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PXD011354-1

PXD011354 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSupervised learning predicts the in vivo fate of engineered nanomaterials
DescriptionDespite 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.
HostingRepositoryPRIDE
AnnounceDate2024-09-14
AnnouncementXMLSubmission_2024-09-14_12:53:14.515.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJonathan Krieger
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListiodoacetamide derivatized residue
InstrumentLTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-10-15 02:02:15ID requested
12024-09-14 12:53:15announced
22024-10-22 06:58:23announced2024-10-22: Updated project metadata.
Publication List
10.1021/acsnano.9b02774;
Lazarovits J, Sindhwani S, Tavares AJ, Zhang Y, Song F, Audet J, Krieger JR, Syed AM, Stordy B, Chan WCW, Fate of Nanomaterials. ACS Nano, 13(7):8023-8034(2019) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: Nanoparticles, protein corona, mass spectrometry, neural networks, predictive biology
Contact List
Warren Chan
contact affiliationInstitute of Biomaterials and Biomedical Engineering, Department of Chemical Engineering, Department of Chemistry, Department of Materials Science and Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
contact emailchanwarr@me.com
lab head
Jonathan Krieger
contact affiliationBruker
contact emailJRKrieger@gmail.com
dataset submitter
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Dataset FTP location
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