Project description:Background: Organ dysfunction, especially liver injury, caused by dengue virus (DENV) infection has been associated with fatal cases in dengue patients around the world. However, the pathophysiological mechanisms of liver involvement in dengue remain unclear. There is accumulating evidence that miRNAs are playing an important role in regulating viral pathogenesis, and it can help in diagnostic and anti-viral therapies development. Methods: We collected liver tissues of DENV-infected for small RNA sequencing to identify significantly different express miRNAs during dengue virus infection, and the identified target genes of these miRNAs were annotated by biological function and pathway enrichment. Results: 31 significantly altered miRNAs were identified, including 16 up-regulated and 15 down-regulated miRNAs. By performing a series of miRNA prediction and signaling pathway enrichment analyses, the down-regulated miRNAs of mmu-miR-484, mmu-miR-1247-5p and mmu-miR-6538 were identified to be the crucial miRNAs. Further analysis revealed that the inflammation and immune responses involving Hippo, PI3K-Akt, MAPK, Wnt, mTOR, TGF-beta, Tight junction, and Platelet activation were modulated collectively by these three key miRNAs during DENV infection. These pathways are considered to be closely associated with the pathogenic mechanism and treatment strategy of dengue patients. Conclusion: The miRNAs identified by sequencing, especially miR-484 may be the potential therapeutic targets for liver involvement in dengue patients which involves the regulation of vascular permeability and expression of inflammatory cytokines. In this study, RNA-Seq analysis of liver tissues from a mouse model after DENV infection was performed to identify differential miRNA expression profiles, predicted target genes, and analyzed the biological functions and pathways involved in the regulation of differential miRNAs, contributing to the understanding of the mechanisms of liver tissue involvement after DENV infection.

Project description:Dengue virus (DENV) infection is associated with a range of clinical manifestations, from self-limiting dengue fever (DF) to life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Although DENV-specific CD4 T cells are capable of producing inflammatory cytokines and can acquire cytotoxic functions in previously DENV-exposed individuals, much less is known related to DENV-specific CD4 T cells during acute DENV infection and disease. In this study, we set out to characterize the immune signatures of DENV-specific CD4 T cells during acute infection and investigate whether DENV-specific CD4 T cell response differs between DF and DHF. Previous studies suggest that increased IL-10 level in the blood is associated with severe dengue disease. Here we show evidence of DENV-specific IL-10-producing CD4 T cells during acute DENV infection. More specifically, an IL-10+IFN-γ+ double positive (DP) CD4 T cell population was prominent in acute hospitalized DENV cases but disappeared at the convalescent stage. RNA-sequencing analysis revealed that these cells were associated with gene signatures that marginally overlapped with previously identified signatures of cytotoxic CD4 T cells and type 1 regulatory T (Tr1)-like cells. However, the majority of the genes differentially expressed by DP cells were not related to cytotoxic CD4 T cells or Tr1-like cells. These genes include IL-21, IL-22, CD86, CD109, and CCR1, which are involved in T cell activation, function, cytokine signaling, and migration. Notably, the magnitude of DP cell response was higher in DHF than DF, whereas the gene expression profile of DP cells was similar between DF and DHF. Finally, our data show that DENV-specific DP cells are largely homogeneous based on the expression of 31 selected markers. Overall, this study reveals unique phenotypes of virus-specific IL-10/IFN-γ co-producing CD4 cells and indicates that the quantity but not quality of these cells may be positively correlated with dengue disease severity.

Project description:Background: Dengue virus (DENV) infection often leads to acute illness lasting 2-7 days with severity ranging from dengue fever (DF) to hemorrhagic fever (DHF) and fatal dengue shock syndrome (DSS). The dynamic changes of host responses on the gene transcription level that accompany DENV infection and differences between DF and DHF cases have been poorly understood, particularly for South American population. Methodology/Principal Findings: Supported by a longitudinal active surveillance program for dengue transmission in Maracay, Venezuela, we conducted a prospective study to investigate host responses in dengue patients. Blood specimens and clinical information were collected on a daily basis from febrile cases confirmed with DENV infection from their first day of enrollment to early defervescence together with one convalescent sample. A total of 49 and 13 study participants were defined as DF and DHF cases respectively based on their clinical and hematological information. Using convalescent specimens as baseline, day-to-day gene expression was evaluated ex vivo in peripheral blood mononuclear cells of the study participants. Two waves of gene expression were detected: the first wave peaked at day 1 from the onset of fever (day 0) then declined at days 3-4; the second wave emerged from day 4 and peaked around day 5-6. Genes associated with innate immune process, including type I interferon signaling, cytokine-mediated signaling, chemotaxis, and antiviral responses, dominated the first wave; whereas genes involved in cell cycle processes, including cell division, mitosis, DNA replication, chromosome, and spindle organization dominated the second wave. Measureable genomic markers predicted early acute, late acute and convalescent phases with 91% accuracy. Gene signatures expressed in early acute phase predicted disease severity (DF vs DHF) with 96% accuracy. Conclusions/Significance: Our study established a dynamic pattern of detailed host immune responses to DENV infection and revealed genomic signatures valuable for diagnostics purposes.

Project description:Background. Dengue caused by dengue virus (DENV) serotypes -1 to -4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood. Methods. Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expression of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection. Results. A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were accessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection. Conclusion. This study provides the first insight into the global miRNA expressions of mouse livers in response to DENV-1 infection in vivo and the possible roles of miRNAs in modulating the adaptive immune responses during DENV-1 infection.

Project description:Hepatitis C virus (HCV)-induced chronic liver disease is one of the leading causes of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying HCC development following chronic HCV infection remain poorly understood. MicroRNAs (miRNAs) play an important role in cellular homeostasis within the liver and deregulation of the miRNome has been associated with liver disease including HCC. While host miRNAs are essential for HCV replication, viral infection in turn appears to induce alterations of intrahepatic miRNA networks. Although the cross-talk between HCV and liver cell miRNAs most likely contributes to liver disease pathogenesis, the functional involvement of miRNAs in HCV-driven hepatocyte injury and HCC remains elusive. Here, we combined a hepatocyte-like based model system, high-throughput small RNA-sequencing, computational analysis and functional studies to investigate HCV-miRNA interactions that may contribute to liver disease and HCC. Profiling analyses indicated that HCV infection differentially regulated the expression of 72 miRNAs by at least two-fold including miRNAs that were previously described to target genes associated with inflammation, fibrosis and cancer development. Further investigation demonstrated that miR-146a-5p was consistently increased in HCV-infected hepatocyte-like cells and primary human hepatocytes as well as in liver tissues from HCV-infected patients. Genome-wide microarray and computational analyses indicated that miR-146a-5p over-expression is related to liver disease and HCC development. Furthermore, we showed that miR-146a-5p positively impacts on late steps of the viral replication cycle thereby increasing HCV infection. Collectively, our data indicate that the HCV-induced increase in miR-146a-5p expression both promotes viral infection and is relevant for pathogenesis of liver disease. To explore the functional relevance of miR-146a-5p up-regulation, we performed a genome-wide transcriptomic analysis of hepatocyte-like cells upon ectopic miR-146a-5p expression.

Project description:Background: Dengue virus (DENV) infection often leads to acute illness lasting 2-7 days with severity ranging from dengue fever (DF) to hemorrhagic fever (DHF) and fatal dengue shock syndrome (DSS). The dynamic changes of host responses on the gene transcription level that accompany DENV infection and differences between DF and DHF cases have been poorly understood, particularly for South American population. Methodology/Principal Findings: Supported by a longitudinal active surveillance program for dengue transmission in Maracay, Venezuela, we conducted a prospective study to investigate host responses in dengue patients. Blood specimens and clinical information were collected on a daily basis from febrile cases confirmed with DENV infection from their first day of enrollment to early defervescence together with one convalescent sample. A total of 49 and 13 study participants were defined as DF and DHF cases respectively based on their clinical and hematological information. Using convalescent specimens as baseline, day-to-day gene expression was evaluated ex vivo in peripheral blood mononuclear cells of the study participants. Two waves of gene expression were detected: the first wave peaked at day 1 from the onset of fever (day 0) then declined at days 3-4; the second wave emerged from day 4 and peaked around day 5-6. Genes associated with innate immune process, including type I interferon signaling, cytokine-mediated signaling, chemotaxis, and antiviral responses, dominated the first wave; whereas genes involved in cell cycle processes, including cell division, mitosis, DNA replication, chromosome, and spindle organization dominated the second wave. Measureable genomic markers predicted early acute, late acute and convalescent phases with 91% accuracy. Gene signatures expressed in early acute phase predicted disease severity (DF vs DHF) with 96% accuracy. Conclusions/Significance: Our study established a dynamic pattern of detailed host immune responses to DENV infection and revealed genomic signatures valuable for diagnostics purposes. Total 64 subjects representing 51 DF (dengue fever) and 13 DHF (dengue hemorrhagic fever) cases were used to study gene expression during the course of dengue acute illness. Sample information regarding Patient No., Infecting serotype, fever status (fever days or defervescent (df) days), and disease severity (DF vs DHF) were provided. The date for a sample for gene chip hybridization and image scanning was marked as Scan date. Samples from study subjects were collected once a patient was enrolled. Over 200 samples were collected. Two genechip platforms were used, the HG-focus and HG-U133plus2. A total of 168 samples were assayed on the HG-focus platform, 2 were excluded for further analysis as they failed on quality control (i.e. VFP-0003_G7_DF, VFP-0029_G1_DF samples). A total of 101 samples were assayed on the HG-U133plus2 platform, 4 were excluded for further analysis as they failed on quality control (i.e. VFP_0186_G4_DF, VFP-0213_G3_DF, VFP_0213_G5_DF, VFP_0220_G3_DHF). Data generated by HG-focus platform were used to explore significantly expressed genes in individual Gs, phases, and for prediction analysis for disease phases. Whereas data generated by HG-U133plus2 were first used to assess the reproducibility of results generated by the HG-focus platform. Secondarily, they were used to perform prediction analysis for disease severity. Samples were grouped into stages (G) based on the timepoint when they were collected: G0=day0 (on the day of fever onset); G1=day 1 (one day after fever onset); G2=day2 (two days after fever onset)M-bM-^@M-&until G5; G6=day6-10 (6-10 days after fever onset); G7= convalescent time point (around day 28 after the first sample). Samples were also grouped into early acute (G0-G3), late acute (G4-G6) and convalescent phases (G7). References for the protocols; PMID 12803996 and 20078211

Project description:Background: Dengue virus (DENV) infection has a global impact on public health. The clinical outcomes (of DENV) can vary from a flu-like illness called dengue fever (DF), to a more severe form, known as dengue hemorrhagic fever (DHF). The underlying innate immune mechanisms leading to protective or detrimental outcomes have not been fully elucidated. Helper innate lymphoid cells (hILCs), an innate lymphocyte recently discovered, functionally resemble T-helper cells and are important in inflammation and homeostasis. However, the role of hILCs in DENV infection had been unexplored. Methods: We performed flow cytometry to investigate the frequency and phenotype of hILCs in peripheral blood mononuclear cells from DENV-infected patients of different disease severities (DF and DHF), and at different phases (febrile and convalescence) of infection. Intracellular cytokine staining of hILCs from DF and DHF were also evaluated by flow cytometry after ex vivo stimulation. Further, the hILCs were sorted and subjected to transcriptome analysis using RNA sequencing. Differential gene expression analysis was performed to compare the febrile and convalescent phase samples in DF and DHF. Selected differentially expressed genes were then validated by quantitative PCR. Results: Phenotypic analysis showed marked activation of all three hILC subsets during the febrile phase as shown by higher CD69 expression when compared to paired convalescent samples, although the frequency of hILCs remained unchanged. Upon ex vivo stimulation, hILCs from febrile phase DHF produced significantly higher IFN-g and IL-4 when compared to those of DF. Transcriptomic analysis showed unique hILCs gene expression in DF and DHF, suggesting that divergent functions of hILCs may be associated with different disease severities. Differential gene expression analysis indicated that hILCs function both in cytokine secretion and cytotoxicity during the febrile phase of DENV infection. Conclusions: Helper ILCs are activated in the febrile phase of DENV infection and display unique transcriptomic changes as well as cytokine production that correlate with severity. Targeting hILCs during early innate response to DENV might help shape subsequent immune responses and potentially lessen the disease severity in the future.

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Hepatic miRNA profile in dengue hemorrhagic fever associated with apoptosis regulation, vascular injury and inflammation

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