PXD039387

PXD039387 is an original dataset announced via ProteomeXchange.

Title	Spatiotemporal glycoproteome remodelling in neutrophils
Description	Neutrophils are short-lived yet vital innate immune cells equipped with bioactive glycoproteins packed in cytosolic granules that can readily be mobilised to elicit an effective and timely response against invading pathogens. Since the dynamic glycosylation processes underpinning the dramatic metamorphosis associated with myeloid progenitor-to-neutrophil differentiation remain unmapped, we here perform a comprehensive spatiotemporal profiling of the complex N-glycoproteome of isolated granule populations from blood-derived neutrophils and during maturation of bone marrow-derived progenitors using glycomics-assisted glycoproteomics. Firstly, glycomics indicated that the granule populations of mature (resting) neutrophils exhibit distinctive glycophenotypes including, most strikingly, unusual paucimannosidic- and monoantennary complex-type N-glycans in azurophilic granules. The granule-specific N-glycosylation features were recapitulated by glycoproteomics, which also uncovered extensive site- and protein-specific N-glycosylation decorating 4,772 N-glycopeptides from 352 N-glycoproteins across the neutrophil granules. Excitingly, comprehensive mining of proteomics and transcriptomics data collected from discrete myeloid progenitor stages for glycopeptide and glyco-enzyme expression revealed that dramatic glycoproteome remodelling underpins the promyelocytic-to-metamyelocyte transition and that remodelling is driven predominantly by proteome expression changes rather than modulation of the glycosylation machinery. Notable exceptions were the oligosaccharyltransferase subunits responsible for initiation of N-glycoprotein biosynthesis that were strongly reduced with myeloid differentiation leading to reduced N-glycosylation efficiency in late-stage neutrophil maturation and in corresponding granules. Our study provides new spatiotemporal insights into the dynamic neutrophil N-glycoproteome, which exhibits intriguingly complex site-, protein- and granule-specific N-glycosylation features and which undergoes strong remodelling during myeloid progenitor-to-neutrophil metamorphosis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:20.305.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rebeca Kawahara
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-13 05:44:49	ID requested
1	2023-09-18 08:16:53	announced
⏵ 2	2023-11-14 09:05:28	announced	2023-11-14: Updated project metadata.

Kawahara R, Ugonotti J, Chatterjee S, Tjondro HC, Loke I, Parker BL, Venkatakrishnan V, Dieckmann R, Sumer-Bayraktar Z, Karlsson-Bengtsson A, Bylund J, Thaysen-Andersen M, -glycosylation accompany neutrophil granulopoiesis. Proc Natl Acad Sci U S A, 120(36):e2303867120(2023) [pubmed]

submitter keyword: Remodelling, neutrophil, glycoproteomics, maturation, granule, glycoproteome

Morten Thaysen-Andersen
contact affiliation	School of Natural Sciences, Macquarie University, Sydney, Australia Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
contact email	morten.andersen@mq.edu.au
lab head
Rebeca Kawahara
contact affiliation	Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
contact email	rebecasakuma@gmail.com
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/2023/09/PXD039387

PRIDE project URI

• PRIDE
  1. PXD039387
     1. Label: PRIDE project
     2. Name: Spatiotemporal glycoproteome remodelling in neutrophils