PXD025940

PXD025940 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide and matrisome-specific atlas of the human ovary from prepuberty to menopause
Description	Our modern era is witnessing an increasing infertility rate worldwide. Although some of the causes can be attributed to our modern lifestyle (eg. persistent organic polluants, late pregnancy), our knowledge of the human ovarian tissue has remained limited and insufficient to reverse the infertility statistics. Indeed, all efforts have been focused on the endocrine and cellular function in support of the cell theory that dates back to the 18th century, while the human ovarian matrisome is still under-described. Therefore, hereby we provide the first systematic study focusing on the human ovarian matrisome and its remodeling during a woman lifetime, from prepuberty til menopause. We apply our matrisome tailored fractionation method, the DC-MaP strategy and mass spectrometry-based quantitative proteomics using TMT pro 16-plex isobaric labeling to delineate proteome-wide and ECM-specific shifts between prepubertal, reproductive-age and menopausal stages. Post-translational modifications, namely proline hydroxylation and advanced glycation ends products have also been detected at different intensities according to age. Matrisome age-biomarkers have been validated with lightsheet microscopy-based-3D imaging, following immunofluorescence and tissue clearing with an ovary-tailored protocol. We used machine learning and statistics to build a neural network that can predict predict the probability of a specific ovarian tissue matrisome to resemble to prepubertal, reproductive-age or menopausal tissue and potentially conclude its fertility potency or evaluate in the future the efficiency of ovarian rejuvenation treatments. We also used NLP medscan technology for advanced literature text-mining to predict all possible-connections between the extra- and intra-cellular compartments and how chemo-radiotherapy, known for its gonadotoxicity can also affect key matrisome proteins.This comprehensive proteomics analysis represents the ovarian proteomic codex and contributes to an improved understanding of the critical roles that ECM plays throughout ovarian life span. By publishing our proteomic data, we hope to open new avenues in fertility restoration, ovarian rejuvenation and reproductive tissue engineering
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:57.069.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025940
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Didier Vertommen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	N6-1-carboxyethyl-L-lysine; acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-11 04:39:08	ID requested
1	2022-04-06 03:29:12	announced
⏵ 2	2023-11-14 08:52:57	announced	2023-11-14: Updated project metadata.

10.6019/PXD025940;

submitter keyword: human ovary, matrisome, reproduction

Christiani Andrade Amorim
contact affiliation	UCLouvain Institut de Recherche Expérimentale et Clinique Pôle de Recherche en Gynécologie Avenue Mounier, 52 Bte. B1.52.02 1200 Bruxelles, Belgique
contact email	christiani.amorim@uclouvain.be
lab head
Didier Vertommen
contact affiliation	UCL - de Duve Institute, Brussels Belgium
contact email	didier.vertommen@uclouvain.be
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/2022/04/PXD025940

PRIDE project URI

• PRIDE
  1. PXD025940
     1. Label: PRIDE project
     2. Name: Proteome-wide and matrisome-specific atlas of the human ovary from prepuberty to menopause