PXD058075-1

PXD058075 is an original dataset announced via ProteomeXchange.

Title	Proteome changes of RPE-1 cells in response to lysosomal damage with the TAK1 inhibitor
Description	The lysosomal damage response plays a critical role in the maintenance of cellular homeostasis. While the repair and autophagic elimination mechanisms of damaged lysosomes have been elucidated, the early signal transduction and subsequent gene expression in response to lysosomal damage remain elusive. Here, we employed transcriptome and proteome analyses to demonstrate that the TAB–TAK1–IKK–NF-κB pathway is activated by K63-linked ubiquitin chains that accumulate on damaged lysosomes. This results in the gene expression of a diverse range of transcription factors and cytokines, which subsequently promote anti-apoptosis and intercellular signaling. These findings indicate that the ubiquitin-directed signal transduction and gene expression play a crucial role in cell survival and cell-cell communication in response to lysosomal damage. The results highlight that the ubiquitin system is involved not only in the removal of damaged lysosomes by lysophagy, but also in the activation of cellular signaling for cell survival.
HostingRepository	PRIDE
AnnounceDate	2025-08-30
AnnouncementXML	Submission_2025-08-29_23:21:05.787.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akinori Endo
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	2024-11-19 22:59:23	ID requested
⏵ 1	2025-08-29 23:21:06	announced

10.7554/ELIFE.106901.1;

submitter keyword: DIA,Human cell, LC-MS, lysosomal damage

Akinori Endo
contact affiliation	Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
contact email	endo-ak@igakuken.or.jp
lab head
Akinori Endo
contact affiliation	Tokyo Metropolitan Institute of Medical Science
contact email	endo-ak@igakuken.or.jp
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/2025/08/PXD058075

PRIDE project URI

• PRIDE
  1. PXD058075
     1. Label: PRIDE project
     2. Name: Proteome changes of RPE-1 cells in response to lysosomal damage with the TAK1 inhibitor