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Badu P, Baniulyte G, Sammons MA, Pager CT. Activation of ATF3 via the integrated stress response pathway regulates innate immune response to restrict Zika virus. J Virol 2024:e0105524. [PMID: 39212382 DOI: 10.1128/jvi.01055-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that can have devastating health consequences. The developmental and neurological effects of a ZIKV infection arise in part from the virus triggering cellular stress pathways and perturbing transcriptional programs. To date, the underlying mechanisms of transcriptional control directing viral restriction and virus-host interaction are understudied. Activating Transcription Factor 3 (ATF3) is a stress-induced transcriptional effector that modulates the expression of genes involved in a myriad of cellular processes, including inflammation and antiviral responses, to restore cellular homeostasis. While ATF3 is known to be upregulated during ZIKV infection, the mode by which ATF3 is activated, and the specific role of ATF3 during ZIKV infection is unknown. In this study, we show via inhibitor and RNA interference approaches that ZIKV infection initiates the integrated stress response pathway to activate ATF4 which in turn induces ATF3 expression. Additionally, by using CRISPR-Cas9 system to delete ATF3, we found that ATF3 acts to limit ZIKV gene expression in A549 cells. We also determined that ATF3 enhances the expression of antiviral genes such as STAT1 and other components in the innate immunity pathway to induce an ATF3-dependent anti-ZIKV response. Our study reveals crosstalk between the integrated stress response and innate immune response pathways and highlights an important role for ATF3 in establishing an antiviral effect during ZIKV infection. IMPORTANCE Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that co-opts cellular mechanisms to support viral processes that can reprogram the host transcriptional profile. Such viral-directed transcriptional changes and the pro- or anti-viral outcomes remain understudied. We previously showed that ATF3, a stress-induced transcription factor, is significantly upregulated in ZIKV-infected mammalian cells, along with other cellular and immune response genes. We now define the intracellular pathway responsible for ATF3 activation and elucidate the impact of ATF3 expression on ZIKV infection. We show that during ZIKV infection, the integrated stress response pathway stimulates ATF3 which enhances the innate immune response to antagonize ZIKV infection. This study establishes a link between viral-induced stress response and transcriptional regulation of host defense pathways and thus expands our knowledge of virus-mediated transcriptional mechanisms and transcriptional control of interferon-stimulated genes during ZIKV infection.
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Affiliation(s)
- Pheonah Badu
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Gabriele Baniulyte
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Morgan A Sammons
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Cara T Pager
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
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Kousa YA, Singh S, Horvath A, Tomasso F, Nazarian J, Henderson L, Mansour TA. Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika's Oncolytic Impact in Glioblastoma Multiforme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.04.605859. [PMID: 39372798 PMCID: PMC11452190 DOI: 10.1101/2024.08.04.605859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Glioblastoma multiforme (GBM) is an aggressive and lethal form of brain cancer with few effective treatments. In this context, Zika virus has emerged as a promising therapeutic agent due to its ability to selectively infect and kill GBM cells. To elucidate these mechanisms and expand the landscape of oncolytic virotherapy, we pursued a transcriptomic meta-analysis comparing the molecular signatures of Zika infection in GBM and neuroblastoma (NBM). Over-representation analysis of dysregulated coding genes showed significant enrichment of tumor necrosis factor (TNF), NF-κB, and p53 signaling pathways. A refined list of long non-coding RNAs consistently dysregulated in Zika-infected GBMs was also developed. Functional review of these candidates revealed their potential regulatory role in Zika-mediated oncolysis. We performed validation of the less-researched targets in adult and pediatric GBM cell lines and found significant differential regulation, as predicted. Altogether, our results provide novel insights into the molecular mechanisms underlying the effect of Zika on GBM. We highlight potential therapeutic targets that could be further interrogated to improve the efficacy of tumor cell death and the utility of Zika as an adjuvant virotherapy for GBM and other related cancers.
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Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Transcriptomic Signatures of Zika Virus Infection in Patients and a Cell Culture Model. Microorganisms 2024; 12:1499. [PMID: 39065267 PMCID: PMC11278784 DOI: 10.3390/microorganisms12071499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
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Affiliation(s)
- Gillian Berglund
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Claudia D. Lennon
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Pheonah Badu
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - John Andrew Berglund
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T. Pager
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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4
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Badu P, Baniulyte G, Sammons MA, Pager CT. Activation of ATF3 via the Integrated Stress Response Pathway Regulates Innate Immune Response to Restrict Zika Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550716. [PMID: 37546954 PMCID: PMC10402074 DOI: 10.1101/2023.07.26.550716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that can have devastating health consequences. The developmental and neurological effects from a ZIKV infection arise in part from the virus triggering cellular stress pathways and perturbing transcriptional programs. To date, the underlying mechanisms of transcriptional control directing viral restriction and virus-host interaction are understudied. Activating Transcription Factor 3 (ATF3) is a stress-induced transcriptional effector that modulates the expression of genes involved in a myriad of cellular processes, including inflammation and antiviral responses, to restore cellular homeostasis. While ATF3 is known to be upregulated during ZIKV infection, the mode by which ATF3 is activated and the specific role of ATF3 during ZIKV infection is unknown. In this study, we show via inhibitor and RNA interference approaches that ZIKV infection initiates the integrated stress response pathway to activate ATF4 which in turn induces ATF3 expression. Additionally, by using CRISPR-Cas9 system to delete ATF3, we found that ATF3 acts to limit ZIKV gene expression in A549 cells. We also determined that ATF3 enhances the expression of antiviral genes such as STAT1 and other components in the innate immunity pathway to induce an ATF3-dependent anti-ZIKV response. Our study reveals crosstalk between the integrated stress response and innate immune response pathways and highlights an important role for ATF3 in establishing an antiviral effect during ZIKV infection.
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Affiliation(s)
- Pheonah Badu
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
| | - Gabriele Baniulyte
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
| | - Morgan A. Sammons
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
| | - Cara T. Pager
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222
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Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595842. [PMID: 38826459 PMCID: PMC11142252 DOI: 10.1101/2024.05.25.595842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
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Affiliation(s)
- Gillian Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Claudia D. Lennon
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Pheonah Badu
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - J. Andrew Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T. Pager
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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Sherwood M, Zhou Y, Sui Y, Wang Y, Skipp P, Kaid C, Gray J, Okamoto K, Ewing RM. Integrated re-analysis of transcriptomic and proteomic datasets reveals potential mechanisms for Zika viral-based oncolytic therapy in neuroblastoma. F1000Res 2024; 12:719. [PMID: 38903860 PMCID: PMC11187533 DOI: 10.12688/f1000research.132627.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Background Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is poor despite intensive multi-modal therapies with significant toxicity. Novel therapies are desperately needed. The Zika virus (ZIKV) can access the nervous system and there is growing interest in employing ZIKV as a potential therapy against paediatric nervous system tumours, including neuroblastoma. Methods Here, we perform extensive data mining, integration and re-analysis of ZIKV infection datasets to highlight molecular mechanisms that may govern the oncolytic response in neuroblastoma cells. We collate infection data of multiple neuroblastoma cell lines by different ZIKV strains from a body of published literature to inform the susceptibility of neuroblastoma to the ZIKV oncolytic response. Integrating published transcriptomics, interaction proteomics, dependency factor and compound datasets we propose the involvement of multiple host systems during ZIKV infection. Results Through data mining of published literature, we observed most paediatric neuroblastoma cell lines to be highly susceptible to ZIKV infection and propose the PRVABC59 ZIKV strain to be the most promising candidate for neuroblastoma oncolytic virotherapy. ZIKV induces TNF signalling, lipid metabolism, the Unfolded Protein Response (UPR), and downregulates cell cycle and DNA replication processes. ZIKV infection is dependent on sterol regulatory element binding protein (SREBP)-regulated lipid metabolism and three protein complexes; V-ATPase, ER Membrane Protein Complex (EMC) and mammalian translocon. We propose ZIKV non-structural protein 4B (NS4B) as a likely mediator of ZIKVs interaction with IRE1-mediated UPR, lipid metabolism and mammalian translocon. Conclusions Our work provides a significant understanding of ZIKV infection in neuroblastoma cells, which will facilitate the progression of ZIKV-based oncolytic virotherapy through pre-clinical research and clinical trials.
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Affiliation(s)
- Matt Sherwood
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yilu Zhou
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yi Sui
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yihua Wang
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Paul Skipp
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Carolini Kaid
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Juliet Gray
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, England, UK
| | - Keith Okamoto
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Rob M. Ewing
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
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Lin C, Zeng M, Song J, Li H, Feng Z, Li K, Pei Y. PRRSV alters m 6A methylation and alternative splicing to regulate immune, extracellular matrix-associated function. Int J Biol Macromol 2023; 253:126741. [PMID: 37696370 DOI: 10.1016/j.ijbiomac.2023.126741] [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: 11/17/2022] [Revised: 08/07/2023] [Accepted: 08/25/2023] [Indexed: 09/13/2023]
Abstract
The alternative splicing and N6-methyladenosine (m6A) modifications occurring during porcine reproductive and respiratory syndrome virus (PRRSV) infections remain poorly understood. Transcriptome and MeRIP-seq analyses were performed to identify the gene expression changes, splicing and m6A modifications in the lungs of PRRSV-infected pigs. In total, 1624 differentially expressed genes (DEGs) were observed between PRRSV-infected and uninfected pigs. We observed significant alterations in alternative splicing (54,367 events) and m6A modifications (2265 DASEs) in numerous genes, including LMO7, SLC25A27, ZNF185, and ECM1, during PRRSV infection. LMO7 and ZNF185 exhibited alternative splicing variants and reduced mRNA expression levels following PRRSV infection. Notably, LMO7 inhibited c-JUN, SMAD3, and FAK expression, whereas ZNF185 affected the expression of FAK, CDH1, and GSK3β downstream. Additionally, ECM1 influenced FAK expression by targeting ITGB3 and AKT2, suggesting its involvement in extracellular matrix accumulation through the ITGB3-AKT2/FAK pathway. These changes may facilitate viral invasion and replication by modulating the expression of genes and proteins participating in crucial cellular processes associated with immunity and the extracellular matrix. We highlight the importance of these genes and their associated pathways in PRRSV infections and suggest that targeting these may be a promising therapeutic approach for treating viral infections.
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Affiliation(s)
- Chenghong Lin
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Mu Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jia Song
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
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Pei Y, Lin C, Li H, Feng Z. Genetic background influences pig responses to porcine reproductive and respiratory syndrome virus. Front Vet Sci 2023; 10:1289570. [PMID: 37929286 PMCID: PMC10623566 DOI: 10.3389/fvets.2023.1289570] [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: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly infectious and economically significant virus that causes respiratory and reproductive diseases in pigs. It results in reduced productivity and increased mortality in pigs, causing substantial economic losses in the industry. Understanding the factors affecting pig responses to PRRSV is crucial to develop effective control strategies. Genetic background has emerged as a significant determinant of susceptibility and resistance to PRRSV in pigs. This review provides an overview of the basic infection process of PRRSV in pigs, associated symptoms, underlying immune mechanisms, and roles of noncoding RNA and alternative splicing in PRRSV infection. Moreover, it emphasized breed-specific variations in these aspects that may have implications for individual treatment options.
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Affiliation(s)
- Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Chenghong Lin
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
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Mehta P, Chattopadhyay P, Ravi V, Tarai B, Budhiraja S, Pandey R. SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing. Microbiol Spectr 2023; 11:e0135123. [PMID: 37604131 PMCID: PMC10580830 DOI: 10.1128/spectrum.01351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023] Open
Abstract
Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism. IMPORTANCE The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.
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Affiliation(s)
- Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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10
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Brand C, Deschamps-Francoeur G, Bullard-Feibelman KM, Scott MS, Geiss BJ, Bisaillon M. Kunjin Virus, Zika Virus, and Yellow Fever Virus Infections Have Distinct Effects on the Coding Transcriptome and Proteome of Brain-Derived U87 Cells. Viruses 2023; 15:1419. [PMID: 37515107 PMCID: PMC10385720 DOI: 10.3390/v15071419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
As obligate intracellular parasites, viruses rely heavily on host cells for replication, and therefore dysregulate several cellular processes for their benefit. In return, host cells activate multiple signaling pathways to limit viral replication and eradicate viruses. The present study explores the complex interplay between viruses and host cells through next generation RNA sequencing as well as mass spectrometry (SILAC). Both the coding transcriptome and the proteome of human brain-derived U87 cells infected with Kunjin virus, Zika virus, or Yellow Fever virus were compared to the transcriptome and the proteome of mock-infected cells. Changes in the abundance of several hundred mRNAs and proteins were found in each infection. Moreover, the alternative splicing of hundreds of mRNAs was found to be modulated upon viral infection. Interestingly, a significant disconnect between the changes in the transcriptome and those in the proteome of infected cells was observed. These findings provide a global view of the coding transcriptome and the proteome of Flavivirus-infected cells, leading to a better comprehension of Flavivirus-host interactions.
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Affiliation(s)
- Carolin Brand
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada; (C.B.); (G.D.-F.); (M.S.S.)
| | - Gabrielle Deschamps-Francoeur
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada; (C.B.); (G.D.-F.); (M.S.S.)
| | - Kristen M. Bullard-Feibelman
- Department of Microbiology, Immunology, and Pathology, School of Biomedical Engineering, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA; (K.M.B.-F.); (B.J.G.)
| | - Michelle S. Scott
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada; (C.B.); (G.D.-F.); (M.S.S.)
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, School of Biomedical Engineering, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA; (K.M.B.-F.); (B.J.G.)
| | - Martin Bisaillon
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada; (C.B.); (G.D.-F.); (M.S.S.)
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11
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Li R, Gao S, Chen H, Zhang X, Yang X, Zhao J, Wang Z. Virus usurps alternative splicing to clear the decks for infection. Virol J 2023; 20:131. [PMID: 37340420 DOI: 10.1186/s12985-023-02098-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Since invasion, there will be a tug-of-war between host and virus to scramble cellular resources, for either restraining or facilitating infection. Alternative splicing (AS) is a conserved and critical mechanism of processing pre-mRNA into mRNAs to increase protein diversity in eukaryotes. Notably, this kind of post-transcriptional regulatory mechanism has gained appreciation since it is widely involved in virus infection. Here, we highlight the important roles of AS in regulating viral protein expression and how virus in turn hijacks AS to antagonize host immune response. This review will widen the understandings of host-virus interactions, be meaningful to innovatively elucidate viral pathogenesis, and provide novel targets for developing antiviral drugs in the future.
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Affiliation(s)
- Ruixue Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Shenyan Gao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Huayuan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, People's Republic of China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Zeng Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China.
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12
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Xu Y, Zhu J, Huang W, Xu K, Yang R, Zhang QC, Sun L. PrismNet: predicting protein-RNA interaction using in vivo RNA structural information. Nucleic Acids Res 2023:7151359. [PMID: 37140045 DOI: 10.1093/nar/gkad353] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/13/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Fundamental to post-transcriptional regulation, the in vivo binding of RNA binding proteins (RBPs) on their RNA targets heavily depends on RNA structures. To date, most methods for RBP-RNA interaction prediction are based on RNA structures predicted from sequences, which do not consider the various intracellular environments and thus cannot predict cell type-specific RBP-RNA interactions. Here, we present a web server PrismNet that uses a deep learning tool to integrate in vivo RNA secondary structures measured by icSHAPE experiments with RBP binding site information from UV cross-linking and immunoprecipitation in the same cell lines to predict cell type-specific RBP-RNA interactions. Taking an RBP and an RNA region with sequential and structural information as input ('Sequence & Structure' mode), PrismNet outputs the binding probability of the RBP and this RNA region, together with a saliency map and a sequence-structure integrative motif. The web server is freely available at http://prismnetweb.zhanglab.net.
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Affiliation(s)
- Yiran Xu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wenze Huang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Rui Yang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Lei Sun
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
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13
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da Silva EV, Fontes-Dantas FL, Dantas TV, Dutra A, Nascimento OJM, Alves-Leon SV. Shared Molecular Signatures Across Zika Virus Infection and Multiple Sclerosis Highlight AP-1 Transcription Factor as a Potential Player in Post-ZIKV MS-Like Phenotypes. Mol Neurobiol 2023:10.1007/s12035-023-03305-y. [PMID: 37046138 DOI: 10.1007/s12035-023-03305-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/08/2023] [Indexed: 04/14/2023]
Abstract
Zika virus (ZIKV) is an arbovirus of the Flaviviridae genus that has rapidly disseminated from across the Pacific to the Americas. Robust evidence has indicated a crucial role of ZIKV in congenital virus syndrome, including neonatal microcephaly. Moreover, emerging evidence suggests an association between ZIKV infection and the development of an extensive spectrum of central nervous system inflammatory demyelinating diseases (CNS IDD), such as multiple sclerosis-like clinical phenotypes. However, the underlying mechanisms of host-pathogen neuro-immune interactions remain to be elucidated. This study aimed to identify common transcriptional signatures between multiple sclerosis (MS) and ZIKV infection to generate molecular interaction networks, thereby leading to the identification of deregulated processes and pathways, which could give an insight of these underlying molecular mechanisms. Our investigation included publicly available transcriptomic data from MS patients in either relapse or remission (RR-MS) and datasets of subjects acutely infected by ZIKV for both immune peripheral cells and central nervous system cells. The protein-protein interaction (PPI) analysis showed upregulated AP-1 transcription factors (JUN and FOS) among the top hub and bottleneck genes in RR-MS and ZIKV data. Gene enrichment analysis retrieved a remarkable presence of ontologies and pathways linked to oxidative stress responses, immune cell function, inflammation, interleukin signaling, cell division, and transcriptional regulation commonly enriched in both scenarios. Considering the recent findings concerning AP-1 function in immunological tolerance breakdown, regulation of inflammation, and its function as an oxidative stress sensor, we postulate that the ZIKV trigger may contribute as a boost for the activation of such AP-1-regulated mechanisms that could favor the development of MS-like phenotypes following ZIKV infection in a genetically susceptible individual.
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Affiliation(s)
- Elielson Veloso da Silva
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de pós-graduação em Medicina (Neurologia/Neurociências), Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Farmacologia e Psicobiologia, Instituto de Biologia Roberto Alcântara Gomes, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago Viana Dantas
- Programa de Engenharia de Sistemas e Computação-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Dutra
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Osvaldo J M Nascimento
- Programa de pós-graduação em Medicina (Neurologia/Neurociências), Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Soniza Vieira Alves-Leon
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
- Hospital Universitário Clementino Fraga Filho, Centro de Referência em Doenças Inflamatórias Desmielinizantes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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14
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Dong CL, Zhu F, Du YZ, Lu MX. Depending on different apoptosis pathways, the effector Cscaspase-3 in Chilo suppressalis exposed to temperature and parasitic stress was induced. Int J Biol Macromol 2023; 238:124270. [PMID: 37003373 DOI: 10.1016/j.ijbiomac.2023.124270] [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: 02/21/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Apoptosis is a form of programmed cell death (PCD) that is largely triggered by caspases through both the mitochondria-dependent and mitochondria-independent pathways. The rice stem borer, Chilo suppressalis, serves as an economically important pest of rice, which is often suffered by temperature and parasitic stress under natural conditions. In the present study, effector Cscaspase-3 encoding caspase was obtained from the rice pest Chilo suppressalis. CsCaspase-3 possesses p20 and p10 subunits, two active sites, four substrate-binding sites, and two cleavage motifs. Real-time quantitative PCR showed that Cscaspase-3 was expressed at maximal levels in hemocytes; furthermore, transcription was most highly in female adults. Expression of Cscaspase-3 was induced by hot and cold temperatures, with the highest expression at 39 °C. Cscaspase-3 expression was also significantly induced at 10 h, 2 d, 5 d, and 7 d of parasitism. Flow cytometry results showed that both temperature and parasitism trigger apoptosis, but only parasitism induces apoptosis via the mitochondrial apoptosis pathway in C. suppressalis. RNAi-mediated silencing of Cscaspase-3 expression reduced C. suppressalis survival at -3 °C. This study provides a foundation for further studies of caspases in insects during biotic and abiotic stress.
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Affiliation(s)
- Chuan-Lei Dong
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China
| | - Feng Zhu
- Plant Protection and Quarantine Station of Jiangsu Province, Nanjing 210000, PR China
| | - Yu-Zhou Du
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Ming-Xing Lu
- College of Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China.
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15
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Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
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Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
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16
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Genome-wide characterization of alternative splicing in blood cells of COVID-19 and respiratory infections of relevance. Virol Sin 2023; 38:309-312. [PMID: 36690184 PMCID: PMC9854207 DOI: 10.1016/j.virs.2023.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023] Open
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17
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Sotcheff SL, Chen JYC, Elrod N, Cao J, Jaworski E, Kuyumcu-Martinez MN, Shi PY, Routh AL. Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells. Pathogens 2022; 11:pathogens11080936. [PMID: 36015056 PMCID: PMC9414685 DOI: 10.3390/pathogens11080936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
Flaviviruses are small RNA viruses that are mainly transmitted via arthropod vectors and are found in tropic and sub-tropical regions. Most infections are asymptomatic (90-95%), but symptoms can be as severe as hemorrhagic fever and encephalitis. One recently emerged flavivirus is Zika virus (ZIKV), which was originally isolated from rhesus monkeys in Uganda roughly 70 years ago but has recently spread east, reaching S. America in 2015-2016. This outbreak was associated with the development of Guillain-Barré syndrome in adults and microcephaly in infants born to expectant mothers infected early in pregnancy. ZIKV must traverse the placenta to impact the development of the fetus, but the mechanisms responsible are unknown. While flaviviruses are known to disrupt splicing patterns in host cells, little is known about how flaviviruses such as ZIKV impact the alternative polyadenylation (APA) of host transcripts. This is important as APA is well-established as a mechanism in the regulation of mRNA metabolism and translation. Thus, we sought to characterize transcriptomic changes including APA in human placental (JEG3) cells in response to ZIKV infection using Poly(A)-ClickSeq (PAC-Seq). We used our differential Poly(A)-cluster (DPAC) analysis pipeline to characterize changes in differential gene expression, alternative poly-adenylation (APA) and the use of alternative terminal exons. We identified 98 upregulated genes and 28 downregulated genes. Pathway enrichment analysis indicated that many RNA processing and immune pathways were upregulated in ZIKV-infected JEG3 cells. We also updated DPAC to provide additional metrics of APA including the percentage-distal usage index (PDUI), which revealed that APA was extensive and the 3' UTRs of 229 genes were lengthened while 269 were shortened. We further found that there were 214 upregulated and 59 downregulated poly(A)-clusters (PACs). We extracted the nucleotide sequences surrounding these PACs and found that the canonical signals for poly-adenylation (binding site for poly-A binding protein (PABP) upstream and a GU-rich region down-stream of the PAC) were only enriched in the downregulated PACs. These results indicate that ZIKV infection makes JEG3 cells more permissive to non-canonical poly-adenylation signals.
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Affiliation(s)
- Stephanea L. Sotcheff
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - John Yun-Chung Chen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nathan Elrod
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jun Cao
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Elizabeth Jaworski
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mugé N. Kuyumcu-Martinez
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew L. Routh
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence:
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18
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Zika Virus Infection Leads to Demyelination and Axonal Injury in Mature CNS Cultures. Viruses 2021; 13:v13010091. [PMID: 33440758 PMCID: PMC7827345 DOI: 10.3390/v13010091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 01/03/2023] Open
Abstract
Understanding how Zika virus (Flaviviridae; ZIKV) affects neural cells is paramount in comprehending pathologies associated with infection. Whilst the effects of ZIKV in neural development are well documented, impact on the adult nervous system remains obscure. Here, we investigated the effects of ZIKV infection in established mature myelinated central nervous system (CNS) cultures. Infection incurred damage to myelinated fibers, with ZIKV-positive cells appearing when myelin damage was first detected as well as axonal pathology, suggesting the latter was a consequence of oligodendroglia infection. Transcriptome analysis revealed host factors that were upregulated during ZIKV infection. One such factor, CCL5, was validated in vitro as inhibiting myelination. Transferred UV-inactivated media from infected cultures did not damage myelin and axons, suggesting that viral replication is necessary to induce the observed effects. These data show that ZIKV infection affects CNS cells even after myelination-which is critical for saltatory conduction and neuronal function-has taken place. Understanding the targets of this virus across developmental stages including the mature CNS, and the subsequent effects of infection of cell types, is necessary to understand effective time frames for therapeutic intervention.
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19
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Yang S, Gorshkov K, Lee EM, Xu M, Cheng YS, Sun N, Soheilian F, de Val N, Ming G, Song H, Tang H, Zheng W. Zika Virus-Induced Neuronal Apoptosis via Increased Mitochondrial Fragmentation. Front Microbiol 2020; 11:598203. [PMID: 33424801 PMCID: PMC7785723 DOI: 10.3389/fmicb.2020.598203] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
The 2015 to 2016 outbreak of Zika virus (ZIKV) infections in the Americas coincided with a dramatic increase in neurodevelopmental abnormalities, including fetal microcephaly, in newborns born to infected women. In this study, we observed mitochondrial fragmentation and disrupted mitochondrial membrane potential after 24 h of ZIKV infection in human neural stem cells and the SNB-19 glioblastoma cell line. The severity of these changes correlated with the amount of ZIKV proteins expressed in infected cells. ZIKV infection also decreased the levels of mitofusin 2, which modulates mitochondria fusion. Mitochondrial division inhibitor 1 (Mdivi-1), a small molecule inhibiting mitochondria fission, ameliorated mitochondria disruptions and reduced cell death in ZIKV-infected cells. Collectively, this study suggests that abnormal mitochondrial fragmentation contributes to ZIKV-induced neuronal cell death; rebalancing mitochondrial dynamics of fission-fusion could be a therapeutic strategy for drug development to treat ZIKV-mediated neuronal apoptosis.
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Affiliation(s)
- Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Emily M Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yu-Shan Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Nuo Sun
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Ferri Soheilian
- Electron Microscopy Laboratory, National Cancer Institute, Center for Cancer Research, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, United States
| | - Natalia de Val
- Electron Microscopy Laboratory, National Cancer Institute, Center for Cancer Research, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, United States
| | - Guoli Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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20
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Rogan PK, Mucaki EJ, Shirley BC. A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections. F1000Res 2020; 9:943. [PMID: 33299552 PMCID: PMC7676395 DOI: 10.12688/f1000research.25390.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N1), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.
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Affiliation(s)
- Peter K. Rogan
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C8, Canada
- CytoGnomix Inc, London, Ontario, N5X 3X5, Canada
| | - Eliseos J. Mucaki
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C8, Canada
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21
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Rogan PK, Mucaki EJ, Shirley BC. A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections. F1000Res 2020; 9:943. [PMID: 33299552 PMCID: PMC7676395 DOI: 10.12688/f1000research.25390.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N2), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.
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Affiliation(s)
- Peter K. Rogan
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C8, Canada
- CytoGnomix Inc, London, Ontario, N5X 3X5, Canada
| | - Eliseos J. Mucaki
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C8, Canada
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