PXD020367-2

PXD020367 is an original dataset announced via ProteomeXchange.

Title	Autophagosome Proteomics of HEK293 cells
Description	Pan-caspase inhibitor Z-VAD-fmk acts as an inhibitor of peptide:N-glycanase (NGLY1); an endoglycosidase which cleaves N-linked glycans from glycoproteins exported from the endoplasmic reticulum during ER-associated degradation (ERAD). Pharmacological N-glycanase inhibition by Z-VAD-fmk or siRNA knockdown (KD) induces GFP-LC3 positive puncta in HEK293 cells. Activation of ER stress markers or reactive oxygen species (ROS) induction are not observed. In NGLY1 inhibition or KD, upregulation of autophagosome formation without impairment of autophagic flux are observed. Enrichment and proteomics analysis of autophagosomes after Z-VAD-fmk treatment or NGLY1 KD reveals similar autophagosomal protein content. Autophagy represents a cellular adaptation to NGLY1 inhibition or KD, and ATG13-deficient mouse embryonic fibroblasts (MEFs) show reduced viability under these conditions. In contrast, treatment with pan-caspase inhibitor, Q-VD-OPh does not induce cellular autophagy. Therefore, experiments with Z-VAD-fmk are complicated by the effects of NGLY1 inhibition and Q-VD-OPh represents an alternative caspase inhibitor free from this limitation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:22.342.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Holger Kramer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-14 22:50:28	ID requested
1	2022-01-12 14:33:16	announced
⏵ 2	2023-11-14 08:50:22	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: autophagy

autophagosome

NGLY1

N-Glycanase

Z-VAD-fmk

off-target

Holger Kramer
contact affiliation	Proteomics & Metabolomics Facility, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, United Kingdom
contact email	h.kramer@lms.mrc.ac.uk
lab head
Holger Kramer
contact affiliation	MRC London Institute of Medical Sciences
contact email	h.kramer@lms.mrc.ac.uk
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/2022/01/PXD020367

PRIDE project URI

• PRIDE
  1. PXD020367
     1. Label: PRIDE project
     2. Name: Autophagosome Proteomics of HEK293 cells