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Sha Y, Liu X, Yan W, Wang M, Li H, Jiang S, Wang S, Ren Y, Zhang K, Yin R. Long Non-Coding RNA Analysis: Severe Pathogenicity in Chicken Embryonic Visceral Tissues Infected with Highly Virulent Newcastle Disease Virus-A Comparison to the Avirulent Vaccine Virus. Microorganisms 2024; 12:971. [PMID: 38792800 PMCID: PMC11123907 DOI: 10.3390/microorganisms12050971] [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: 02/06/2024] [Revised: 04/12/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
There are significant variations in pathogenicity among different virulent strains of the Newcastle disease virus (NDV). Virulent NDV typically induces severe pathological changes and high mortality rates in infected birds, while avirulent NDV usually results in asymptomatic infection. Currently, the understanding of the specific mechanisms underlying the differences in host pathological responses and symptoms caused by various virulent NDV strains remains limited. Long non-coding RNA (lncRNA) can participate in a range of biological processes and plays a crucial role in viral infection and replication. Therefore, this study employed RNA-Seq to investigate the transcriptional profiles of chicken embryos' visceral tissues (CEVTs) infected with either the virulent NA-1 strain or avirulent LaSota strain at 24 hpi and 36 hpi. Using bioinformatic methods, we obtained a total of 2532 lncRNAs, of which there were 52 and 85 differentially expressed lncRNAs at 24 hpi and 36 hpi, respectively. LncRNA analysis revealed that the severe pathological changes and symptoms induced by virulent NDV infection may be partially attributed to related target genes, regulated by differentially expressed lncRNAs such as MSTRG.1545.5, MSTRG.14601.6, MSTRG.7150.1, and MSTRG.4481.1. Taken together, these findings suggest that virulent NDV infection exploits the host's metabolic resources and exerts an influence on the host's metabolic processes, accompanied by excessive activation of the immune response. This impacts the growth and development of each system of CEVTs, breaches the blood-brain barrier, inflicts severe damage on the nervous system, and induces significant lesions. These observations may be attributed to variations in pathology. Consequently, novel insights were obtained into the intricate regulatory mechanisms governing NDV and host interactions. This will aid in unraveling the molecular mechanisms underlying both virulent and avirulent forms of NDV infection.
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Affiliation(s)
- Yuxin Sha
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Xinxin Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Weiwen Yan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Mengjun Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Hongjin Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Shanshan Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Sijie Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Yongning Ren
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Kexin Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
| | - Renfu Yin
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (Y.S.); (X.L.); (W.Y.); (M.W.); (H.L.); (S.J.); (S.W.); (Y.R.); (K.Z.)
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Yao X, Zhong L, Wang M, Wang M, Han Y, Wang Y, Zhou J, Song J, Li Y, Xu Y. Up-regulated lncRNA CYLD as a ceRNA of miR-2383 facilitates bovine viral diarrhea virus replication by promoting CYLD expression to counteract RIG-I-mediated type-I IFN production. Int J Biol Macromol 2023; 253:127351. [PMID: 37839600 DOI: 10.1016/j.ijbiomac.2023.127351] [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: 04/24/2023] [Revised: 09/17/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Bovine viral diarrhea virus (BVDV) is one of the most important pathogens of cattle, causing numerous economic losses to the cattle industry. To date, many potential mechanisms of BVDV evading or subverting innate immunity are still unknown. In this study, an lnc-CYLD/miR-2383/CYLD axis involved in BVDV-host interactions was screened from RNA-seq-based co-expression networks analysis of long noncoding RNAs, microRNAs and mRNAs in BVDV-infected bovine cells, and underlying mechanisms of lnc-CYLD/miR-2383/CYLD axis regulating BVDV replication were explored. Results showed that BVDV-induced up-regulation of the lnc-CYLD competed for binding to the miR-2383, and then promoted CYLD expression, thereby inhibiting RIG-I-mediated type-I interferon (IFN) production, which was subsequently confirmed by treatment with lnc-CYLD overexpression and miR-2383 inhibitor. However, miR-2383 transfection and small interfering RNA-mediated lnc-CYLD knockdown inhibited CYLD expression and enhanced RIG-I-mediated type-I IFN production, inhibiting BVDV replication. In addition, interaction relationship between lnc-CYLD and miR-2383, and colocalization relationship of lnc-CYLD, miR-2383 and CYLD were confirmed by dual-luciferase assay and in situ hybridization assay. Conclusively, up-regulation of the lnc-CYLD as a competing endogenous RNA binds to the miR-2383 to reduce inhibitory effect of the miR-2383 on the CYLD expression, playing an important role in counteracting type-I IFN-dependent antiviral immunity to facilitate BVDV replication.
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Affiliation(s)
- Xin Yao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Key Laboratory for Animal Disease Control and Pharmaceutical Development of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Linhan Zhong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mengmeng Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mei Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yanyan Han
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yixin Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jiaying Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jingge Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yuan Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
| | - Yigang Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics and Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
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Zhang X, Xie T, Li X, Feng M, Mo G, Zhang Q, Zhang X. Transcriptome Sequencing Reveals That Intact Expression of the Chicken Endogenous Retrovirus chERV3 In Vitro Can Possibly Block the Key Innate Immune Pathway. Animals (Basel) 2023; 13:2720. [PMID: 37684986 PMCID: PMC10486640 DOI: 10.3390/ani13172720] [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: 07/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Endogenous retroviruses (ERVs) are viral sequences that have integrated into the genomes of vertebrates. Our preliminary transcriptome sequencing analysis revealed that chERV3 is active and is located on chromosome 1:32602284-32615631. We hypothesized that chERV3 may have a role in the host innate immune response to viral infection. In this study, using reverse genetics, we constructed the puc57-chERV3 full-length reverse cloning plasmid in vitro. We measured the p27 content in culture supernatant by enzyme-linked immunosorbent assay (ELISA). Finally, transcriptome analysis was performed to analyze the function of chERV3 in innate immunity. The results showed that chERV3 may generate p27 viral particles. We found that compared to the negative control (NC) group (transfected with pMD18T-EGFP), the chERV3 group exhibited 2538 up-regulated differentially expressed genes (DEGs) and 1828 down-regulated DEGs at 24 hours (h) and 1752 up-regulated DEGs and 1282 down-regulated DEGs at 48 h. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the down-regulated DEGs were enriched mainly in immune-related processes such as the inflammatory response, innate immune response, and Toll-like receptor signaling pathway. GSEA showed that the Toll-like receptor signaling pathway was suppressed by chERV3 at both time points. We hypothesized that chERV3 can influence the activation of the innate immune pathway by blocking the Toll-like receptor signaling pathway to achieve immune evasion.
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Affiliation(s)
- Xi Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiaoqi Li
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Qihong Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
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4
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Fandiño S, Gomez-Lucia E, Benítez L, Doménech A. Avian Leukosis: Will We Be Able to Get Rid of It? Animals (Basel) 2023; 13:2358. [PMID: 37508135 PMCID: PMC10376345 DOI: 10.3390/ani13142358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Avian leukosis viruses (ALVs) have been virtually eradicated from commercial poultry. However, some niches remain as pockets from which this group of viruses may reemerge and induce economic losses. Such is the case of fancy, hobby, backyard chickens and indigenous or native breeds, which are not as strictly inspected as commercial poultry and which have been found to harbor ALVs. In addition, the genome of both poultry and of several gamebird species contain endogenous retroviral sequences. Circumstances that support keeping up surveillance include the detection of several ALV natural recombinants between exogenous and endogenous ALV-related sequences which, combined with the well-known ability of retroviruses to mutate, facilitate the emergence of escape mutants. The subgroup most prevalent nowadays, ALV-J, has emerged as a multi-recombinant which uses a different receptor from the previously known subgroups, greatly increasing its cell tropism and pathogenicity and making it more transmissible. In this review we describe the ALVs, their different subgroups and which receptor they use to infect the cell, their routes of transmission and their presence in different bird collectivities, and the immune response against them. We analyze the different systems to control them, from vaccination to the progress made editing the bird genome to generate mutated ALV receptors or selecting certain haplotypes.
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Affiliation(s)
- Sergio Fandiño
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain
- Research Group, "Animal Viruses" of Complutense University of Madrid, 28040 Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain
- Research Group, "Animal Viruses" of Complutense University of Madrid, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain
- Research Group, "Animal Viruses" of Complutense University of Madrid, 28040 Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain
- Research Group, "Animal Viruses" of Complutense University of Madrid, 28040 Madrid, Spain
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Wu H, Zaib G, Luo H, Guo W, Wu T, Zhu S, Wang C, Chai W, Xu Q, Cui H, Hu X. CCL4 participates in the reprogramming of glucose metabolism induced by ALV-J infection in chicken macrophages. Front Microbiol 2023; 14:1205143. [PMID: 37333648 PMCID: PMC10272584 DOI: 10.3389/fmicb.2023.1205143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Interferon and chemokine-mediated immune responses are two general antiviral programs of the innate immune system in response to viral infections and have recently emerged as important players in systemic metabolism. This study found that the chemokine CCL4 is negatively regulated by glucose metabolism and avian leukosis virus subgroup J (ALV-J) infection in chicken macrophages. Low expression levels of CCL4 define this immune response to high glucose treatment or ALV-J infection. Moreover, the ALV-J envelope protein is responsible for CCL4 inhibition. We confirmed that CCL4 could inhibit glucose metabolism and ALV-J replication in chicken macrophages. The present study provides novel insights into the antiviral defense mechanism and metabolic regulation of the chemokine CCL4 in chicken macrophages.
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Affiliation(s)
- Huixian Wu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Gul Zaib
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agricultural and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Huan Luo
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wang Guo
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ting Wu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shutong Zhu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chenjun Wang
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wenxian Chai
- Changzhou Animal Disease Prevention and Control Center, Changzhou, Jiangsu, China
| | - Qi Xu
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agricultural and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agricultural and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xuming Hu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agricultural and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
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Wang D, Gomes MT, Mo Y, Prohaska CC, Zhang L, Chelvanambi S, Clauss MA, Zhang D, Machado RF, Gao M, Bai Y. Human Endogenous Retrovirus, SARS-CoV-2, and HIV Promote PAH via Inflammation and Growth Stimulation. Int J Mol Sci 2023; 24:7472. [PMID: 37108634 PMCID: PMC10138839 DOI: 10.3390/ijms24087472] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a pulmonary vascular disease characterized by the progressive elevation of pulmonary arterial pressures. It is becoming increasingly apparent that inflammation contributes to the pathogenesis and progression of PAH. Several viruses are known to cause PAH, such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), human endogenous retrovirus K(HERV-K), and human immunodeficiency virus (HIV), in part due to acute and chronic inflammation. In this review, we discuss the connections between HERV-K, HIV, SARS-CoV-2, and PAH, to stimulate research regarding new therapeutic options and provide new targets for the treatment of the disease.
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Affiliation(s)
- Desheng Wang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Marta T. Gomes
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Yanfei Mo
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Clare C. Prohaska
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Lu Zhang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Sarvesh Chelvanambi
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthias A. Clauss
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Dongfang Zhang
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Roberto F. Machado
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Mingqi Gao
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Yang Bai
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
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7
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Mo G, Wei P, Hu B, Nie Q, Zhang X. Advances on genetic and genomic studies of ALV resistance. J Anim Sci Biotechnol 2022; 13:123. [PMID: 36217167 PMCID: PMC9550310 DOI: 10.1186/s40104-022-00769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022] Open
Abstract
Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.
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Affiliation(s)
- Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530001, Guangxi, China
| | - Bowen Hu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Activation of lnc-ALVE1-AS1 inhibited ALV-J replication through triggering the TLR3 pathway in chicken macrophage like cell line. Vet Res Commun 2022; 47:431-443. [PMID: 35715584 DOI: 10.1007/s11259-022-09960-1] [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: 11/23/2021] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
Endogenous retroviruses (ERVs) are remnants of the historical retroviral infections, and their derived transcripts with viral signatures are important sources of long noncoding RNAs (lncRNAs). We have previously shown that the chicken ERV-derived lncRNA lnc-ALVE1-AS1 exerts antiviral innate immunity in chicken embryo fibroblasts. However, it is not clear whether this endogenous retroviral RNA has a similar function in immune cells. Here, we found that lnc-ALVE1-AS1 was persistently inhibited in chicken macrophages after avian leukosis virus subgroup J (ALV-J) infection. Furthermore, overexpression of lnc-ALVE1-AS1 significantly inhibited the replication of exogenous ALV-J, whereas knockdown of lnc-ALVE1-AS1 promoted the replication of ALV-J in chicken macrophages. This phenomenon is attributed to the induction of antiviral innate immunity by lnc-ALVE1-AS1 in macrophages, whereas knockdown of lnc-ALVE1-AS1 had the opposite effect. Mechanistically, lnc-ALVE1-AS1 can be sensed by the cytosolic pattern recognition receptor TLR3 and trigger the type I interferons response. The present study provides novel insights into the antiviral defense of ERV-derived lncRNAs in macrophages and offers new strategies for future antiviral solutions.
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9
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Dai M, Xie T, Feng M, Zhang X. Endogenous retroviruses transcriptomes in response to four avian pathogenic microorganisms infection in chicken. Genomics 2022; 114:110371. [PMID: 35462029 DOI: 10.1016/j.ygeno.2022.110371] [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: 10/13/2021] [Revised: 02/20/2022] [Accepted: 04/17/2022] [Indexed: 01/14/2023]
Abstract
The impact of Endogenous retroviruses (ERVs) on chicken disease is not well understood. Here, we systematically identified 436 relatively complete ChERVs from the chicken genome. Subsequently, ChERV transcriptomes were analyzed in chicken after subgroup J avian leukosis virus (ALV-J), avian influenza virus (AIV), Marek's disease virus (MDV) and avian pathogenic Escherichia coli (APEC) infection. We found that about 50%-68% of ChERVs were transcriptionally active in infected and uninfected-samples, although the abundance of most ChERVs is relatively low. Moreover, compared to uninfected-samples, 49, 18, 66 and 17 ChERVs were significantly differentially expressed in ALV-J, AIV, MDV and APEC infected-samples, respectively. These findings may be of significance for understanding the role and function of ChERVs to response the pathogenic microorganism infection.
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Affiliation(s)
- Manman Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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10
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Ji X, Meng W, Liu Z, Mu X. Emerging Roles of lncRNAs Regulating RNA-Mediated Type-I Interferon Signaling Pathway. Front Immunol 2022; 13:811122. [PMID: 35280983 PMCID: PMC8914027 DOI: 10.3389/fimmu.2022.811122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The type-I interferon (IFN-I) signaling pathway plays pivot roles in defending against pathogen invasion. Exogenous ssRNA and dsRNA could be immunogenic. RNA-mediated IFN signaling is extensively studied in the field. The incorrect functioning of this pathway leads to either autoimmune diseases or suffering from microorganism invasion. From the discrimination of “self” and “non-self” molecules by receptors to the fine-tune modulations in downstream cascades, all steps are under the surveillance featured by complex feedbacks and regulators. Studies in recent years highlighted the emerging roles of long noncoding RNAs (lncRNAs) as a reservoir for signaling regulation. LncRNAs bind to targets through the structure and sequence, and thus the mechanisms of action can be complex and specific. Here, we summarized lncRNAs modulating the RNA-activated IFN-I signaling pathway according to the event order during the signaling. We hope this review help understand how lncRNAs are participating in the regulation of IFN-I signaling.
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Affiliation(s)
- Xiaoxin Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Wei Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
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11
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Chen S, Zhao R, Wu T, Wang D, Wang B, Pan S, Hu X, Pan Z, Cui H. An Endogenous Retroviral LTR-Derived Long Noncoding RNA lnc-LTR5B Interacts With BiP to Modulate ALV-J Replication in Chicken Cells. Front Microbiol 2021; 12:788317. [PMID: 34912323 PMCID: PMC8667585 DOI: 10.3389/fmicb.2021.788317] [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: 10/02/2021] [Accepted: 11/05/2021] [Indexed: 01/25/2023] Open
Abstract
Infection with the avian leukosis virus subgroup J (ALV-J) impairs host genes and facilitates the establishment of chronic infection and the viral life cycle. However, the involvement of long noncoding RNAs (lncRNAs) in ALV-J infection remains largely unknown. In this study, we identified a novel chicken lncRNA derived from LTR5B of the ERV-L family (namely lnc-LTR5B), which is significantly downregulated in ALV-J infected cells. lnc-LTR5B was localized in the cytoplasm and was relatively high expressed in the chicken lung and liver. Notably, the replication of ALV-J was inhibited by the overexpression of lnc-LTR5B but enhanced when lnc-LTR5B expression was knocked down. We further confirmed that lnc-LTR5B could bind to the binding immunoglobulin protein (BiP), a master regulator of endoplasmic reticulum (ER) function. Mechanistically, lnc-LTR5B serves as a competing endogenous RNA for BiP, restricting its physical availability. Upon ALV-J infection, the reduction of lnc-LTR5B released BiP, which facilitated its translocation to the cell surface. This is crucial for ALV-J entry as well as pro-survival signaling. In conclusion, we identified an endogenous retroviral LTR-activated lnc-LTR5B that is involved in regulating the cell surface translocation of BiP, and such regulatory machinery can be exploited by ALV-J to complete its life cycle and propagate.
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Affiliation(s)
- Shihao Chen
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Ruihan Zhao
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ting Wu
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Dedong Wang
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Biao Wang
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Shiyu Pan
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Xuming Hu
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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12
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Srinivasachar Badarinarayan S, Sauter D. Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. J Virol 2021; 95:e02299-20. [PMID: 33883223 PMCID: PMC8315955 DOI: 10.1128/jvi.02299-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 01/15/2023] Open
Abstract
Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.
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MESH Headings
- Animals
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/physiology
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Humans
- Immunity, Cellular
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Pattern Recognition/metabolism
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/metabolism
- Retroelements
- Viral Proteins/metabolism
- Virion/metabolism
- Virus Diseases/genetics
- Virus Diseases/immunology
- Virus Diseases/virology
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Affiliation(s)
- Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
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13
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Mason AS. Falling fowl of the chicken reference genome: pitfalls of studying polymorphic endogenous retroviruses. Retrovirology 2021; 18:10. [PMID: 33879155 PMCID: PMC8059273 DOI: 10.1186/s12977-021-00555-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/24/2022] Open
Abstract
High quality reference genomes have facilitated the study of endogenous retroviruses (ERVs). However, there are an increasing number of published works which assume the ERVs in reference genomes are universal; even those of evolutionarily recent integrations. Consequently, these studies fail to properly characterise polymorphic ERVs, and even propose biological functions for ERVs that may not actually be present in the genomes of interest. Here, I outline the pitfalls of three studies of chicken endogenous Avian Leukosis Viruses (ALVEs or "ev genes": the "original" ERVs), all confounded by the assumption that the reference genome provides a representative ALVE baseline.
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Affiliation(s)
- Andrew S Mason
- Jack Birch Unit for Molecular Carcinogenesis, The Department of Biology and York Biomedical Research Institute, The University of York, York, YO10 5DD, UK.
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14
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The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation. Stem Cells Int 2021; 2021:6660936. [PMID: 33727936 PMCID: PMC7937486 DOI: 10.1155/2021/6660936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
Endogenous retroviruses (ERVs) are repetitive sequences in the genome, belonging to the retrotransposon family. During the course of life, ERVs are associated with multiple aspects of chromatin and transcriptional regulation in development and pathological conditions. In mammalian embryos, ERVs are extensively activated in early embryo development, but with a highly restricted spatial-temporal pattern; and they are drastically silenced during differentiation with exceptions in extraembryonic tissue and germlines. The dynamic activation pattern of ERVs raises questions about how ERVs are regulated in the life cycle and whether they are functionally important to cell fate decision during early embryo and somatic cell development. Therefore, in this review, we focus on the pieces of evidence demonstrating regulations and functions of ERVs during stem cell differentiation, which suggests that ERV activation is not a passive result of cell fate transition but the active epigenetic and transcriptional regulation during mammalian development and stem cell differentiation.
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15
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Chen S, Wang D, Liu Y, Zhao R, Wu T, Hu X, Pan Z, Cui H. Targeting the Histone Methyltransferase Disruptor of Telomeric Silencing 1-Like Restricts Avian Leukosis Virus Subgroup J Replication by Restoring the Innate Immune Response in Chicken Macrophages. Front Microbiol 2020; 11:603131. [PMID: 33363525 PMCID: PMC7752946 DOI: 10.3389/fmicb.2020.603131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/20/2020] [Indexed: 01/31/2023] Open
Abstract
Avian leukosis virus subgroup J (ALV-J), an oncogenic retrovirus, is known to cause immunosuppression and various types of cancer in chickens. Recent reports have shown that epigenetic changes in DNA and chromatin are widely implicated in the life cycle of diverse viruses, and reversal of these changes in host cells can lead to alterations in the propagation of viruses. In the present study, we found that disruptor of telomeric silencing 1-like (DOT1L), a histone H3 lysine79 (H3K79) methyltransferase, was upregulated during ALV-J infection in chicken macrophage HD11 cells. Subsequently, we show that targeting DOT1L with a specific inhibitor can significantly decrease the ALV-J replication and viral production. By generating of DOT1L-knockout (KO) HD11 cells using the CRISPR/Cas9 system, we show that deletion of the DOT1L led to an increase in the induction of IFNβ and interferon-stimulated genes (ISGs) in HD11 cells in response to ALV-J infection. Importantly, we confirmed that ALV-J infection impaired the activation of the melanoma differentiation-associated protein 5 (MDA5)-mediated-IFN pathway by suppressing the MDA5 expression, and knockout DOT1L rescued the expression of MDA5 and signal transducer and activator of transcription 1 (STAT1), both of which tightly control the antiviral innate immunity. Collectively, it can be deduced from the current data that blocking DOT1L activity or deletion of DOT1L can lead to ALV-J replication inhibition and restoration of the virally suppressed host innate immunity. Thus, we suggest that DOT1L might be a potential drug target for modulating host innate immune responses to combat ALV-J infection.
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Affiliation(s)
- Shihao Chen
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yinyin Liu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Ruihan Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ting Wu
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xuming Hu
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agricultural and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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16
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Zhu T, Fernandez-Sesma A. Innate Immune DNA Sensing of Flaviviruses. Viruses 2020; 12:v12090979. [PMID: 32899347 PMCID: PMC7552040 DOI: 10.3390/v12090979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Flaviviruses are arthropod-borne RNA viruses that have been used extensively to study host antiviral responses. Often selected just to represent standard single-stranded positive-sense RNA viruses in early studies, the Flavivirus genus over time has taught us how truly unique it is in its remarkable ability to target not just the RNA sensory pathways but also the cytosolic DNA sensing system for its successful replication inside the host cell. This review summarizes the main developments on the unexpected antagonistic strategies utilized by different flaviviruses, with RNA genomes, against the host cyclic GAMP synthase (cGAS)/stimulator of interferon genes (STING) cytosolic DNA sensing pathway in mammalian systems. On the basis of the recent advancements on this topic, we hypothesize that the mechanisms of viral sensing and innate immunity are much more fluid than what we had anticipated, and both viral and host factors will continue to be found as important factors contributing to the host innate immune system in the future.
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Affiliation(s)
- Tongtong Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-241-5182
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17
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Wang Y, Wang Y, Luo W, Song X, Huang L, Xiao J, Jin F, Ren Z, Wang Y. Roles of long non-coding RNAs and emerging RNA-binding proteins in innate antiviral responses. Am J Cancer Res 2020; 10:9407-9424. [PMID: 32802200 PMCID: PMC7415804 DOI: 10.7150/thno.48520] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022] Open
Abstract
The diseases caused by viruses posed a great challenge to human health, the development of which was driven by the imbalanced host immune response. Host innate immunity is an evolutionary old defense system that is critical for the elimination of the virus. The overactive innate immune response also leads to inflammatory autoimmune diseases, which require precise control of innate antiviral response for maintaining immune homeostasis. Mounting long non-coding RNAs (lncRNAs) transcribed from the mammalian genome are key regulators of innate antiviral response, functions of which greatly depend on their protein interactors, including classical RNA-binding proteins (RBPs) and the unconventional proteins without classical RNA binding domains. In particular, several emerging RBPs, such as m6A machinery components, TRIM family members, and even the DNA binding factors recognized traditionally, function in innate antiviral response. In this review, we highlight recent progress in the regulation of type I interferon signaling-based antiviral responses by lncRNAs and emerging RBPs as well as their mechanism of actions. We then posed the future perspective toward the role of lncRNA-RBP interaction networks in innate antiviral response and discussed the promising and challenges of lncRNA-based drug development as well as the technical bottleneck in studying lncRNA-protein interactions. Our review provides a comprehensive understanding of lncRNA and emerging RBPs in the innate antiviral immune response.
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18
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Yao M, Xu C, Shen H, Liu T, Wang X, Shao C, Shao S. The regulatory role of miR-107 in Coxsackie B3 virus replication. Aging (Albany NY) 2020; 12:14467-14479. [PMID: 32674073 PMCID: PMC7425430 DOI: 10.18632/aging.103488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 05/20/2020] [Indexed: 11/25/2022]
Abstract
Coxsackie B3 virus (CVB3) is a member of small RNA viruses that belongs to the genus Enterovirus of the family Picornaviridae and CVB3 is the main pathogen of acute and chronic viral myocarditis. In this study RT-qPCR was used to determine the expression of miR-107 in CVB3-infected and uninfected HeLa cells. The experimental results show that the level of miR-107 began to rise at 4 h after the infection, and significantly boosted at 6 h. Based on the results of this experiment, we consider that miR-107 expression is related to CVB3 infection. In order to further clarify the effect of miR-107 in the process of CVB3 infection, we studied the effect of miR-107 upstream and downstream target genes on CVB3 replication. Levels of the target RNAs were detected by RT-qPCR after CVB3 infection, and the expression of CVB3 capsid protein VP1 by western blot analysis. Then the virus in the supernatant was quantitated via a viral plaque assay, reflecting the release of the virus. The experimental results showed that miRNA-107 expression is associated with CVB3 replication and proliferation, while KLF4 and BACE1 as the downstream of miR-107 weakened CVB3 replication. Overexpressions of KLF4 and BACE1 negatively regulated CVB3 replication, this effect on CVB3 was completely opposite to that of miR-107. Further experiments revealed that the upstream lncRNA004787, a new lncRNA that had not been reported, was located on chromosome 5, strand - from 37073250 to 37070908 (genome assembly: hg19). We sequenced and studied lncRNA004787 and found that it partially inhibited CVB3 replication. This prompted us to speculate that lncRNA004787 probably impacted the replication by other means. In conclusion, miR-107 interfered with CVB3 replication and release.
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Affiliation(s)
- Min Yao
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chi Xu
- Marshall International Center for Digestive Diseases, Shanghai East Hospital, Tongji University, Shanghai 200120, China
| | - Hongxing Shen
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Tingjun Liu
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiuping Wang
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Chen Shao
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shihe Shao
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.,Marshall International Center for Digestive Diseases, Shanghai East Hospital, Tongji University, Shanghai 200120, China
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19
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Hildebrandt E, Penzes JJ, Gifford RJ, Agbandje-Mckenna M, Kotin RM. Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors. Virus Evol 2020; 6:veaa043. [PMID: 32913662 PMCID: PMC7474932 DOI: 10.1093/ve/veaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.
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Affiliation(s)
- Evin Hildebrandt
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
| | - Judit J Penzes
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Genomics & Bioinformatics, Sir Michael Stoker Building Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Mavis Agbandje-Mckenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert M Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
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