PXD055081

PXD055081 is an original dataset announced via ProteomeXchange.

Title	Proteomic characterization of ubiquitin carboxyl-terminal hydrolase 19 deficient cells reveals a role for USP19 in secretion of lysosomal proteins
Description	Ubiquitin carboxyl-terminal hydrolase 19 (USP19) is a unique deubiquitinase (DUB), characterized by multiple variants generated by alternative splicing. Several variants bear a C-terminal transmembrane domain that anchors them to the endoplasmic reticulum (ER). Other than regulating protein stability by preventing proteasome degradation, USP19 has been reported to rescue substrates from ER-associated protein degradation (ERAD) in a catalytic-independent manner, promote autophagy and address proteins to lysosomal degradation via chaperone-mediated autophagy. In addition, USP19 has recently emerged as the protein responsible for the unconventional secretion of misfolded proteins including Parkinson’s disease associated protein α-synuclein. Despite mounting evidence that USP19 plays crucial roles in a number of biological processes, the underlying mechanisms are unclear due to lack of information on the physiological substrates of USP19. Herein, we used high-resolution quantitative proteomics to analyze changes in the secretome and cell proteome induced by loss of USP19, in order to identify proteins whose secretion or turnover is regulated by USP19. We found that ablation of USP19 induced significant proteomic alterations both in and out of the cell. Loss of USP19 impaired release of several lysosomal proteins, including legumain (LGMN) and several cathepsins. In order to understand the underlaying mechanism, we dissected the USP19-regulated secretion of LGMN in several cell types. We found that LGMN was not a DUB substrate of USP19 and that its USP19-dependent release did not require their direct interaction. LGMN secretion occurred by a mechanism that involved the Golgi apparatus, autophagosome formation and lysosome function. This mechanism resembled the recently described “lysosomal exocytosis”, by which LGMN and other lysosomal hydrolases are secreted, that involves ubiquitination of p62 and is regulated by other DUBs such as USP15 and USP17. In conclusion, our proteomic characterization of USP19 has identified a collection of proteins in the secretome and within the cell that are regulated by USP19, which link USP19 to secretion of lysosomal proteins, including LGMN.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_01:10:43.581.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simone Bonelli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-22 09:13:37	ID requested
⏵ 1	2025-05-07 01:10:44	announced

10.1016/j.mcpro.2024.100854;

Bonelli S, Lo Pinto M, Ye Y, M, ü, ller SA, Lichtenthaler SF, Scilabra SD, Proteomic Characterization of Ubiquitin Carboxyl-Terminal Hydrolase 19 Deficient Cells Reveals a Role for USP19 in the Secretion of Lysosomal Proteins. Mol Cell Proteomics, 23(11):100854(2024) [pubmed]

submitter keyword: lysosome, cathepsins.,ubiquitin carboxyl-terminal hydrolase 19

proteomics

unconventional secretion

secretome

legumain

Simone Dario
contact affiliation	Fondazione Ri.MED
contact email	sdscilabra@fondazionerimed.com
lab head
Simone Bonelli
contact affiliation	Ri.MED Foundation
contact email	sbonelli@fondazionerimed.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/PXD055081

PRIDE project URI

• PRIDE
  1. PXD055081
     1. Label: PRIDE project
     2. Name: Proteomic characterization of ubiquitin carboxyl-terminal hydrolase 19 deficient cells reveals a role for USP19 in secretion of lysosomal proteins