Browse
Submit Data
Databases
API
Help

Dataset Information

237 Views

0 Connections

1 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanoparticle protein corona LC-MS/MS

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Bos Taurus (bovine)

TISSUE(S): Cell Culture

SUBMITTER: Jacob Kuruvilla

LAB HEAD: Susana Christobal

PROVIDER: PXD004636 | Pride | 2017-02-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PC_10nm_1.msf	Msf
	PC_10nm_1.mzid.gz	Mzid
	PC_10nm_1.mzid_PC_10nm_1.MGF	Mzid
	PC_10nm_1.mzid_PC_10nm_1.pride.mgf.gz	Mzid
	PC_10nm_1.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 138

Similar Datasets

Interaction of TiO2 nanoparticles with lung fluid proteins and the resulting macrophage inflammatory response

Project description:Inhalation is a major nanoparticle exposure pathway. Following inhalation, nanoparticles first interact with the lung lining fluid, a complex mixture of proteins, lipids, and mucins. We measure the concentration and composition of lung fluid proteins adsorbed on the surface of titanium dioxide (TiO2) nanoparticles. Using proteomics, we find that lung fluid results in a unique protein corona on the surface of the TiO2 nanoparticles.

2023-11-10 | PXD041036 | Pride

Supervised learning predicts the in vivo fate of engineered nanomaterials

Project description:Despite having exquisite control over nanoparticle design, controlling nanoparticle fate in vivo remains a major barrier for clinical translation. This is because we do not understand how nanoparticles interact with the surrounding environment in vivo and how this lack of control contributes towards organ accumulation. The suggested link between nanoparticle interactions and organ accumulation are the proteins that adsorb to the nanoparticle surface following administration. How this network of proteins changes during nanoparticle transport, and its influence over the fate of where nanoparticles distribute inside of the body is fundamentally not understood. Here we developed a simple workflow to show that the evolution of proteins on the surface of nanoparticles predicts the biological fate of nanoparticles in vivo. This workflow involves extracting nanoparticles at multiple time points from circulation, isolating the proteins off the surface, and training a neural network to predict nanoparticle biological fate using the proteins as inputs and clearance and organ accumulation as outputs. In a double-blind study, we validated the model by predicting nanoparticle clearance and spleen and liver accumulation with 76-97% accuracy. This work demonstrates that a link between surface adsorbed proteins and the biological fate of nanomaterials exists, and that it can be predicted using the workflow we designed. As we acquire more training data, the strength of these relationships will become more powerful. With more training data we will use more sophisticated neural networks to identify proteins and pathways to target, or create more effective nanomaterial designs to improve clinical translation.

2024-09-14 | PXD011354 | Pride

Global genetic impact of surface-modified gold nanoparticles on two model human cell lines

Project description:Gold nanoparticles (Au NPs) are uniquely suited for various biomedical applications due to the combination of their optical properties with their easily functionalized surfaces. The Au NP surface can be tailored to improve biocompatibility while also attaching targeting ligands or drugs. However, information on how these tailored surface chemistries may affect cell gene expression is scarce. Using two model human cells line, human dermal fibroblasts and prostate cancer cells, microarray experiments measured gene expression over 27,000 human genes. Each of the cell lines was exposed to four related types of surface-modified Au NPs at two different concentrations, and the microarray data was analyzed by weighted gene correlation network analysis and gene functional annotation. Au NPs were shown to affect genes associated with a variety of cellular functions, and surface charge and chemistry were linked with the types of parthways changed and the degree of which those changes occured. Nanoparticle induced gene expression in PC3 and HDF cells was measured after 24 hour exposure to nanoparticles of four different surface coating types. RNA from three separate culture samples were used for each nanoparticle-cell combinations, along with three control samples not exposed to nanoparticles at all.

2014-10-01 | E-GEOD-56432 | biostudies-arrayexpress

Expression data from primary human hepatic stellate cells treated with coated and uncoated ZnO nanoparticles, or ZnSO4

2014-08-07 | GSE60159 | GEO

Expression data from primary human hepatic stellate cells treated with coated and uncoated ZnO nanoparticles, or ZnSO4

Project description:ZnO nanoparticles can elicit a range of perturbed cell responses in vitro. The liver is a target for ZnO nanoparticle-, or Zn2+ released from ZnO nanoparticles-induced accumulation and/or impact in vitro and in vivo. The response of human hepatic stellate cells to ZnO nanoparticles has not yet been assessed. We aimed to determine whether the presence of surface coatings could protect human hepatic stellate cells from ZnO nanoparticle-induced cytotoxicity. Primary human hepatic stellate cells were treated with one of two types of uncoated ZnO nanoparticles (Z-COTE or Nanosun), two types of coated ZnO nanoparticles (HP1, MAX), a mass equivalent of ZnSO4, or were left untreated. After 24 h, RNA was isolated and processed for whole genome transcriptional profiling, comparing the expresson profiles of treated cells to the untreated controls. Each treatment was prepared in duplicate.

2014-08-07 | E-GEOD-60159 | biostudies-arrayexpress

Non-labelled proteomics expression analysis of PC-3 cells treated with transferrin conjugated gold nanoparticles

Project description:Nanoparticles-based therapeutics are being clinically translated for treating cancer. Meanwhile nanoparticles are increasingly being identified as impacting cell regulation and protein expression. Here, we sought to understand how a model of a relatively inert nanoparticle without any therapeutic agent itself interact with the cells and what are the key biological mechanisms.

2023-10-24 | PXD039433 | Pride

Gene expression profile of STAT3 in ovarian cancer cell (SKOV3ip1)

Project description:RNA interference (RNAi) holds tremendous potential as a therapeutic approach, especially in the treatment of malignant tumors. However, efficient and biocompatible delivery methods are needed for systemic delivery of siRNA. To achieve this goal, we have established a novel formulation of siRNA by incorporating it into reconstituted high density lipoprotein (rHDL) nanoparticles. Here, we demonstrate that rHDL nanoparticles facilitate highly efficient systemic delivery of siRNA in vivo, mediated by the scavenger receptor type B1 (SR-B1). Moreover, in therapeutic proof-of-concept studies, these nanoparticles were effective in targeting either signal transducer and activator of transcription 3 (STAT3) or focal adhesion kinase (FAK) expression in orthotopic mouse models of ovarian and colorectal cancer. These data indicate that an rHDL nanoparticle is a novel and highly efficient siRNA carrier, and therefore this novel technology could serve as the foundation for new cancer therapeutic approaches. To identify the role of STAT3 in ovarian cancer cell, we performed microarray after knocking down STAT3 in ovarican cancer cells (3 siCon and 3 siSTAT3).

2011-12-22 | E-GEOD-20597 | biostudies-arrayexpress

The effect of CuO nanoparticles on gene expression patterns in Daphnia magna

Project description:There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions. 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank

2014-03-01 | E-GEOD-54738 | biostudies-arrayexpress

The effect of ZnO nanoparticles on gene expression patterns in Daphnia magna

2014-03-01 | E-GEOD-54736 | biostudies-arrayexpress

RNAseq of human epithelial lung carcinoma cell line A549 exposed to ceria, silver or zinc ions, micron-sized particles or nanoparticles

Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .

2018-02-01 | E-MTAB-5734 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data