Proteomics of Culex tarsalis cells persistently infected with Culex narnavirus 1
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ XL
ORGANISM(S): Culex Tarsalis (ncbitaxon:7177) Culex Narnavirus 1 (ncbitaxon:2562539)
SUBMITTER: 
Joseph L. DeRisi
PROVIDER: MSV000086532 | MassIVE | Fri Nov 27 21:32:00 GMT 2020
REPOSITORIES: MassIVE
Similar Datasets
Project description:Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High-throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a pathogenic mechanism. Since SARS-CoV2 is a positive sense RNA virus that replicates in the cytoplasm it does not have a nuclear phase in its life cycle, so it is biologically unlikely to be in a location where splicing events could result in genome integration. Here, we investigated the biological authenticity of HVC events. In contrast to true biological events, e.g. mRNA splicing and genome rearrangement events, which generate reproducible chimeric sequencing fragments across different biological isolates, we found that HVC events across >100 RNA-seq libraries from patients with COVID-19 and SARS-CoV2 infected cell lines, were highly irreproducible. RNA-seq library preparation is inherently error-prone due to random template switching during reverse transcription of RNA to cDNA. By counting chimeric events observed when constructing an RNA-seq library from human RNA and spike-in RNA from an unrelated species, such as fruit-fly, we estimated that ~1% of RNA-seq reads are artifactually chimeric. In SARS-CoV2 RNA-seq we found that the frequency of HVC events were, in fact, no more frequent than this background “noise”. Finally, we developed a novel experimental approach to enrich SARS-CoV2 sequences from bulk RNA of infected cells. This method enriched viral sequences but did not enrich for HVC events, suggesting that the majority of HVC events are, in all likelihood, artifacts of library construction. In conclusion, our findings indicate that HVC events observed in RNA-sequencing libraries from SARS-CoV2 infected cells are extremely rare and are likely artifacts arising from either random template switching of reverse-transcriptase and/or sequence alignment errors. Therefore, the observed HVC events do not support SARS-CoV2 fusion to cellular genes and/or integration into human genomes.
2021-02-19 | GSE167131 | GEO
Project description:GFP-tagged viral peptide sequences and their controls were used to pull down interactors from human (uninfected) or green monkey (viral infected) cell lysate. After sample preparation, digestion and bottom-up LC-MS/MS analysis, the enriched proteins were identified.
2023-03-09 | PXD033874 | Pride
Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943 viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.
2016-09-06 | E-GEOD-81392 | biostudies-arrayexpress
Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.
2016-09-05 | E-GEOD-81391 | biostudies-arrayexpress
Project description:Wolbachia is a vertically transmitted intracellular bacteria that infect most than 60% of insect species. The strains wMelPop and wMel were introduced in the dengue virus vector Aedes aegypti, naturally not infected by Wolbachia. Recently, it was shown that those two strains inhibit dengue virus replication into their new host, A. aegypti (Moreira et al. 2009 and Walker et al. in preparation). The aim of this project is to look at the transcriptional response of Aedes aegypti to infection with wMel and wMelPop and try to find some genes or pathway potentially involved in the viral interference.Four laboratory lines of A. aegypti were used throughout this study. The PGYP1 and Mel2 lines were generated by transinfection with wMelPop and wMel strains respectively. PGYP1.tet and Mel2tet lines were treated with the antibiotic tetracycline and cured from Wolbachia infection (McMeniman et al., 2009 and Walker et al in preparation). The Mosquitoes were reared under standard laboratory conditions (26 ± 2 °C, 12:12 light/dark cycle, 75% relative humidity). Mosquito larvae were fed 0.1mg/larvae of TetraMin Tropical Tablets once a day. Adults were transferred to cages (measuring 30 x 30 x 30 cm) at emergence at 400 individuals per cage. Adults were supplied with a basic diet of 10% sucrose solution (Turley et al., 2009).
2012-01-01 | E-MEXP-2931 | biostudies-arrayexpress
Project description:The mosquito-borne chikungunya virus (CHIKV) poses a threat to human health in tropical countries throughout the world. The molecular interactions of CHIKV with its mosquito vector, Aedes aegypti are not fully understood. Following oral acquisition of CHIKV via salinemeals, we analyzed changes in the proteome of Ae. aegypti in 12 h intervals by label-free timsTOF Pro mass spectrometry. For each of the seven time points, between 2647 and 3167 proteins were identified among CHIKV infected and non-infected mosquito samples and fewer than 6% of those identified proteins were affected by the virus.
2020-03-18 | MSV000085115 | MassIVE
Project description:Background: The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it be responsible for transposon silencing in this mosquito. Results: Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions: Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster. 5 small RNA libraries were generated from total RNA of whole adult Aedes aegypti tissues, two of these libraries were sequenced twice (technical replicates). 1 small RNA library was generated from total RNA of a whole adult Drosophila melanogaster tissue.
2014-03-18 | E-GEOD-33595 | biostudies-arrayexpress
Project description:In the context of studying visceral leishmaniasis, neutrophils infected with Leishmania donovani have been compared to uninfected neutrophils. Compared time points are 0, 6 and 24 hours post infection. Neutrophils of three human donors have been used. Overall 6 samples for infected neutrophils at time point 6 hours and 6 samples for infected neutrophils at time point 24 hours exist, including three biological samples and two technical samples. Uninfected neutrophils represent 3 samples at time point 0 hours, 3 samples at time point 6 hours and 3 samples at time point 24 hours. Transcriptome of Leishmania donovani culture has been assessed in two replicates.
| EGAS00001004912 | EGA
Project description:Interleukin (IL)-10 is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper cell (TFH) differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph node (LN) are induced by infection and not normalized with ART. During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were significantly correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including TFH, and predicted the frequency of CD4+ TFH and their cell- associated SIV-DNA content during ART, respectively. Notably, in ART-treated RMs, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B-cell follicle in close proximity to IL-10. Finally, we demonstrate that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques significantly reduces B cell follicle maintenance and, by extension, cellular sites of viral persistence, including LN TFH and memory CD4+ T-cells expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T-cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.
2022-02-09 | GSE196182 | GEO
Project description:Wolbachia endosymbionts are widespread intracellular, maternally inherited bacteria which manipulate the host to favour their spread through a population. Cytoplasmic incompatibility (CI) and viral suppression are two such manipulations driven by uncharacterised mechanisms. To gain insight into potential molecular mechanisms responsible for these effects, we performed the first in-depth proteomic characterisation of the host response to Wolbachia infection. We find that the presence of the Wolbachia wMelPop in Aedes aegypti mosquito cells alters levels of proteins involved in cell cycle control, DNA replication, autophagy, vesicular trafficking, iron homeostasis, amino acid degradation, purine metabolism, lipid metabolism and immunity. The majority of the cell cycle/DNA replication proteins were downregulated in the presence of Wolbachia, in particular, a member of the anoctamin family was strongly down regulated which may be related to the chromosomal segregation defects observed in CI crosses. We found clear evidence for perturbed lipid metabolism, Wolbachia infected cells expressed higher levels of Apolipoprotein D and the cholesterol efflux transporter ABCA1, while the LDL receptor and fatty acid synthase were downregulated. ABCA1 was also upregulated at the mRNA level in adult Wolbachia infected Aedes aegypti mosquitoes. Wolbachia therefore perturbs cholesterol homeostasis causing the host cell to respond to an apparent cholesterol excess which may contribute to viral inhibition.
2017-09-19 | PXD003429 | Pride