PXD071681

PXD071681 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 Cell Surface
Description	Targeting tumor-associated macrophages (TAMs) holds great promise for cancer immunotherapy. Surface glycoproteins in macrophages regulate their interactions with tumor cells and represent emerging therapeutic targets. Given the crucial roles of protein glycosylation in immune function and cancer, we systematically investigate the total and surface glycoproteomes in polarized macrophages using multiplexed proteomics coupled with selective enrichment. Using THP-1 monocyte-derived macrophages, we uncovered distinct N-glycosylation patterns between M1 and M2 phenotypes, with differential regulation primarily driven by changes in protein expression and nucleotide sugar biosynthesis. Furthermore, we performed systematic analysis of surface glycoproteins in primary human macrophages with M1 or M2 phenotype (HM1 and HM2), and the results revealed extensive, phenotype-specific remodeling of the cell-surface glycoproteome: HM1 macrophages displayed enhanced innate immune signaling, whereas in HM2 macrophages, surface glycoproteins related to adhesion, endocytosis, and angiogenesis were upregulated. Comparative analysis between THP-1-derived and primary human macrophages highlights both shared and divergent features of surface remodeling, emphasizing the value of primary cell systems for physiological relevance. Integrative analyses combining cell-surface glycoproteomic, transcriptomic, and tissue-specific datasets identified surface proteins as potential targets for inhibiting M2 macrophages, including some previously underexplored ones (such as LIPA, CD200R1, and CR1). Together, this study provides a comprehensive macrophage glycoproteome atlas and establishes a framework for developing TAM-directed cancer immunotherapies.
HostingRepository	PRIDE
AnnounceDate	2026-08-22
AnnouncementXML	Submission_2026-08-22_09:30:43.387.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD071681
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xing Xu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT: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	2025-12-07 15:19:57	ID requested
⏵ 1	2026-08-22 09:30:43	announced

10.6019/PXD071681;

submitter keyword: primary human macrophages

LC-MS-based proteomics

cell surface proteins

glycosylation

Xing Xu
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	xingxu@gatech.edu
lab head
Xing Xu
contact affiliation	Georgia Institute of Technology
contact email	xingxu@gatech.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/2026/08/PXD071681

PRIDE project URI

• PRIDE
  1. PXD071681
     1. Label: PRIDE project
     2. Name: Deciphering the Mechanisms of Macrophage Polarization through Comprehensive Analysis of Protein Glycosylation in Cells and on the Cell Surface