Genome-wide forward genetic screening to identify receptors and proteins mediating nanoparticle uptake and intracellular processing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB71925 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12495491.fastq.gz | Fastqsanger.gz | |||
| ERR12495492.fastq.gz | Fastqsanger.gz | |||
| ERR12495493.fastq.gz | Fastqsanger.gz | |||
| ERR12495494.fastq.gz | Fastqsanger.gz | |||
| ERR12495495.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Rational design of nanocarriers for drug delivery approaches requires an unbiased knowledge of uptake mechanisms and intracellular trafficking pathways. Here we dissected these processes using a quantitative proteomics approach. We isolated intracellular vesicles containing superparamagnetic iron oxide polystyrene nanoparticles and analyzed their protein composition by label free quantitative mass spectrometry. The proteomic snapshot of organelle marker proteins revealed that an atypical macropinocytic-like mechanism mediated the entry of nanoparticles. We show that the entry mechanism is controlled by actin reorganization, atypical macropinocytic signaling and ADP-ribosylation factor 1. Additionally, our proteomics data demonstrated a central role for multivesicular bodies and multilamellar lysosomes in trafficking and final nanoparticle storage. This was confirmed by confocal microscopy and cryo-TEM measurements. By quantitatively analyzing the protein composition of nanoparticle-containing vesicles, our study clearly defines the routes of nanoparticle entry, intracellular trafficking and the proteomic milieu of a nanoparticle-containing vesicle.
2014-09-25 | PXD001175 | Pride
Project description:Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model
| PRJNA613652 | ENA
Project description:Engineered nanoparticles for biomedical applications require increased effectiveness in targeting specific cells while preserving non-target cells’ safety. Native nanoparticles entering a protein-rich liquid media quickly form a macromolecular structure called protein corona. This protein structure defines the physical interaction between nanoparticles and target cells. We describe SUSTU (surface proteomics for nanoparticle safety, targeting and uptake) a proteomics-based method to analyze the surface of a nanoparticle protein corona. This method provides qualitative and quantitative analysis from the protein corona surface. Those exposed proteins compose the first line of interaction between this macromolecular structure and the cell surface of a target cell. With SUSTU, the spatial and temporal dynamics of the protein corona surface can be studied. Data from SUSTU would ascertain the nanoparticle functionalized groups exposed at destiny; circumventing preliminary in vitro experiments. Therefore this method evaluates nanoparticle targeting and uptake capability and could be integrated into a rapid prototyping strategy which is a major challenge in nanomaterial science.
2017-02-28 | PXD004636 | Pride
Project description:We report the development of a new multiomic nanoparticle delivery system called Single cEll Nanoparticle Transcriptome-sequencing (SENT-seq), which quantifies how dozens of lipid nanoparticles (LNPs) deliver DNA barcodes and mRNA into cells, subsequent protein production, and the transcriptome, with single cell resolution. We show from the sequencing data that cell heterogeneity influences the efficiency with which LNPs deliver mRNA therapies, and identify cell subtypes that exhibit particularly high or low LNP uptake as well as genes associated with those subtypes. These data suggest that cell subsets have distinct responses to LNPs, and that these differential interactions can affect mRNA therapies.
2023-01-23 | GSE186395 | GEO
Project description:We sequenced the transcroptome of isolated nanoparticle positive and nanoparticle negative tumour endothelial cells from mouse 4T1 mammary tumours
2021-09-07 | GSE172496 | GEO
Project description:An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection. P. aeruginosa Genechip Genome Array (Affymetrix, P/N 900339) was used in order to study the cells after the addition of ZnO nanoparticles. DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).
2015-05-25 | E-GEOD-46947 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Shewanella oneidensis MR-1 to Fe nanoparticle decorated anodes, compared to the carbon plate anodes in microbial electrolysis cells. Whole genome microarray analysis of the gene expression showed that the encoding biofilm formation genes were significantly up-regulated as response to nanoparticle decorated anodes which indicated thickness improvements contributed to enhance current density. The increased expression genes related to nanowire, flavins and c-type cytochromes also have partially contributed to enhance current density by Fe nanoparticle decorated anode. The majority of additional differentially expressed genes associated with electron transport, anaerobic metabolism in response to the nanostructured anodes possibly play roles in current density enhancement. A six chip study using total RNA recovered from three separate replicates of biofilm on Fe Nanoparticle decorated anode of Shewanella oneidensis MR-1 and three separate replicates of carbon plate control. Each chip measures the expression level of 4,295 genes .
2011-08-19 | E-GEOD-31535 | biostudies-arrayexpress
Project description:The use of engineered nano-sized materials led to revolutionary developments in many industrial applications and in the medical field. These materials, however, also may cause cytotoxicity. In addition to size, surface properties and shape were identified as relevant parameters for cell damage. Cell damage may occur as disruption of membrane integrity, induction of apoptosis and by organelle damage. Generation of oxidative stress may serve as an indicator for cytotoxicity. Effects occurring upon short contact of particles with cells, for instance in the systemic blood circulation, could be identified according to increases of intracellular [Ca(2+) ] levels, which are caused by variety of toxic stimuli. Negatively charged, neutral and positively charged polystyrene particles of different sizes were used to study the role of size and surface properties on viability, membrane disruption, apoptosis, lysosome function, intracellular [Ca(2+) ] levels and generation of oxidative stress. Silica particles served to test this hypothesis. Twenty nm polystyrene particles as well as 12 nm and 40 nm silica particles caused membrane damage and apoptosis with no preference of the surface charge. Only 20 nm plain and amine functionalized polystyrene particles cause oxidative stress and only the plain particles lysosomal damage. A potential role of surface charge was identified for 200 nm polystyrene particles, where only the amidine particles caused lysosomal damage. Increases in intracellular [Ca(2+) ] levels and cytotoxicity after 24 h was often linked but determination of intracellular [Ca(2+) ] levels could serve to characterize further the type of membrane damage.
| S-EPMC4606983 | biostudies-literature
Project description:In this study, we attempted to compare among the stress of Y2O3 nanoparticle and YCl3 to yeast cells. Yttrium oxide (Y2O3) nanoparticle is used in widespread applications. It has been reported that Y2O3 nanoparticle showed toxic activities. However, we assumed that the most important toxic factor of nanoparticles was metal ion release. We tried to prove the toxicity of yttrium nanoparticles comes from yttrium ion. Therefore, we used YCl3 as a positive control for evaluation of effects of yttrium ion.
2016-04-27 | GSE80677 | GEO
Project description:The aim of this study was to investigate the effects of administration of carbon black nanoparticle (CB-NP) to pregnant mice on the development of lymphoid tissues in infantile mice. Pregnant ICR mice were treated with a suspension of CB-NP 95 microg/kg/time) by intranasal instillation, twice, on gestational day 5 and 9. Spleen and thymus were collected from offspring mice at 5 days post-partum. RNA sample was taken from spleen of 5-day-old mouse prenatally received carbon black nanoparticle, while control RNA was taken from control counterpart prenatally received distilled water. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
2013-08-30 | E-GEOD-50432 | biostudies-arrayexpress