PXD061286

PXD061286 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis of viral infection in neurons
Description	Endemic viral infections with low pathogenicity are often overlooked due to their mild symptoms, yet they can exert long-term effects on cellular function and contribute to disease pathogenesis. While viral infections have been implicated in neurodegenerative disorders, their impact on the neuronal proteome remains poorly understood. Here, we differentiated human induced pluripotent stem cells (KOLF2.1J) into mature neurons to investigate virus-induced proteomic changes following infection with five neurotropic endemic human viruses: Herpes simplex virus 1 (HSV-1), Human coronavirus 229E (HCoV-229E), Epstein-Barr virus (EBV), Varicella-Zoster virus (VZV), and Influenza A virus (H1N1). Given that these viruses can infect adults and have the potential to cross the placental barrier, their molecular impact on neurons may be relevant across the lifespan. Using mass spectrometry-based proteomics with a customized library for simultaneous detection of human and viral proteins, we confirmed successful infections and identified virus-specific proteomic signatures. Notably, virus-induced protein expression changes converged on key neuronal pathways, including those associated with neurodegeneration. Gene co-expression network analysis revealed virus-specific protein modules linked to Alzheimer’s and Parkinson’s disease pathways. Remarkably, several viral-induced proteomic alterations overlapped with changes observed in postmortem Alzheimer’s patient brains, suggesting a mechanistic connection between viral exposure and neurodegenerative disease progression. These findings provide molecular insights into how common viral infections perturb neuronal homeostasis and may contribute to neurodegenerative pathology, highlighting the need to consider endemic viruses as potential environmental risk factors in neurological disorders.
HostingRepository	PRIDE
AnnounceDate	2026-06-25
AnnouncementXML	Submission_2026-06-25_08:21:28.812.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yue Andy Qi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-27 15:38:06	ID requested
1	2026-06-23 15:29:43	announced
⏵ 2	2026-06-25 08:21:29	announced	2026-06-25: Updated project metadata.

Li Z, Martin NP, Epstein J, Chen SH, Hao Y, Ramos DM, Andersh KM, Jarreau P, Weller C, Nalls MA, Pantazis CB, Ferrucci L, Cookson MR, Singleton AB, Qi YA, Yakel JL, Proteomic Analysis of Endemic Viral Infections in Neurons offers Insights into Neurodegenerative Diseases. bioRxiv, ():(2025) [pubmed]

10.1101/2025.03.17.643709;

submitter keyword: virus,IPSC-derived neurons

Yue Andy Qi
contact affiliation	Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
contact email	andy.qi@nih.gov
lab head
Yue Andy Qi
contact affiliation	Center for Alzheimer’s Disease and Related Dementias (CARD)/NIH
contact email	andy.qi@nih.gov
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/2026/06/PXD061286

PRIDE project URI

• PRIDE
  1. PXD061286
     1. Label: PRIDE project
     2. Name: Proteomics analysis of viral infection in neurons