Transcriptional Profiling of the Immune Response to Ebola Infection
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ABSTRACT:
ORGANISM(S): Homo sapiens Macaca fascicularis
PROVIDER: GSE68809 | GEO | 2017/02/10
SECONDARY ACCESSION(S): PRJNA283829
REPOSITORIES: GEO
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Project description:<p align="left"><b>Title: </b> Ebola-infected non-human primates - PBMCs<br> <p align="left"><b>Summary: </b> Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever. In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions we have examined the molecular features of EBOV infection in vivo. Using self-spotted cDNA microarrays, we analyzed genome-wide host expression patterns in sequential blood samples from nonhuman primates (NHP) infected with EBOV. <br> <p align="left"><b>Overall Design: </b> Ebola infection of non-human primates (cynomolgus macaques). We took sequential samples of peripheral blood mononuclear cells (PBMC) from 15 cynomolgus macaques infected intramuscularly with 1000 plaque forming units (PFUs) of EBOV, Zaire strain. Peripheral blood samples (2.5mL) were collected on days 1, 4, or 6 prior to infection, in order to define a robust baseline, and then on successive days after infection, until death (immediately prior to euthanasia). Animals were euthanized at days 1, 2, 3, 4, 5, and 6 postinfection. PBMC's were collected at days post-infection as noted, preserved in Trizol, Trizol-extracted total RNA, 1 round amplified (Ambion MessageAmp I), directly labeled by Cy5 incorporation during reverse transcription of amplified RNA. Each blood sample was hybridized versus a common reference. The same reference is used for all samples - Stratagene Universal Human Reference RNA, 1 round of amplification (Ambion MessageAmp I), directly labeled by Cy3 incorporation during reverse transcription of amplified reference RNA. Two to three biological replicates of pre-infection samples were taken for each animal, as well as two to nine biological replicates (from different animals) at each day post-infection. A total of 50 arrays, representing 15 animals is included in this dataset.
2008-03-11 | E-SMDB-4098 | biostudies-arrayexpress
Project description:Ebola virus disease (EVD) is a serious illness associated with 20-90% fatalities. EVD is characterized by robust virus replication and strong host inflammatory immune response. Analyzing the host immune response has increasingly involved multimodal approaches including transcriptomics to profile gene expression. We studied cynomolgus macaques exposed to Ebola virus (EBOV) Makona via different routes with the intent of comparing RNA-Seq to a NanoString nCounter codeset targeting 769 non-human primate (NHP) genes. RNA-Seq analysis of serial blood samples showed different routes led to the same overall transcriptional response seen in previously reported EBOV-exposed NHP studies. Similar profiles were observed using the NanoString codeset. Both platforms displayed a strong correlation in gene expression patterns, thus cross-validating the two methods. This included a strong induction of innate immune response genes at early time points post-infection, and neutrophil-associated genes at later time points. Using data generated from either platform, we could deploy a 41-gene classifier to cluster samples by EBOV infection status. Finally, NanoString and RNA-Seq identified changes in circulating immune cell populations that matched traditional hematology. Together, these results show the complementarity of RNA-Seq and NanoString for gene expression analysis, verifying host biomarkers of infection, and predicting changes in cell types.
2017-11-09 | GSE99463 | GEO
Project description:RNA deep sequencing analysis was perfromed on PBMCs obtained from cynomolgus macaques (CMs) prior to and after immunization with VSV carrying ZEBOVgp (VSVΔG/ZEBOVgp) and at multiple points after ZEBOV challenge
2014-12-29 | GSE64538 | GEO
Project description:The 2013-2016 Ebola Zaire virus (EBV) outbreak in West Africa resulted in over 28,000 cases and 11,000 deaths. Ebola virus disease (EVD) is a highly virulent systemic disease with a high case fatality rate of ~ 50%. EVD results in hemorrhagic fever marked by an exaggerated systemic inflammatory response, and impaired vascular and coagulation systems. The immune response of patients who either survived or died is characterized by strong differences. Notably, fatalities showed a diminished capacity to mount an appropriate immune response, resulting in high viremia and increased pro-inflammatory cytokine production. In this study, we analyzed 38 sequential samples collected from 12 patients: 8 survivors and 4 fatalities. Our analytical strategy combined three protein-based platforms covering three different fractions of the plasma proteome: the undepleted classical plasma proteome, the depleted plasma proteome, and cytokines/chemokines, using LC/MS- and antibody-based assays, resulting in over 1000 quantified host and pathogen proteins. For depletion of the most abundant plasma proteins, we advanced a perchloric acid-based precipitation method. This method is low cost, high-throughput and robust.
2022-03-29 | PXD030260 | Pride
Project description:Ebola (EBOV) virus causes severe and often lethal hemorrhagic fever in humans and nonhuman primates (NHP), and has been classified as a Category A bioweapon agent. There are currently no approved preventive vaccines or postexposure treatments for EBOV hemorrhagic fever. The mechanisms of EBOV pathogenesis are only partially understood, but the dysregulation of normal host immune responses (including destruction of lymphocytes, increases in levels of circulating proinflammatory cytokines, and development of coagulation abnormalities) is thought to play a major role. Accumulating evidence suggests that much of the observed pathology is not the direct result of virus-induced structural damage but rather is due to the release of soluble immune mediators from EBOV-infected cells. It is therefore essential to understand how the candidate therapeutic may be interrupting the disease process and/or targeting the infectious agent. Identification of effective treatment strategies may greatly benefit based on identification of molecular features of the host response to infection and treatment. In order to identify these gene signatures related to correlates of protection, we used a DNA microarray-based approach to compare the host genome-wide responses of EBOV-infected NHP responding to candidate therapeutics. With this approach, we have identified genes that appear to correlate with survival, including chemokine ligand 8 (CCL8/MCP-2), and revealed a subset of distinctly differently expressed genes that may provide possible targets for future diagnostics or therapeutics. These analyses will assist us in understanding the pathogenic mechanisms of EBOV infection as well as identify improved therapeutic strategies. Transcriptional analysis of global gene expression changes in Zaire Ebola Virus (ZEBOV)-infected rhesus macaques that were treated with either recombinant nematode anticoagulant protein c2 (rNAPc2) or recombinant human activated protein C (rhAPC). Animals were infected with 1000pfu ZEBOV, then subsequently treated with rNAPc2 or rhAPC. Four animals were left untreated for controls. Blood samples were taken at specified days post-infection and PBMCs were isolated from the samples and inactivated in TRIzol reagent. Total RNA was isolated from the samples, then linearly amplified and hybridized to a whole genome long-oligonucleotide microarray in a two color comparative format with a commercially available human reference RNA from Stratagene as a consistent control in dataset comparisons.
2010-11-30 | E-GEOD-24943 | biostudies-arrayexpress
Project description:The purpose of this experiment was to obtain samples for transcriptome analysis using wild-type viruses: Zaire Ebola (ZEBOV '76) and Reston Ebola (REBOV '08). Overview of Experiment: Cells: Immortalized Human Hepatocytes (IHH); seed 60,000 cells per well in a 24-well plate. Infected with a multiplicity of infection (MOI) of 0.5. After infection, 3x wash with PBS and replace with 5% FCS DMEM without NaPyr or NEAA. Time matched mocks done in triplicate from same cell stock as rest of samples. Time Points = 0, 8, 24, 48, and 72 hrs post infection in triplicate. (For miRNA: 8, 24, 48, 72 hours.)
2015-02-04 | E-GEOD-65573 | biostudies-arrayexpress
Project description:Zaire ebolavirus (ZEBOV) is among the deadliest known human pathogens, causing severe hemorrhagic fever with high case fatality rates ranging from 70-90%. The lack of effective vaccines or treatment available for ZEBOV renders this pathogen as a significant global biodefense threat, as evidenced by the current, highly lethal outbreak of a novel ZEBOV variant in western Africa. Existing mouse models of lethal ZEBOV infection do not reproduce hallmark symptoms of Ebola hemorrhagic fever (EHF) including prolonged blood coagulation, acute hepatitis, disseminated intravascular coagulation (DIC), and death from hemorrhagic shock, thus restricting pathogenesis studies to non-human primates (NHP). This has prevented rapid evaluation of countermeasures in outbreak scenarios, and impeded a comprehensive understanding of how host responses to infection contribute to severe EHF disease. Here we demonstrate that mice from the Collaborative Cross (CC), a panel of reproducible, recombinant inbred animals that span the genetic breadth of three murine subspecies, are susceptible to a spectrum of disease phenotypes following ZEBOV infection. In contrast to C57Bl6/J mice, which develop lethal disease without symptoms of EHF, CC recombinant inbred intercrossed (CC-RIX) lines develop either complete resistance to lethal disease or severe EHF characterized by prolonged coagulation times and 100% mortality. Disease resistance and survival is not dependent on viral tropism, as both resistant and EHF-susceptible lines show similar inflammation and cytopathic effect in target organs. Transcriptomics reveal potential mechanisms for both induction of severe hemorrhage in EHF mediated by IL-6 and vascular activation, and resistance to lethal infection by induction of lymphocyte differentiation and cellular adhesion. These data demonstrate that host responses specific to unique genetic backgrounds determine susceptibility to hemorrhagic syndrome independent of virus replication. The CC represents a novel mouse model for studying EHF pathogenesis, and we anticipate that it will be applied immediately to developing and evaluating therapeutic countermeasures. Microarrays were performed on liver and spleen samples from mice collected at days 1, 3, and 5 post-infection with mouse adapted Zaire ebolavirus or from time-matched mock-infected animals.
2014-05-01 | E-GEOD-57214 | biostudies-arrayexpress
Project description:Ebola Virus Disease (EVD), caused by the Ebola virus (EBOV), recently made headlines as it cause a large outbreak in West Africa killing more than 11,000 individuals. One aspect of an outbreak of this scale is understanding disease transmission and differences in the host response to infection. In animal models for disease, particularly non-human primate models of disease, a large infectious dose of 1000PFU through intramuscular injection results if a fairly uniformly lethal disease were the animals die after 6-9 days. However, this is not representative of actual transmission routes of infection as humans tend to have variable exposures through cuts and mucosal surfaces and have variable times to death. To determine if a low dose infection through a mucosal surface results in a different host response to infection, we infected 12 cynomologus macaques with 100PFU of EBOV-Makona (EBOV-Mak). To follow the host response to infection, we utilized RNA-Sequencing and a newly developed NanoString codeset to monitor changes in RNA transcripts. We found that despite different onset of disease and some animals presenting with delayed time to death, there was a highly conserved and predictable host response to infection. When animals were aligned based on onset of fever, the first clinical sign of severe disease, the host response to infection was able to be modeled showing a predictable pattern of gene expression with ISG appearing as early as 4 days before fever onset. Together, this shows that lethal EVD has a uniform and predictable response to infection and that expression of a subst of genes is present before the onset of fever.
2018-04-12 | GSE103825 | GEO
Project description:Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever. In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions we have examined the molecular features of EBOV infection in vivo. Using self-spotted cDNA microarrays, we analyzed genome-wide host expression patterns in sequential blood samples from nonhuman primates (NHP) infected with EBOV. A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design
2007-06-28 | GSE8317 | GEO
Project description:The purpose of this experiment was to obtain samples for mRNA analysis in IHH cells infected with Zaire Ebola virus and mutants: Zaire Ebola virus: This wild-type Ebola virus - strain Mayinga - was isolated from a fatal human case in Zaire (now known as the Democratic Republic of Congo) in 1976 Zaire Ebola virus, VP35 R312A possesses a R312A mutation in the VP35 protein. Zaire Ebola virus, delta sGP. Lacks the ability to produce non-structural protein, the secreted glycoprotein (sGP). Zaire Ebola virus, delta mucin. Lacks the mucin-like domain (MLD), which contains both N-linked and O-linked glycosylation sites, for the glycoproteins. Overview of Experiment: Cells: Immortalized Human Hepatocytes (IHH); seed 60,000 cells per well in a 24-well plate. Infected with a multiplicity of infection (MOI) of 0.5. After infection, 3x wash with PBS and replace with 5% FCS DMEM without NaPyr or NEAA. Time matched mocks done in triplicate from same cell stock as rest of samples. Time Points = 0, 6, 12, 24, 48, and 72 hrs post infection in triplicate.
2015-06-18 | E-GEOD-69943 | biostudies-arrayexpress