PXD020225

PXD020225 is an original dataset announced via ProteomeXchange.

Title	Silica-cSilica-coated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysisoated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysis
Description	Exposure to nanoparticles leads to their accumulation in the brain, but drug development to counteract this nanotoxicity remains challenging. Here we assessed the effect of silica-coated-magnetic nanoparticles containing the rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)] on microglia through integration of transcriptomics, proteomics, and metabolomics. Intracellular reactive oxygen species production, an inflammatory response, and morphological activation of cells were greater, but glucose uptake was lower in MNPs@SiO2(RITC)-treated BV2 microglia and primary rat microglia. Expression of 121 genes, and levels of 45 proteins and 17 metabolites related to the above phenomena changed in MNPs@SiO2(RITC)-treated microglia. We integrated the three omics datasets and generated a single network using a machine learning algorithm. We screened 19 compounds and predicted their effects on nanotoxicity within the triple-omics network. A combination of glutathione and citrate attenuated nanotoxicity induced by MNPs@SiO2(RITC) and ten other nanoparticles in vitro and in the murine brain, protecting mostly the hippocampus and thalamus.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:32:11.681.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020225
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ju Yeon Lee
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-06 15:12:08	ID requested
1	2022-02-16 03:50:31	announced
⏵ 2	2024-10-22 05:32:14	announced	2024-10-22: Updated project metadata.

10.6019/PXD020225;

10.1186/s12989-021-00433-y;

Shin TH, Manavalan B, Lee DY, Basith S, Seo C, Paik MJ, Kim SW, Seo H, Lee JY, Kim JY, Kim AY, Chung JM, Baik EJ, Kang SH, Choi DK, Kang Y, Mouradian MM, Lee G, Silica-coated magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate identified using integrated omics. Part Fibre Toxicol, 18(1):42(2021) [pubmed]

submitter keyword: machine learning,silica-coated- magnetic nanoparticles

nanotoxicity

integrated omics, microglia

Gwang Lee
contact affiliation	Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea Immune-network pioneer research center, Ajou University School of Medicine, Suwon, Republic of Korea
contact email	glee@ajou.ac.kr
lab head
Ju Yeon Lee
contact affiliation	Korea Basic Science Institute
contact email	jylee@kbsi.re.kr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD020225

PRIDE project URI

• PRIDE
  1. PXD020225
     1. Label: PRIDE project
     2. Name: Silica-cSilica-coated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysisoated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysis