumar
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. INFECTION GENETICS AND EVOLUTION 2020; 87:104672. [PMID: 33309772 DOI: 10.1016/j.meegid.2020.104672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 01/04/2023]
Abstract
H5N8 subtype highly pathogenic avian influenza viruses (HPAIVs) pose a huge threat to poultry industry and general public health. Our previous study demonstrated that synergistic effect of 283M and 526R in PB2 gene was a critical factor for viral high pathogenicity in mammals. However, the potential pathogenic mechanism of the mutant virus is still unclear. Here, RNA-seq method was used to analyze the global host response of murine lungs after infecting with parental r-JY virus and JY-PB2-I283M-K526R mutant virus. We found that both amounts and the expression levels of host differentially expressed genes (DEGs) were higher in mutant virus-infected mice compared with the group of parental virus. Furthermore, the DEGs mainly related with innate immune response by GO and KEGG analysis. Especially, PB2-I283M-K526R mutation strongly induced a sharp expression of cytokine storm-related genes, including MX1, CXCL10, and IFN-γ, performed by qRT-PCR. We also found that PB2-I283M-K526R mutation accelerated the level of cell apoptosis by heat map analysis of apoptosis-related DEGs in lungs and apoptosis assay in vitro. Taken together, our data demonstrated that PB2-I283M-K526R of H5N8 subtype HPAIV exacerbated the innate immune response and the level of cell apoptosis, which might be a key pathogenic mechanism for the enhanced pathogenicity of mutants in mammals.
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12
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Mostafa A, Blaurock C, Scheibner D, Müller C, Blohm U, Schäfer A, Gischke M, Salaheldin AH, Nooh HZ, Ali MA, Breithaupt A, Mettenleiter TC, Pleschka S, Abdelwhab EM. Genetic incompatibilities and reduced transmission in chickens may limit the evolution of reassortants between H9N2 and panzootic H5N8 clade 2.3.4.4 avian influenza virus showing high virulence for mammals. Virus Evol 2020; 6:veaa077. [PMID: 33343923 PMCID: PMC7733613 DOI: 10.1093/ve/veaa077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The unprecedented spread of H5N8- and H9N2-subtype avian influenza virus (AIV) in birds across Asia, Europe, Africa, and North America poses a serious public health threat with a permanent risk of reassortment and the possible emergence of novel virus variants with high virulence in mammals. To gain information on this risk, we studied the potential for reassortment between two contemporary H9N2 and H5N8 viruses. While the replacement of the PB2, PA, and NS genes of highly pathogenic H5N8 by homologous segments from H9N2 produced infectious H5N8 progeny, PB1 and NP of H9N2 were not able to replace the respective segments from H5N8 due to residues outside the packaging region. Furthermore, exchange of the PB2, PA, and NS segments of H5N8 by those of H9N2 increased replication, polymerase activity and interferon antagonism of the H5N8 reassortants in human cells. Notably, H5N8 reassortants carrying the H9N2-subtype PB2 segment and to lesser extent the PA or NS segments showed remarkably increased virulence in mice as indicated by rapid onset of mortality, reduced mean time to death and increased body weight loss. Simultaneously, we observed that in chickens the H5N8 reassortants, particularly with the H9N2 NS segment, demonstrated significantly reduced transmission to co-housed chickens. Together, while the limited capacity for reassortment between co-circulating H9N2 and H5N8 viruses and the reduced bird-to-bird transmission of possible H5N8 reassortants in chickens may limit the evolution of such reassortant viruses, they show a higher replication potential in human cells and increased virulence in mammals.
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Affiliation(s)
| | | | | | - Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Ulrike Blohm
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Alexander Schäfer
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | | | | | - Hanaa Z Nooh
- Department of Anatomy and Histology, College of Medicine, Jouf University, Sakaka 72442, Aljouf Province, Saudi Arabia
| | - Mohamed A Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Dokki, 12622, Giza, Egypt
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | | | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
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13
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Cha JY, Kang SH, Ali I, Lee SC, Ji MG, Jeong SY, Shin GI, Kim MG, Jeon JR, Kim WY. Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis. Sci Rep 2020; 10:15042. [PMID: 32929162 PMCID: PMC7490348 DOI: 10.1038/s41598-020-71701-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Imdad Ali
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sang Cheol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, PMBBRC, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jong-Rok Jeon
- Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Department of Agricultural Chemistry and Food Science & Technology, Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, 52828, Republic of Korea.
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14
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Nahand JS, Jamshidi S, Hamblin MR, Mahjoubin-Tehran M, Vosough M, Jamali M, Khatami A, Moghoofei M, Baghi HB, Mirzaei H. Circular RNAs: New Epigenetic Signatures in Viral Infections. Front Microbiol 2020; 11:1853. [PMID: 32849445 PMCID: PMC7412987 DOI: 10.3389/fmicb.2020.01853] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Covalent closed circular RNAs (circRNAs) can act as a bridge between non-coding RNAs and coding messenger RNAs. CircRNAs are generated by a back-splicing mechanism during post-transcriptional processing and are abundantly expressed in eukaryotic cells. CircRNAs can act via the modulation of RNA transcription and protein production, and by the sponging of microRNAs (miRNAs). CircRNAs are now thought to be involved in many different biological and pathological processes. Some studies have suggested that the expression of host circRNAs is dysregulated in several types of virus-infected cells, compared to control cells. It is highly likely that viruses can use these molecules for their own purposes. In addition, some viral genes are able to produce viral circRNAs (VcircRNA) by a back-splicing mechanism. However, the viral genes that encode VcircRNAs, and their functions, are poorly studied. In this review, we highlight some new findings about the interaction of host circRNAs and viral infection. Moreover, the potential of VcircRNAs derived from the virus itself, to act as biomarkers and therapeutic targets is summarized.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Sogol Jamshidi
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States.,Department of Dermatology, Harvard Medical School, Boston, MA, United States.,Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marzieh Jamali
- Department of Gynecology and Obstetrics, Mahdieh Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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15
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Mitamura Y, Nunomura S, Furue M, Izuhara K. IL-24: A new player in the pathogenesis of pro-inflammatory and allergic skin diseases. Allergol Int 2020; 69:405-411. [PMID: 31980374 DOI: 10.1016/j.alit.2019.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 12/24/2022] Open
Abstract
Interleukin (IL)-24 is a member of the IL-20 family of cytokines and is produced by various types of cells, such as CD4+ T cells, NK cells, mast cells, keratinocytes, bronchial epithelial cells, and myofibroblasts. Previous studies suggest that IL-24 plays an essential role in the pathogenesis of pro-inflammatory autoimmune disorders such as psoriasis, arthritis, and inflammatory bowel diseases. However, the role of IL-24 in the pathogenesis of allergic diseases has been elusive. It has already been reported that IL-24 is involved in the pathogenesis of allergic lung and skin diseases. Moreover, we have recently revealed for the first time the pivotal functions of IL-24 in IL-13-mediated skin barrier dysfunction in atopic dermatitis (AD), which is known to be a characteristic of AD caused by Th2 cytokines such as IL-4 or IL-13. In this review, we show recent advances in the basic characteristics of IL-24 and its novel functions in the pathogenesis of allergic skin inflammation, focusing on AD. A better understanding of the role of IL-24 in allergic diseases can lead to the development of new therapeutic options.
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Affiliation(s)
- Yasutaka Mitamura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan; Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Satoshi Nunomura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan
| | - Masutaka Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenji Izuhara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga Medical School, Saga, Japan
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16
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Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martinez-Colon GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response to severe COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 32511639 DOI: 10.1101/2020.04.17.20069930] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2. Here, we apply single-cell RNA sequencing (scRNA-seq) to peripheral blood mononuclear cells (PBMCs) of 7 patients hospitalized with confirmed COVID-19 and 6 healthy controls. We identify substantial reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a novel B cell-derived granulocyte population appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines, suggesting that circulating leukocytes do not significantly contribute to the potential COVID-19 cytokine storm. Collectively, we provide the most thorough cell atlas to date of the peripheral immune response to severe COVID-19.
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17
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Transcriptome Profile of Nicotinic Receptor-Linked Sensitization of Beta Amyloid Neurotoxicity. Sci Rep 2020; 10:5696. [PMID: 32231242 PMCID: PMC7105468 DOI: 10.1038/s41598-020-62726-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 03/18/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the specific gene changes underlying the prodromic stages of Alzheimer’s disease pathogenesis will aid the development of new, targeted therapeutic strategies for this neurodegenerative disorder. Here, we employed RNA-sequencing to analyze global differential gene expression in a defined model nerve cell line expressing α4β2 nicotinic receptors (nAChRs), high-affinity targets for beta amyloid (Aβ). The nAChR-expressing neuronal cells were treated with nanomolar Aβ1–42 to gain insights into the molecular mechanisms underlying Aβ-induced neurotoxicity in the presence of this sensitizing target receptor. We identified 15 genes (out of 15,336) that were differentially expressed upon receptor-linked Aβ treatment. Genes up-regulated with Aβ treatment were associated with calcium signaling and axonal vesicle transport (including the α4 nAChR subunit, the calcineurin regulator RCAN3, and KIF1C of the kinesin family). Downregulated genes were associated with metabolic, apoptotic or DNA repair pathways (including APBA3, PARP1 and RAB11). Validation of the differential expression was performed via qRT-PCR and immunoblot analysis in the defined model nerve cell line and primary mouse neurons. Further verification was performed using immunocytochemistry. In conclusion, we identified apparent changes in gene expression on Aβ treatment in the presence of the sensitizing nAChRs, linked to early-stage Aβ-induced neurotoxicity, which may represent novel therapeutic targets.
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18
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Káňová E, Tkáčová Z, Bhide K, Kulkarni A, Jiménez-Munguía I, Mertinková P, Drážovská M, Tyagi P, Bhide M. Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq. Sci Rep 2019; 9:18763. [PMID: 31822804 PMCID: PMC6904618 DOI: 10.1038/s41598-019-55409-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 11/28/2019] [Indexed: 01/25/2023] Open
Abstract
Interaction of Neisseria meningitidis (NM) with human brain microvascular endothelial cells (hBMECs) initiates of multiple cellular processes, which allow bacterial translocation across the blood-brain barrier (BBB). NM is equipped with several antigens, which interacts with the host cell receptors. Recently we have shown that adhesin MafA (UniProtKB-X5EG71), relatively less studied protein, is one of those surface exposed antigens that adhere to hBMECs. The present study was designed to comprehensively map the undergoing biological processes in hBMECs challenged with NM or MafA using RNA sequencing. 708 and 726 differentially expressed genes (DEGs) were identified in hBMECs exposed to NM and MafA, respectively. Gene ontology analysis of the DEGs revealed that several biological processes, which may alter the permeability of BBB, were activated. Comparative analysis of DEGs revealed that MafA, alike NM, might provoke TLR-dependent pathway and augment cytokine response. Moreover, both MafA and NM were able to induce genes involved in cell surface modifications, endocytosis, extracellular matrix remodulation and anoikis/apoptosis. In conclusion, this study for the first time describes effect of NM on the global gene expression in hBMECs using high-throughput RNA-seq. It also presents ability of MafA to induce gene expression, which might aid NM in breaching the BBB.
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Affiliation(s)
- Evelína Káňová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Zuzana Tkáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Monika Drážovská
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Punit Tyagi
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04001, Kosice, Slovakia. .,Institute of Neuroimmunology of Slovak Academy of Sciences, 84510, Bratislava, Slovakia.
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19
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Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus. Pathogens 2019; 8:pathogens8040183. [PMID: 31658769 PMCID: PMC6963325 DOI: 10.3390/pathogens8040183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/02/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023] Open
Abstract
Licensed live attenuated vaccines have been developed to prevent varicella zoster virus (VZV) infection, which causes chickenpox and shingles. The genomic sequences of both clinical- and vaccine-derived VZV strains have been analyzed previously. To further characterize the molecular signatures and complexity of wildtype (clinical) versus attenuated (vaccine-derived) VZV-mediated host cellular responses, we performed high-throughput next generation sequencing to quantify and compare the expression patterns of mRNAs and microRNAs (miRNAs) in primary human dermal fibroblasts (HDFs) infected with wildtype (YC01 low passage) and attenuated (YC01 high passage, SuduVax, and VarilRix) VZV strains. 3D-multidimensional scaling of the differentially expressed genes demonstrated the distinct grouping of wildtype and attenuated strains. In particular, we observed that HDFs infected with attenuated strains had more differentially expressed genes (DEGs) involved in the retinoic-acid inducible gene–I-like receptor and interferon-mediated signaling pathways compared with wildtype strains. Additionally, miRNA expression patterns were profiled following the infection of HDFs with VZV. Small RNA sequencing identified that several miRNAs were upregulated, including miR-146a-5p, which has been associated with other herpesvirus infections, whereas let-7a-3p was downregulated in both wildtype and attenuated VZV-infected cells. This study identified genes and miRNAs that may be essential in VZV pathogenesis.
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20
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Wani SA, Sahu AR, Khan RIN, Pandey A, Saxena S, Hosamani N, Malla WA, Chaudhary D, Kanchan S, Sah V, Rajak KK, Muthuchelvan D, Mishra B, Tiwari AK, Sahoo AP, Sajjanar B, Singh YP, Gandham RK, Mishra BP, Singh RK. Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats. Front Immunol 2019; 10:1463. [PMID: 31333643 PMCID: PMC6624447 DOI: 10.3389/fimmu.2019.01463] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/10/2019] [Indexed: 01/06/2023] Open
Abstract
In this study, transcriptome analysis of PPRV infected PBMC subsets-T helper cells, T cytotoxic cells, monocytes, and B lymphocytes was done to delineate their role in host response. PPRV was found to infect lymphocytes and not monocytes. The established receptor for PPRV-SLAM was found downregulated in lymphocytes and non-differentially expressed in monocytes. A profound deviation in the global gene expression profile with a large number of unique upregulated genes (851) and downregulated genes (605) was observed in monocytes in comparison to lymphocytes. ISGs-ISG15, Mx1, Mx2, RSAD2, IFIT3, and IFIT5 that play a role in antiviral response and the genes for viral sensors-MDA5, LGP2, and RIG1, were found to be upregulated in lymphocytes and downregulated in monocytes. The transcription factors-IRF-7 and STAT-1 that regulate expression of most of the ISGs were found activated in lymphocytes and not in monocytes. Interferon signaling pathway and RIG1 like receptor signaling pathway were found activated in lymphocytes and not in monocytes. This contrast in gene expression profiles and signaling pathways indicated the predominant role of lymphocytes in generating the antiviral response against PPRV in goats, thus, giving us new insights into host response to PPRV.
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, United States
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Neelima Hosamani
- Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Dheeraj Chaudhary
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Sonam Kanchan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Vaishali Sah
- Division of Animal Genetics and Breeding, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Aditya P Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Mukteswar, India
| | - Basavaraj Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Yash Pal Singh
- ARIS Cell, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
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21
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Khan A, Shin OS, Na J, Kim JK, Seong RK, Park MS, Noh JY, Song JY, Cheong HJ, Park YH, Kim WJ. A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in Humans. Sci Rep 2019; 9:4760. [PMID: 30886186 PMCID: PMC6423257 DOI: 10.1038/s41598-019-41205-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/27/2019] [Indexed: 01/08/2023] Open
Abstract
Hantavax is an inactivated vaccine for hemorrhagic fever with renal syndrome (HFRS). The immunogenic responses have not been elucidated yet. Here we conducted a cohort study in which 20 healthy subjects were administered four doses of Hantavax during 13-months period. Pre- and post- vaccinated peripheral blood mononuclear cells (PBMCs) and sera were analysed by transcriptomic and metabolomic profilings, respectively. Based on neutralizing antibody titers, subjects were subsequently classified into three groups; non responders (NRs), low responders (LRs) and high responders (HRs). Post vaccination differentially expressed genes (DEGs) associated with innate immunity and cytokine pathways were highly upregulated. DEG analysis revealed a significant induction of CD69 expression in the HRs. High resolution metabolomics (HRM) analysis showed that correlated to the antibody response, cholesteryl nitrolinoleate, octanoyl-carnitine, tyrosine, ubiquinone-9, and benzoate were significantly elevated in HRs, while chenodeoxycholic acid and methyl palmitate were upregulated in NRs and LRs, compared with HRs. Additionally, gene-metabolite interaction revealed upregulated gene-metabolite couplings in, folate biosynthesis, nicotinate and nicotinamide, arachidonic acid, thiamine and pyrimidine metabolism in a dose dependent manner in HR group. Collectively, our data provide new insight into the underlying mechanisms of the Hantavax-mediated immunogenicity in humans.
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Affiliation(s)
- Adnan Khan
- Metabolomics Laboratory, Korea University College of Pharmacy, Sejeong city, Republic of Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jinhyuk Na
- Metabolomics Laboratory, Korea University College of Pharmacy, Sejeong city, Republic of Korea
| | - Jae Kwan Kim
- Metabolomics Laboratory, Korea University College of Pharmacy, Sejeong city, Republic of Korea
| | - Rak-Kyun Seong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Youngja Hwang Park
- Metabolomics Laboratory, Korea University College of Pharmacy, Sejeong city, Republic of Korea.
| | - Woo Joo Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea. .,Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea.
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22
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Park SJ, Kim YI, Park A, Kwon HI, Kim EH, Si YJ, Song MS, Lee CH, Jung K, Shin WJ, Zeng J, Choi Y, Jung JU, Choi YK. Ferret animal model of severe fever with thrombocytopenia syndrome phlebovirus for human lethal infection and pathogenesis. Nat Microbiol 2018; 4:438-446. [PMID: 30531978 DOI: 10.1038/s41564-018-0317-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 11/06/2018] [Indexed: 01/06/2023]
Abstract
Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV), listed in the most dangerous pathogens by the World Health Organization, has 12-30% fatality rates with a characteristic thrombocytopenia syndrome. With a majority of clinically diagnosed SFTSV patients older than ~50 years of age, age is a critical risk factor for SFTSV morbidity and mortality. Here, we report an age-dependent ferret model of SFTSV infection and pathogenesis that fully recapitulates the clinical manifestations of human infections. Whereas young adult ferrets (≤2 years of age) did not show any clinical symptoms and mortality, SFTSV-infected aged ferrets (≥4 years of age) demonstrated severe thrombocytopenia, reduced white blood cell counts and high fever with 93% mortality rate. Moreover, a significantly higher viral load was observed in aged ferrets. Transcriptome analysis of SFTSV-infected young ferrets revealed strong interferon-mediated anti-viral signalling, whereas inflammatory immune responses were markedly upregulated and persisted in aged ferrets. Thus, this immunocompetent age-dependent ferret model should be useful for anti-SFTSV therapy and vaccine development.
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Affiliation(s)
- Su-Jin Park
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Young-Il Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Angela Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hyeok-Il Kwon
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Eun-Ha Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Young-Jae Si
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Min-Suk Song
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Kyle Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Woo-Jin Shin
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jianxiong Zeng
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Younho Choi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Young Ki Choi
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea. .,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Republic of Korea.
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23
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Son Y, Kwon SM, Cho JY. CD276 (B7-H3) Maintains Proliferation and Regulates Differentiation in Angiogenic Function in Late Endothelial Progenitor Cells. Stem Cells 2018; 37:382-394. [PMID: 30379377 DOI: 10.1002/stem.2944] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/22/2018] [Accepted: 10/16/2018] [Indexed: 12/24/2022]
Abstract
Endothelial progenitor cells (EPCs) provide an important source of recovery from blood vessel dysfunction. Late EPCs (LEPCs) are circulating blood cells that are capable of promoting vascular repair. Using transcriptome analysis, we identified distinctive LEPC profiles and found that CD276 (B7-H3) mRNA is strongly expressed in LEPCs. CD276 protein is present abundantly on the cell surface of LEPC when analyzed by fluorescence-activated cell sorter and immunocytochemistry. CD276, a B7 family member, is a type I transmembrane glycoprotein. The role of CD276 in LEPCs remains unknown. CD276 knockdown by lentivirus transduction in LEPCs significantly decreased proliferation and increased apoptosis of LEPCs in vitro. After CD276 silencing, the cell cycle of LEPCs was prone to remain at the G0/G1 phase, and the cell migration rates as well as transwell and wound-healing migration were decreased. CD276 knockdown in LEPCs increased the G1 phase regulators cyclin D2/D3/E1-cyclin-dependent kinases (CDK2/4/6), but decreased the S-G2-M phase regulators cyclin A/B-CDK1. However, LEPCs with CD276 knockdown resulted in increased tube formation in vitro and angiogenesis in a Matrigel plug assay in vivo. FoxC1/C2, an upstream signal of Notch in arterial cell proliferation, and Hey1/2, which is known to promote arterial differentiation in the vasculature, were upregulated in CD276 knockdown LEPCs. In LEPCS, CD276 has a positive effect on proliferation and migration of endothelial cells, but negative effects on angiogenesis, particularly endothelial cell differentiation. Our data indicate, for therapeutic purpose, that CD276 can be used to acquire and maintain cell populations of LEPCs and blocking CD276 will promote angiogenetic differentiation. We found that CD276 (B7-H3) is enriched on the cell membrane of LEPCs. CD276 knockdown reduced proliferation and migration of LEPCs by increasing cell cycle inhibitors such as p21cip1 and pRb and decreasing pErk1/2 and pAkt but promoted angiogenesis and endothelial cell differentiation by elevating vascular endothelial growth factor-vascular endothelial growth factor receptor 1 and p-p38. Stem Cells 2019;37:382-394.
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Affiliation(s)
- YeonSung Son
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Sang-Mo Kwon
- Laboratory for Vascular Medicine & Stem Cell Biology, Medical Research Institute, Department of Physiology, School of Medicine, Pusan National University, Yangsan, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
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24
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Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis FJ. MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data. Gigascience 2018; 7:5036539. [PMID: 29901703 PMCID: PMC6025204 DOI: 10.1093/gigascience/giy070] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts. Findings We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource. Conclusions Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.
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Affiliation(s)
- L M Simon
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - S Karg
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - A J Westermann
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research, Würzburg, Germany
| | - M Engel
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Helmholtz Zentrum München, German Research Center for Environmental Health, Scientific Computing Research Unit, Neuherberg, Germany
| | - A H A Elbehery
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - B Hense
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - M Heinig
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - L Deng
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - F J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Department of Mathematics, Technische Universität München, Munich, Germany
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25
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Frönicke L, Bronner DN, Byndloss MX, McLaughlin B, Bäumler AJ, Westermann AJ. Toward Cell Type-Specific In Vivo Dual RNA-Seq. Methods Enzymol 2018; 612:505-522. [PMID: 30502956 DOI: 10.1016/bs.mie.2018.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Dual RNA-seq has emerged as a genome-wide expression profiling technique, simultaneously measuring RNA transcript levels in a given host and its pathogen during an infection. Recently, the method was transferred from cell culture to in vivo models of bacterial infections; however, specific host cell-type resolution has not yet been achieved. Here we present a detailed protocol that describes the application of Dual RNA-seq to murine colonocytes isolated from mice infected with the enteric pathogen Salmonella Typhimurium. At day 5 after oral infection, the mice were humanely euthanized, their colons extracted, and colonocytes isolated and fixed. Upon antibody staining of cell type-specific surface markers, the fraction of Salmonella-invaded colonocytes was collected by fluorescence-activated cell sorting based on a fluorescent signal emitted by the internalized bacteria. Total RNA was extracted from cells enriched by this method, and ribosomal transcripts from host and microbial cells were removed prior to cDNA synthesis and library generation. We compared different protocols for library preparation and discuss their respective advantages and caveats when applied to minute RNA amounts that constitute an inherent challenge for in vivo transcriptomics. Our results introduce an ultralow input protocol that holds promise for cell type-specific in vivo Dual RNA-seq for charting gene expression of a bacterial pathogen within its respective in vivo niche, along with the consequent host response.
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Affiliation(s)
- Lutz Frönicke
- University of California Davis Genome Center, Davis, CA, United States
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Bridget McLaughlin
- Comprehensive Cancer Center Flow Cytometry Shared Resource, University of California Davis, Davis, CA, United States
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany.
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26
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TLR4-mediated activation of the ERK pathway following UVA irradiation contributes to increased cytokine and MMP expression in senescent human dermal fibroblasts. PLoS One 2018; 13:e0202323. [PMID: 30118525 PMCID: PMC6097681 DOI: 10.1371/journal.pone.0202323] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/01/2018] [Indexed: 02/02/2023] Open
Abstract
Exposure to ultraviolet (UV) radiation is a major contributing factor to premature aging (photoaging) and skin cancer. In vitro models of cellular senescence have proven to be very useful for the study of slow and progressive accumulation of damage resulting in the growth arrest of aging skin cells. In this study, we compared UVA-induced cellular responses in non-senescent (NS) vs. senescent (S) human dermal fibroblasts (HDFs). HDFs were irradiated with a single dose of UVA (7.5 J/cm2) and QuantSeq 3' mRNA sequencing was performed to assess differential gene expression. Both NS and S HDFs expressed similar numbers of differentially expressed genes, although distinct sets of genes were differentially expressed between the two groups. Higher expression of matrix metalloproteinases (MMPs) and Toll-like receptor (TLR) pathway genes, such as TLR4, MyD88, and CXCL-8, was detected in S HDFs as compared with NS HDFs, and UVA exposure led to a downregulation of collagen genes, such as COL8A2 and COL5A3. Consistent with gene expression profiling, enhanced IL-6 and IL-8 secretion was observed in S HDFs compared with NS HDFs, in response to UVA. Furthermore, we show that TLR4-mediated ERK pathway is responsible for the UVA-mediated mitochondrial dysfunction as well as increased secretion of MMP-1 and IL-8 in S HDFs. Taken together, our results demonstrate the UVA-induced common and distinct molecular patterns of cellular responses between NS and S HDFs and suggest TLR4/ERK pathways as candidate targets to reduce senescent phenotypes.
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27
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Strand-Specific Dual RNA Sequencing of Bronchial Epithelial Cells Infected with Influenza A/H3N2 Viruses Reveals Splicing of Gene Segment 6 and Novel Host-Virus Interactions. J Virol 2018; 92:JVI.00518-18. [PMID: 29976658 DOI: 10.1128/jvi.00518-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/24/2018] [Indexed: 02/08/2023] Open
Abstract
Host-influenza virus interplay at the transcript level has been extensively characterized in epithelial cells. Yet, there are no studies that simultaneously characterize human host and influenza A virus (IAV) genomes. We infected human bronchial epithelial BEAS-2B cells with two seasonal IAV/H3N2 strains, Brisbane/10/07 and Perth/16/09 (reference strains for past vaccine seasons) and the well-characterized laboratory strain Udorn/307/72. Strand-specific RNA sequencing (RNA-seq) of the infected BEAS-2B cells allowed for simultaneous analysis of host and viral transcriptomes, in addition to pathogen genomes, to reveal changes in mRNA expression and alternative splicing (AS). In general, patterns of global and immune gene expression induced by the three IAVs were mostly shared. However, AS of host transcripts and small nuclear RNAs differed between the seasonal and laboratory strains. Analysis of viral transcriptomes showed deletions of the polymerase components (defective interfering-like RNAs) within the genome. Surprisingly, we found that the neuraminidase gene undergoes AS and that the splicing event differs between seasonal and laboratory strains. Our findings reveal novel elements of the host-virus interaction and highlight the importance of RNA-seq in identifying molecular changes at the genome level that may contribute to shaping RNA-based innate immunity.IMPORTANCE The use of massively parallel RNA sequencing (RNA-seq) has revealed insights into human and pathogen genomes and their evolution. Dual RNA-seq allows simultaneous dissection of host and pathogen genomes and strand-specific RNA-seq provides information about the polarity of the RNA. This is important in the case of negative-strand RNA viruses like influenza virus, which generate positive (complementary and mRNA) and negative-strand RNAs (genome) that differ in their potential to trigger innate immunity. Here, we characterize interactions between human bronchial epithelial cells and three influenza A/H3N2 strains using strand-specific dual RNA-seq. We focused on this subtype because of its epidemiological importance in causing significant morbidity and mortality during influenza epidemics. We report novel elements that differ between seasonal and laboratory strains highlighting the complexity of the host-virus interplay at the RNA level.
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28
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Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiol Mol Biol Rev 2018; 82:e00071-17. [PMID: 29695497 PMCID: PMC5968457 DOI: 10.1128/mmbr.00071-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.
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Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Thomas D Otto
- Centre of Immunobiology, University of Glasgow, Glasgow, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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29
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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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30
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Oh SJ, Choi YK, Shin OS. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases. Yonsei Med J 2018; 59:176-186. [PMID: 29436184 PMCID: PMC5823818 DOI: 10.3349/ymj.2018.59.2.176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/29/2022] Open
Abstract
Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs.
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Affiliation(s)
- Soo Jin Oh
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea.
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31
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Zhang N, Bao YJ, Tong AHY, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SMY. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection. BMC Med Genomics 2018; 11:20. [PMID: 29475453 PMCID: PMC6389164 DOI: 10.1186/s12920-018-0335-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood. Methods To obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection. Results Our data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to pathophysiology of H5N1 virus infection. Conclusions Our study provides important mechanistic insights into the understanding of H5N1 viral pathogenesis and the multi-faceted host immune responses. The dysregulated genes could be potential candidates as therapeutic targets for treating H5N1 disease. Electronic supplementary material The online version of this article (10.1186/s12920-018-0335-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Na Zhang
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China
| | - Yun-Juan Bao
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, USA
| | - Amy Hin-Yan Tong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - J S Malik Peiris
- HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Si Lok
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, China. .,The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada.
| | - Suki Man-Yan Lee
- HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China.
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Cao Y, Cao R, Huang Y, Zhou H, Liu Y, Li X, Zhong W, Hao P. A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza a viruses. BMC Genomics 2018; 19:925. [PMID: 29363430 PMCID: PMC5780764 DOI: 10.1186/s12864-017-4330-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pathways. Cellular RNA editing activity in response to influenza A virus infection has not been fully characterized in human and avian hosts. This study was designed as a big data analysis to investigate the role and response of RNA editing in epithelial cells during the course of infection with various subtypes of influenza A viruses. Results Using a bioinformatics pipeline modified from our previous study, we characterized the profiles of A-to-I and C-to-U RNA editing events in human epithelial cells during the course of influenza A virus infection. Our results revealed a striking diversity of A-to-I RNA editing activities in human epithelial cells in responses to different subtypes of influenza A viruses. The infection of H1N1 and H3N2 significantly up-regulated normalized A-to-I RNA editing levels in human epithelial cells, whereas that of H5N1 did not change it and H7N9 infection significantly down-regulated normalized A-to-I editing level in A549 cells. Next, the expression levels of ADAR and APOBEC enzymes responsible for A-to-I and C-to-U RNA editing during the course of virus infection were examined. The increase of A-to-I RNA editing activities in infections with some influenza A viruses (H1N1 and H3N2) is linked to the up-regulation of ADAR1 but not ADAR2. Further, the pattern recognition receptors of human epithelial cells infected with H1N1, H3N2, H5N1 and H7N9 were examined. Variable responsive changes in gene expression were observed with RIG-I like receptors and Toll like receptors. Finally, the effect of influenza A virus infection on cellular RNA editing activity was also analyzed in avian hosts. Conclusion This work represents the first comprehensive study of cellular RNA editing activity in response to different influenza A virus infections in human and avian hosts, highlighting the critical role of RNA editing in innate immune response and the pathogenicity of different subtypes of influenza A viruses. Electronic supplementary material The online version of this article (10.1186/s12864-017-4330-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Cao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Ruiyuan Cao
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yaowei Huang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Hongxia Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Wu Zhong
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China.
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Sarker S, Wang Y, Warren-Smith B, Helbig KJ. Dynamic Changes in Host Gene Expression following In Vitro Viral Mimic Stimulation in Crocodile Cells. Front Immunol 2017; 8:1634. [PMID: 29213275 PMCID: PMC5702629 DOI: 10.3389/fimmu.2017.01634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/09/2017] [Indexed: 11/21/2022] Open
Abstract
The initial control of viral infection in a host is dominated by a very well orchestrated early innate immune system; however, very little is known about the ability of a host to control viral infection outside of mammals. The reptiles offer an evolutionary bridge between the fish and mammals, with the crocodile having evolved from the archosauria clade that included the dinosaurs, and being the largest living reptile species. Using an RNA-seq approach, we have defined the dynamic changes of a passaged primary crocodile cell line to stimulation with both RNA and DNA viral mimics. Cells displayed a marked upregulation of many genes known to be involved in the mammalian response to viral infection, including viperin, Mx1, IRF7, IRF1, and RIG-I with approximately 10% of the genes being uncharacterized transcripts. Both pathway and genome analysis suggested that the crocodile may utilize the main known mammalian TLR and cytosolic antiviral RNA signaling pathways, with the pathways being responsible for sensing DNA viruses less clear. Viral mimic stimulation upregulated the type I interferon, IFN-Omega, with many known antiviral interferon-stimulated genes also being upregulated. This work demonstrates for the first time that reptiles show functional regulation of many known and unknown antiviral pathways and effector genes. An enhanced knowledge of these ancient antiviral pathways will not only add to our understanding of the host antiviral innate response in non-mammalian species, but is critical to fully comprehend the complexity of the mammalian innate immune response to viral infection.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Yinan Wang
- Genomics Research Platform, La Trobe University, Melbourne, VIC, Australia
| | - Brenden Warren-Smith
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Karla J Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
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Virulence of an H5N8 highly pathogenic avian influenza is enhanced by the amino acid substitutions PB2 E627K and HA A149V. INFECTION GENETICS AND EVOLUTION 2017; 54:347-354. [PMID: 28750900 DOI: 10.1016/j.meegid.2017.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/05/2017] [Accepted: 07/24/2017] [Indexed: 11/23/2022]
Abstract
A novel reassortant H5N8 highly pathogenic avian influenza (HPAI) virus was recently identified in Asia, Europe, and North America. The H5N8 HPAI virus has raised serious concerns regarding the potential risk for human infection. However, the molecular changes responsible for allowing mammalian infection in H5N8 HPAI viruses are not clear. The objective of this study was to identify amino acid substitutions that are potentially associated with the adaptation of H5N8 HPAI viruses to mammals. In this study, an avian-origin H5N8 virus was adapted to mice through serial lung-to-lung passage. The virulence of mouse-adapted virus was increased and adaptive mutations, HA (A149V) and PB2 (E627K), were detected after the ninth passage in each series of mice. Reverse genetics were used to generate reassortants of the wild type and mouse-adapted viruses. Substitutions in the HA (A149V) and PB2 (E627K) proteins led to enhanced viral virulence in mice, the viruses displayed expanded tissue tropism, and increased replication kinetics in mammalian cells. Continued surveillance in poultry for amino acid changes that might indicate H5N8 HPAI viruses pose a threat to human health is required.
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Influenza-Omics and the Host Response: Recent Advances and Future Prospects. Pathogens 2017; 6:pathogens6020025. [PMID: 28604586 PMCID: PMC5488659 DOI: 10.3390/pathogens6020025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza A viruses (IAV) continually evolve and have the capacity to cause global pandemics. Because IAV represents an ongoing threat, identifying novel therapies and host innate immune factors that contribute to IAV pathogenesis is of considerable interest. This review summarizes the relevant literature as it relates to global host responses to influenza infection at both the proteome and transcriptome level. The various-omics infection systems that include but are not limited to ferrets, mice, pigs, and even the controlled infection of humans are reviewed. Discussion focuses on recent advances, remaining challenges, and knowledge gaps as it relates to influenza-omics infection outcomes.
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Zhou B, Li J, Liang X, Yang Z, Jiang Z. Transcriptome profiling of influenza A virus-infected lung epithelial (A549) cells with lariciresinol-4-β-D-glucopyranoside treatment. PLoS One 2017; 12:e0173058. [PMID: 28273165 PMCID: PMC5342222 DOI: 10.1371/journal.pone.0173058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
The influenza A virus is an acute contagious pathogen that affects the human respiratory system and can cause severe lung disease and even death. Lariciresinol-4-β-D-glucopyranoside is a lignan that is extracted from Isatis indigotica, which is a medicinal herb plant that was commonly applied to treat infections, the common cold, fever and inflammatory diseases. Our previous study demonstrated that lariciresinol-4-β-D-glucopyranoside possesses anti-viral and anti-inflammatory properties. However, the comprehensive and detailed mechanisms that underlie the effect of lariciresinol-4-β-D-glucopyranoside interventions against influenza virus infection remain to be elucidated. In this study, we employed high-throughput RNA sequencing (RNA-seq) to investigate the transcriptomic responses of influenza A virus-infected lung epithelial (A549) cells with lariciresinol-4-β-D-glucopyranoside treatment. The transcriptome data show that infection with influenza A virus prompted the activation of 368 genes involved in RIG-I signalling, the inflammatory response, interferon α/β signalling and gene expression that was not affected by lariciresinol-4-β-D-glucopyranoside treatment. Lariciresinol-4-β-D-glucopyranoside exerted its pharmacological actions on the immune system, signal transduction, cell cycle and metabolism, which may be an underlying defense mechanism against influenza virus infection. In addition, 166 differentially expressed genes (DEGs) were uniquely expressed in lariciresinol-4-β-D-glucopyranoside-treated cells, which were concentrated in the cell cycle, DNA repair, chromatin organization, gene expression and biosynthesis domains. Among them, six telomere-associated genes were up-regulated by lariciresinol-4-β-D-glucopyranoside treatment, which have been implicated in telomere regulation and stability. Collectively, we employed RNA-seq analysis to provide comprehensive insight into the mechanism of lariciresinol-4-β-D-glucopyranoside against influenza virus infection.
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Affiliation(s)
- Beixian Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Jing Li
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, National Clinical Centre of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiaoli Liang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, National Clinical Centre of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zifeng Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, National Clinical Centre of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- * E-mail: (ZFY); (ZHJ)
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (ZFY); (ZHJ)
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Seong RK, Choi YK, Shin OS. MDA7/IL-24 is an anti-viral factor that inhibits influenza virus replication. J Microbiol 2016; 54:695-700. [DOI: 10.1007/s12275-016-6383-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 01/10/2023]
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Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis. Sci Rep 2016; 6:26350. [PMID: 27211830 PMCID: PMC4876452 DOI: 10.1038/srep26350] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/26/2016] [Indexed: 01/23/2023] Open
Abstract
Differential host responses may be critical determinants of distinct pathologies of West Nile virus (WNV) NY99 (pathogenic) and WNV Eg101 (non-pathogenic) strains. We employed RNA-seq technology to analyze global differential gene expression in WNV-infected mice brain and to identify the host cellular factors leading to lethal encephalitis. We identified 1,400 and 278 transcripts, which were differentially expressed after WNV NY99 and WNV Eg101 infections, respectively, and 147 genes were common to infection with both the viruses. Genes that were up-regulated in infection with both the viruses were mainly associated with interferon signaling. Genes associated with inflammation and cell death/apoptosis were only expressed after WNV NY99 infection. We demonstrate that differences in the activation of key pattern recognition receptors resulted in the induction of unique innate immune profiles, which corresponded with the induction of interferon and inflammatory responses. Pathway analysis of differentially expressed genes indicated that after WNV NY99 infection, TREM-1 mediated activation of toll-like receptors leads to the high inflammatory response. In conclusion, we have identified both common and specific responses to WNV NY99 and WNV Eg101 infections as well as genes linked to potential resistance to infection that may be targets for therapeutics.
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