PXD058936

PXD058936 is an original dataset announced via ProteomeXchange.

Title	DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation
Description	Aging and DNA damage increase the risk of chronic inflammation and autoimmunity, yet their molecular underpinnings remain unclear. Here, we uncover a DNA damage-driven mechanism in macrophages that triggers immune autoreactivity. Using Er1Lyz2/- animals with a macrophage-specific DNA repair defect in ERCC1-XPF, we demonstrate that monocyte-derived macrophages with persistent DNA damage activate the immune system, drive polyclonal T-cell responses, and generate anti-nuclear autoantibodies. Proteomic and immunopeptidomic analyses reveal a distinct MHC-II antigen repertoire in these macrophages, enriched in nuclear and ribosomal peptides, relying on autophagy for nuclear cargo delivery to MHC-II. Aged macrophages exhibit a similar lysosomal cargo profile, linking autophagy-driven nuclear antigen presentation to immune activation. Notably, inhibiting autophagy in Er1Lyz2/⁻ mice suppresses autoimmune features, pinpointing autophagy-facilitated nuclear antigen processing as a central driver of age-related autoimmunity. These findings establish DNA damage-induced autophagy in macrophages as a pivotal mechanism linking aging to autoimmunity, and unveiling potential targets for interventions to mitigate age-related immune dysregulation.
HostingRepository	PRIDE
AnnounceDate	2025-12-03
AnnouncementXML	Submission_2025-12-03_04:32:31.978.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Beli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-17 02:23:05	ID requested
⏵ 1	2025-12-03 04:32:32	announced

Dataset with its publication pending

submitter keyword: Macrophages, Genome stability, Autophagy,Immunosenescence, Autophagosome profiling

Prof. Dr. Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
lab head
Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
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/2025/12/PXD058936

PRIDE project URI

• PRIDE
  1. PXD058936
     1. Label: PRIDE project
     2. Name: DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation