PXD028895

PXD028895 is an original dataset announced via ProteomeXchange.

Title	Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia
Description	Current techniques to diagnose and/or monitor critically ill neonates with bronchopulmonary dysplasia (BPD) require invasive sampling of body fluids, which can affect the health status of these frail neonate. We tested our hypotheses 1) it is feasible to use early urine samples from extremely low gestational age newborns at risk for bronchopulmonary dysplasia for proteomics, and 2) urine proteomics can confirm previously identified proteins and biomarkers associated with BPD without invasive sample collection. We developed a robust high throughput urine proteomics methodology that requires only 50 microliters of urine. We validated the methodology on urine collected within 72 hours of birth. Urine samples were collected from extremely low gestational age newborns (ELGANS) (gestational age (26 + 1.2) weeks) admitted to a single Neonatal Intensive Care Unit(NICU); half of whom eventually developed BPD, while the other half served as controls. Our high throughput urine proteomics approach clearly identified several BPD-associated changes in the urine proteome recapitulating expected blood proteome changes. Interestingly, sixteen identified urinary proteins are known targets of drugs approved by the Food and Drug Administration (FDA). Urine proteomics can be used for prediction of BPD risk. In addition to identifying numerous proteins implicated in BPD pathophysiology, previously found in invasively collected blood, tracheal aspirate, and broncho-alveolar lavage, urine proteomics also suggested novel potential therapeutic targets. Ease of access to urine for sequential proteomic evaluations could also allow for longitudinal monitoring of disease progression and impact of therapeutic intervention.
HostingRepository	PRIDE
AnnounceDate	2022-05-31
AnnouncementXML	Submission_2022-05-31_06:42:44.071.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Saima Ahmed
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-04 04:00:56	ID requested
⏵ 1	2022-05-31 06:42:45	announced

Ahmed S, Odumade OA, van Zalm P, Smolen KK, Fujimura K, Muntel J, Rotunno MS, Winston AB, Steen JA, Parad RB, Van Marter LJ, Kourembanas S, Steen H, Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia. Neonatology, 119(2):193-203(2022) [pubmed]

submitter keyword: extremely low gestational age newborn, mass spectrometry, chronic lung disease

Dr Hanno Steen
contact affiliation	Director of Proteomics Boston Children's Hospital Associate Professor of Pathology Harvard Medical School
contact email	Hanno.Steen@childrens.harvard.edu
lab head
Saima Ahmed
contact affiliation	Boston Children's Hospital
contact email	saima.ahmed@childrens.harvard.edu
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/PXD028895

PRIDE project URI

• PRIDE
  1. PXD028895
     1. Label: PRIDE project
     2. Name: Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia