PXD028283

PXD028283 is an original dataset announced via ProteomeXchange.

Title	¬Single cell transcriptomics of human iPSC differentiation dynamics reveal a core network of Parkinson’s disease
Description	Parkinson’s disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. The underlying mechanisms are only partly understood and there is no treatment to reverse PD progression. Here, we investigated the disease mechanism using mDA neurons obtained through differentiation of human induced pluripotent stem cells (hiPSCs) carrying the ILE368ASN mutation within the PINK1 gene. Single-cell RNA sequencing (RNAseq) and gene expression analysis of a PINK1 and a control cell line identified genes differentially expressed during mDA neuron differentiation. Network analysis revealed that these genes form a core network, members of which interact with all known 19 protein-coding Parkinson’s disease-associated genes. This core network encompasses key PD-associated pathways, including ubiquitination, mitochondrial, protein processing, RNA metabolism, and vesicular transport. Proteomics analysis showed a consistent alteration in proteins of dopamine metabolism, validating the manifestation of the affected neuronal phenotype. Our findings suggest the existence of a network onto which pathways associated with PD pathology converge, and offers new interpretation of the phenotypic heterogeneity of PD.
HostingRepository	PRIDE
AnnounceDate	2022-02-15
AnnouncementXML	Submission_2022-02-15_13:10:22.533.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gunnar Dittmar
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:10:34	ID requested
⏵ 1	2022-02-15 13:10:23	announced

Novak G, Kyriakis D, Grzyb K, Bernini M, Rodius S, Dittmar G, Finkbeiner S, Skupin A, Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. Commun Biol, 5(1):49(2022) [pubmed]

submitter keyword: Parkinson’s disease

iPSCs, shotgun

Gunnar Dittmar
contact affiliation	Luxembourg Institute of Health
contact email	Gunnar.Dittmar@lih.lu
lab head
Gunnar Dittmar
contact affiliation	LIH
contact email	gunnar.dittmar@lih.lu
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/2022/02/PXD028283

PRIDE project URI

• PRIDE
  1. PXD028283
     1. Label: PRIDE project
     2. Name: ¬Single cell transcriptomics of human iPSC differentiation dynamics reveal a core network of Parkinson’s disease