PXD047011

PXD047011 is an original dataset announced via ProteomeXchange.

Title	Multilayered-proteomics analysis of insulin signaling in insulin sensitive and resistant HepG2 IGF1R KO cell line
Description	This is a mass spectrometry (MS)-based proteomics dataset, generated to study insulin signaling in a hepatocellular cell model (HepG2 insulin-like growth factor knock-down), at the IR interactome, phos-phoproteome, and proteome level. To induce insulin sensitivity and resistance in HepG2 IGF1R KO cells, the following protocol, established based on a previously published study by Dall’Agnese et al. (https://doi.org/10.1038/s41467-022-35176-7), was used. The day after cell seeding, culture medium was changed to serum-free low glucose DMEM for 48 hours. Following the serum washout, cells were treated for 48 hours in low glucose DMEM with 1.25 % HSA (human serum albumin) and either a phys-iologic level of 0.1 nM insulin and a pathologic level of 3 nM insulin, to make the cells either sensitive or resistant to insulin. Insulin sensitive and resistant HepG2 IGF1R KO cells, were subjected to an insulin wash-out over 35 minutes, with 7 media exchanges. Afterwards, the cells were stimulated for 5 minutes with varying insulin concentrations (0, 0.1, 3, or 100 nM) in low glucose DMEM with 1.25% HSA. Note that 0.1 nM is named 100 pM in the files. We performed 5 biological independent experiments, which were used to study the IR interactome, phosphoproteome, and a reference single-shot proteome. These cells were lysed in a co-immunoprecipitation (IP)-lysis buffer, preserving protein-interactions. Additional-ly, we generated SDS-based label-free DIA-MS single-shot proteome dataset, from four independent experiments of the insulin sensitive and resistant HepG2 IGF1R KO cells, directly after the insulin-resistance inducing procedure.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_13:57:02.754.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sarah Jørgensen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-16 01:55:36	ID requested
⏵ 1	2025-05-06 13:57:03	announced

10.1038/s41598-024-77817-5;

J, ø, rgensen SH, Emdal KB, Pedersen AK, Axelsen LN, Kildegaard HF, Demozay D, Pedersen T Å, Gr, ø, nborg M, Slaaby R, Nielsen PK, Olsen JV, Multi-layered proteomics identifies insulin-induced upregulation of the EphA2 receptor via the ERK pathway which is dependent on low IGF1R level. Sci Rep, 14(1):28856(2024) [pubmed]

submitter keyword: insulin resistance, proteomics, insulin receptor,Interactome, label-free DIA LC-MS/MS, phosphoproteomics, hepatoma cell line

Jesper Velgaard Olsen
contact affiliation	Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Sarah Jørgensen
contact affiliation	Universitry of Copenhagen Novo Nordisk A/S
contact email	sjzq@novonordisk.com
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/2025/05/PXD047011

PRIDE project URI

• PRIDE
  1. PXD047011
     1. Label: PRIDE project
     2. Name: Multilayered-proteomics analysis of insulin signaling in insulin sensitive and resistant HepG2 IGF1R KO cell line