PXD053647

PXD053647 is an original dataset announced via ProteomeXchange.

Title	Deciphering the mechanisms of macrophage polarization through comprehensive analysis of protein glycosylation in cells and on the surface
Description	In this work, we conducted an in-depth characterization of protein glycosylation including total glycoproteins and surface ones across different macrophage phenotypes using mass spectrometry (MS)-based proteomics. The global analysis of glycoproteins was performed using the boronic acid-conjugated dendrimer beads-based enrichment method. The N-glycoproteome was found to undergo more pronounced changes in M1 macrophages compared to M2 macrophages. To examine the alterations of surface glycoproteins, we employed enzymatic and chemical reactions to label surface glycoproteins. The remodeling of the glycoproteome in macrophage polarization is primarily driven by changes in protein expression and sugar donors rather than changes in the protein glycosylation machinery. Comparative analysis of cell-surface glycoproteins between M1 and M2 macrophages reveals phenotype-specific N-glycosylation patterns. Moreover, we identified potential targets for suppressing M2 macrophages, including CD36, FLT1, Siglec11, THSD7A, and SLC12A2. Finally, we characterized the site-specific changes of cell-surface glycoproteins between M1 and M2 macrophages related to their local protein structures and adjacent residues. The dramatic alterations in N-glycosylation sites were located within crucial protein domains, including the immunoglobulin (Ig)-like domain, fibronectin type III domain, and growth factor domain. Global and site-specific analysis of protein glycosylation and surface glycoproteins advance our understanding of different types of macrophages and provide valuable and unprecedented information for future functional and mechanistic investigations of human macrophages, leading to a better understanding of cancer immunity and the development of immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:52:51.621.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD053647
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xing Xu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	(18)O label at both C-terminal oxygens; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-04 15:29:40	ID requested
1	2024-08-08 02:47:56	announced
⏵ 2	2024-10-22 06:52:52	announced	2024-10-22: Updated project metadata.

10.6019/PXD053647;

submitter keyword: Glycoproteomics, proteomics, tumor-associated macrophages, M1 macrophage, M2 macrophage, surfaceome, macrophage polarization

Xing Xu, Kejun Yin, and Ronghu Wu
contact affiliation	School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
contact email	ronghu.wu@chemistry.gatech.edu
lab head
Xing Xu
contact affiliation	Georgia Institute of Technology
contact email	xingxu@gatech.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053647
     1. Label: PRIDE project
     2. Name: Deciphering the mechanisms of macrophage polarization through comprehensive analysis of protein glycosylation in cells and on the surface