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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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Zhang Y, Guo J, Gao Y, Li S, Pan T, Xu G, Li X, Li Y, Yang J. Dynamic transcriptome analyses reveal m 6A regulated immune non-coding RNAs during dengue disease progression. Heliyon 2023; 9:e12690. [PMID: 36685392 PMCID: PMC9850062 DOI: 10.1016/j.heliyon.2022.e12690] [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: 08/06/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Dengue infection is one of the most prevalent arthropod-borne viral diseases, which can result in severe complications. Identification of genes and long non-coding RNAs (lncRNAs) involved in dengue infection would help in deciphering potential mechanisms responsible for the disease progression. We comprehensively analyzed the dynamic transcriptome during dengue disease progression and identified critical genes and lncRNAs with expression perturbations. Our findings revealed that the expression of genes (i.e., CCR10 and GNG7) and lncRNAs (i.e., CTBP1-AS and MAFG-AS1) were potentially regulated by m6A RNA methylation. Interestingly, dengue viral proteins prevalently interact with genes or lncRNAs with expression perturbations, which are involved in cell cycle, inflammation signaling pathways and immune response. Dynamically expressed genes and lncRNAs were likely to locate in the central regions of human protein-protein network, which play crucial roles in mediating signaling spread and helping viral replication. Immune microenvironments analysis revealed that plasma cells levels were increased and T cells infiltrations were decreased during dengue disease progression. Dynamically expressed genes and lncRNAs were correlated with immune cell infiltrations. Moreover, network analysis reveals the associations between dengue viral infections and human complex diseases (i.e., digestive diseases and neoplasms). Our comprehensive transcriptome analysis of dengue disease progression identified potential gene and lncRNA biomarkers, providing novel insights for understanding the pathogenesis of and developing effective therapeutic strategies for dengue infection.
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Affiliation(s)
- Ya Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Jing Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Yueying Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Si Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Tao Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Gang Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding author.Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China.
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,Corresponding author.
| | - Jun Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,Corresponding author.
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Xiong N, Sun Q. Identification of stage-related and severity-related biomarkers and exploration of immune landscape for Dengue by comprehensive analyses. Virol J 2022; 19:130. [PMID: 35918744 PMCID: PMC9344228 DOI: 10.1186/s12985-022-01853-8] [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: 01/23/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background At present, there are still no specific therapeutic drugs and appropriate vaccines for Dengue. Therefore, it is important to explore distinct clinical diagnostic indicators. Methods In this study, we combined differentially expressed genes (DEGs) analysis, weighted co-expression network analysis (WGCNA) and Receiver Operator Characteristic Curve (ROC) to screen a stable and robust biomarker with diagnosis value for Dengue patients. CIBERSORT was used to evaluate immune landscape of Dengue patients. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA) were applied to explore potential functions of hub genes. Results CD38 and Plasma cells have excellent Area Under the Curve (AUC) in distinguishing clinical stages for Dengue patients, and activated memory CD4+ T cells and Monocytes have good AUC for this function. ZNF595 has acceptable AUC in discriminating dengue hemorrhagic fever (DHF) from dengue fever (DF) in whole acute stages. Analyzing any serotype, we can obtain consistent results. Negative inhibition of viral replication based on GO, KEGG and GSEA analysis results, up-regulated autophagy genes and the impairing immune system are potential reasons resulting in DHF. Conclusions CD38, Plasma cells, activated memory CD4+ T cells and Monocytes can be used to distinguish clinical stages for dengue patients, and ZNF595 can be used to discriminate DHF from DF, regardless of serotypes. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01853-8.
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Affiliation(s)
- Nan Xiong
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Kunming Medical University, Kunming, 650500, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.
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Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors. Comput Struct Biotechnol J 2022; 20:2759-2777. [PMID: 35685361 PMCID: PMC9167876 DOI: 10.1016/j.csbj.2022.05.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV), the most medically relevant tick-transmitted flavivirus in Eurasia, targets the host central nervous system and frequently causes severe encephalitis. The severity of TBEV-induced neuropathogenesis is highly cell-type specific and the exact mechanism responsible for such differences has not been fully described yet. Thus, we performed a comprehensive analysis of alterations in host poly-(A)/miRNA/lncRNA expression upon TBEV infection in vitro in human primary neurons (high cytopathic effect) and astrocytes (low cytopathic effect). Infection with severe but not mild TBEV strain resulted in a high neuronal death rate. In comparison, infection with either of TBEV strains in human astrocytes did not. Differential expression and splicing analyses with an in silico prediction of miRNA/mRNA/lncRNA/vd-sRNA networks found significant changes in inflammatory and immune response pathways, nervous system development and regulation of mitosis in TBEV Hypr-infected neurons. Candidate mechanisms responsible for the aforementioned phenomena include specific regulation of host mRNA levels via differentially expressed miRNAs/lncRNAs or vd-sRNAs mimicking endogenous miRNAs and virus-driven modulation of host pre-mRNA splicing. We suggest that these factors are responsible for the observed differences in the virulence manifestation of both TBEV strains in different cell lines. This work brings the first complex overview of alterations in the transcriptome of human astrocytes and neurons during the infection by two TBEV strains of different virulence. The resulting data could serve as a starting point for further studies dealing with the mechanism of TBEV-host interactions and the related processes of TBEV pathogenesis.
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Ahmed W, Neelakanta G, Sultana H. Tetraspanins as Potential Therapeutic Candidates for Targeting Flaviviruses. Front Immunol 2021; 12:630571. [PMID: 33968023 PMCID: PMC8097176 DOI: 10.3389/fimmu.2021.630571] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Tetraspanin family of proteins participates in numerous fundamental signaling pathways involved in viral transmission, virus-specific immunity, and virus-mediated vesicular trafficking. Studies in the identification of novel therapeutic candidates and strategies to target West Nile virus, dengue and Zika viruses are highly warranted due to the failure in development of vaccines. Recent evidences have shown that the widely distributed tetraspanin proteins may provide a platform for the development of novel therapeutic approaches. In this review, we discuss the diversified and important functions of tetraspanins in exosome/extracellular vesicle biology, virus-host interactions, virus-mediated vesicular trafficking, modulation of immune mechanism(s), and their possible role(s) in host antiviral defense mechanism(s) through interactions with noncoding RNAs. We also highlight the role of tetraspanins in the development of novel therapeutics to target arthropod-borne flaviviral diseases.
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Affiliation(s)
- Waqas Ahmed
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States
| | - Girish Neelakanta
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States.,Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States
| | - Hameeda Sultana
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States.,Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States
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Wang WH, Urbina AN, Chang MR, Assavalapsakul W, Lu PL, Chen YH, Wang SF. Dengue hemorrhagic fever - A systemic literature review of current perspectives on pathogenesis, prevention and control. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 53:963-978. [PMID: 32265181 DOI: 10.1016/j.jmii.2020.03.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Dengue is an arboviral disease caused by dengue virus. Symptomatic dengue infection causes a wide range of clinical manifestations, from mild dengue fever (DF) to potentially fatal disease, such as dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS). We conducted a literature review to analyze the risks of DHF and current perspectives for DHF prevention and control. METHODS According to the PRISMA guidelines, the references were selected from PubMed, Web of Science and Google Scholar database using search strings containing a combination of terms that included dengue hemorrhagic fever, pathogenesis, prevention and control. Quality of references were evaluated by independent reviewers. RESULTS DHF was first reported in the Philippines in 1953 and further transmitted to the countries in the region of South-East Asia and Western Pacific. Plasma leakages is the main pathophysiological hallmark that distinguishes DHF from DF. Severe plasma leakage can result in hypovolemic shock. Various factors are thought to impact disease presentation and severity. Virus virulence, preexisting dengue antibodies, immune dysregulation, lipid change and host genetic susceptibility are factors reported to be correlated with the development of DHF. However, the exact reasons and mechanisms that triggers DHF remains controversial. Currently, no specific drugs and licensed vaccines are available to treat dengue disease in any of its clinical presentations. CONCLUSION This study concludes that antibody-dependent enhancement, cytokine dysregulation and variation of lipid profiles are correlated with DHF occurrence. Prompt diagnosis, appropriate treatment, active and continuous surveillance of cases and vectors are the essential determinants for dengue prevention and control.
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Affiliation(s)
- Wen-Hung Wang
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Aspiro Nayim Urbina
- Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan.
| | - Max R Chang
- Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan.
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Po-Liang Lu
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Yen-Hsu Chen
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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