PXD033552

PXD033552 is an original dataset announced via ProteomeXchange.

Title	Pharmacoproteomic profiling directed by C. elegans-driven phenotypic quantitative HTS
Description	Quantitative high-throughput screening (qHTS) pharmacologically evaluates libraries of drugs and investigational agents for potential therapeutic uses, toxicological risk assessment, and increasingly for academic chemical tool discovery. Phenotypic HTS assays aim to interrogate molecular pathways and networks, often relying on cell culture systems, historically with less emphasis on multicellular organisms. C. elegans has served as a powerful eukaryotic model organism for human biology and disease by virtue of genetic conservation and experimental tractability. Here we describe a paradigm to enable C. elegans in qHTS using 384-well microtiter plate laser scanning cytometry for rapid signal acquisition with concurrent quantification of the fluorescent protein-expressing organism to select phenotype-modifying compounds for subsequent life-stage and proteomic analysis. E. coli bacterial ghosts, a non-replicating nutrient, allow compound exposures over 7-days spanning two life cycles to mitigate complications from bacterial overgrowth. We demonstrate the method using 643 anti-infective biased agents tested in 7-pt titration to assess feasibility of nematode-based in vivo qHTS. A pharmacological profile from the primary screen confirmed the efficacy of known anti-parasitic molecules, such as ivermectin and levamisole as well as illuminating anthelmintic properties of general chemical classes, including MEK, -secretase, bromodomain and proteasome inhibitors. Subsequent life-stage and proteomics analysis helped elucidate the physiologic consequence of specific compounds on C. elegans viability. For example, bortezomib induced a parallel upregulation of core proteasome subunits and the transcription factor skn-1-activating DDI aspartyl protease, while the kinase inhibitor trametinib upregulated the C. elegans MEK-1 ortholog, Mnk-1, downstream aminoacyl tRNA synthetases and ribosomal survival pathway proteins. We anticipate a broader application of this qHTS-coupled proteomics approach will enable the analysis of C. elegans orthologous transgenic phenotypes of human pathologies to facilitate drug and probe profiling from high-impact chemical libraries for a range of therapeutic indications.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:56:34.756.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD033552
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Dingyin Tao
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-28 02:30:51	ID requested
1	2023-02-21 07:22:55	announced
⏵ 2	2023-11-14 08:56:35	announced	2023-11-14: Updated project metadata.

10.6019/PXD033552;

submitter keyword: model organisms, laser cytometry, proteomics,drug discovery, infectious disease, genetic disorders, high-throughput screening

Dingyin Tao
contact affiliation	National Institutes of Health (NIH) National Center for Advancing Translational Sciences (NCATS)
contact email	dingyin.tao@nih.gov
lab head
Dingyin Tao
contact affiliation	National Institutes of Health (NIH) National Center for Advancing Translational Sciences (NCATS)
contact email	dingyin.tao@nih.gov
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/2023/02/PXD033552

PRIDE project URI

• PRIDE
  1. PXD033552
     1. Label: PRIDE project
     2. Name: Pharmacoproteomic profiling directed by C. elegans-driven phenotypic quantitative HTS