PXD024748

PXD024748 is an original dataset announced via ProteomeXchange.

Title	Polyomic analyses of dopaminergic neurons isolated from human substantia nigra in Parkinson’s disease: An exploratory study.
Description	Dopaminergic neurons of the substantia nigra pars compacta selectively and progressively degenerate in Parkinson’s disease. Until now, molecular analyses of dopaminergic neurons in PD have been limited to genomic and transcriptomic approaches, whereas, to the best of our knowledge, no proteomic or combined polyomic study examining the protein profile of these neurons, is currently available. In this exploratory study, we used laser microdissection to extract dopaminergic neurons from 10 human SNpc samples obtained at autopsy in Parkinson’s disease patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nano-LC-MS/MS, respectively, and the differential expression between Parkinson’s disease and control group was assessed. Qualitative analyses confirmed that the microdissection protocol preserves the integrity of our samples and offers access to specific molecular pathways. This polyomic analysis highlighted differential expression of 52 genes and 33 proteins, including molecules of interest already known to be dysregulated in Parkinson’s disease, such as LRP2, PNMT, CXCR4, MAOA and CBLN1 genes, or the Aldehyde dehydrogenase 1 protein. On the other hand, despite the same samples were used for both analyses, correlation between RNA and protein expression was low, as exemplified by the CST3 gene encoding for the cystatin C protein. This is the first exploratory study analyzing both gene and protein expression of LMD-dissected neurons from substantia nigra pars compacta in Parkinson’s disease.
HostingRepository	PRIDE
AnnounceDate	2021-12-30
AnnouncementXML	Submission_2021-12-30_14:35:16.042.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Affif Zaccaria
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-15 08:57:27	ID requested
⏵ 1	2021-12-30 14:35:16	announced

Zaccaria A, Antinori P, Licker V, K, ö, vari E, Lobrinus JA, Burkhard PR, Multiomic Analyses of Dopaminergic Neurons Isolated from Human Substantia Nigra in Parkinson's Disease: A Descriptive and Exploratory Study. Cell Mol Neurobiol, 42(8):2805-2818(2022) [pubmed]

submitter keyword: Parkinson’s disease, human brain tissue, dopaminergic neurons, laser micro-dissection, Transcriptomics, Proteomics .

Pierre R. Burkhard
contact affiliation	Neuroproteomics Group, University Medical Center, Faculty of Medicine, Geneva University, Geneva, Switzerland
contact email	pierre.burkhard@hcuge.ch
lab head
Affif Zaccaria
contact affiliation	University of Geneva
contact email	affif.zaccaria@unige.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD024748
     1. Label: PRIDE project
     2. Name: Polyomic analyses of dopaminergic neurons isolated from human substantia nigra in Parkinson’s disease: An exploratory study.