PXD027821-1

PXD027821 is an original dataset announced via ProteomeXchange.

Title	Interval-based secretomics unravels the time-dependent acute phase response in hepatocyte model systems
Description	Mass spectrometry based secretomics approaches preferentially utilize serum-free culture conditions to circumvent serum induced interference and enable sufficient analytical depth. However, this negatively affects a wide range of cellular functions and thus reduces the biological relevance. Moreover, the experimental time range is limited by the viability of cells under serum free culture conditions which results in potentially missing out a large fraction of transcriptionally regulated secretion events and feedback-loops. We present an “interval-based” secretomics workflow, that addresses the shortcomings of the serum-free secretomics approach, by probing protein secretion rates in short serum-free time windows. We applied this approach to unravel the time-resolved secretion in the hepatocyte model systems HepG2 and HepaRG after stimulation of the acute-phase response (APR), a cellular reaction to inflammatory stimuli that typically manifests over days. The integration of relative quantification using tandem mass tags (TMT) enabled precise monitoring of time dependent changes in the secretome over days. Cell line and cytokine specific changes were observed: IL1b directed the APR towards pathogen defense over three distinct chronological phases. In contrast, IL6 directed the APR towards regeneration. Cell surface shedding was pronounced upon IL1b stimulation and small molecule inhibition of ADAM and matrix metalloproteases identified induced as well as constitutive shedding events. Inhibition of ADAM proteases by TAPI-0 not only led to reduced shedding of the sorting receptor SORT1, but also an attenuated cytokine response suggesting a direct link between cell surface shedding and cytokine secretion rates.
HostingRepository	PRIDE
AnnounceDate	2022-05-04
AnnouncementXML	Submission_2022-05-04_04:42:29.841.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sascha Knecht
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; methionine oxidation with neutral loss of 64 Da; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-09 06:34:51	ID requested
⏵ 1	2022-05-04 04:42:30	announced

Dataset with its publication pending

submitter keyword: Secretomics, interval-based secretomics, HepG2, HepaRG, IL1b, IL6, acute-phase response, liver, shedding

Marcus Bantscheff
contact affiliation	Cellzome - a GSK company Meyerhofstrasse 1, 69117 HEIDELBERG
contact email	marcus.x.bantscheff@gsk.com
lab head
Sascha Knecht
contact affiliation	Cellzome GmbH, a GSK company
contact email	sascha.knecht@me.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/2022/05/PXD027821

PRIDE project URI

• PRIDE
  1. PXD027821
     1. Label: PRIDE project
     2. Name: Interval-based secretomics unravels the time-dependent acute phase response in hepatocyte model systems