Dataset Information

Proteoglycan sequencing - Deep sequencing of complex proteoglycans: a novel strategy for high coverage and site-specific identification of glycosaminoglycan-linked peptides

ABSTRACT: Proteoglycans are distributed in all animal tissues and play critical, multifaceted, physiological roles. Expressed in a spatially- and temporally-regulated manner, these molecules regulate interactions among growth factors and cell surface receptors and play key roles in basement membranes and other extracellular matrices. Due to the high degree of glycosylation by glycosaminoglycan (GAG), N-glycan and mucin-type O-glycan classes, the peptide sequence coverage of complex proteoglycans is revealed poorly by standard mass spectrometry-based proteomics methods. As a result, there is little information concerning how proteoglycan site specific glycosylation changes during normal and pathological processes. Here, we developed a workflow to improve sequence coverage and identification of glycosylated peptides in proteoglycans. We applied this workflow to the small leucine-rich proteoglycan decorin and the hyalectan proteoglycans; neurocan, brevican, and aggrecan.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Bos Taurus (bovine)

TISSUE(S): Brain, Articular Cartilage

SUBMITTER: Joseph Zaia

LAB HEAD: Joseph Zaia

PROVIDER: PXD008855 | Pride | 2018-05-22

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	171112_gag-ol-muc-nl-bovine-glycans_revised_GAG_JZ_keratanPGarticle.txt	Txt
	171112_gag-ol-muc-nl-human-glycans_revised_GAG_JZ_keratanPGarticle.txt	Txt
	DCN tryptic upper peptides_1_1_0.pride.mztab.gz	Mztab
	DCNtrypticupperpeptides_1_1_0.mzid.gz	Mzid
	agcn_trp_glu_10k_upper.mzML	Mzml

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Publications

Deep Sequencing of Complex Proteoglycans: A Novel Strategy for High Coverage and Site-specific Identification of Glycosaminoglycan-linked Peptides.

Klein Joshua A JA Meng Le L Zaia Joseph J

Molecular & cellular proteomics : MCP 20180517 8

Proteoglycans are distributed in all animal tissues and play critical, multifaceted, physiological roles. Expressed in a spatially and temporally regulated manner, these molecules regulate interactions among growth factors and cell surface receptors and play key roles in basement membranes and other extracellular matrices. Because of the high degree of glycosylation by glycosaminoglycan (GAG), <i>N</i>-glycan and mucin-type <i>O</i>-glycan classes, the peptide sequence coverage of complex proteo ...[more]

PMID: 29773674

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Project description:Glioblastoma (GBM) is the most common and malignant primary brain tumor. The extracellular matrix (ECM), also known as the matrisome, helps determine glioma invasion, adhesion, and growth. Little attention, however, has been paid to glycosylation of the ECM components that constitute the majority of glycosylated protein mass and presumed biological properties. To acquire a comprehensive understanding of the biological functions of the matrisome and its components, including proteoglycans and glycosaminoglycans (GAGs), in GBM tumorigenesis, and to identify potential biomarker candidates, we studied the alterations of GAGs, including heparan sulfate (HS) and chondroitin sulfate (CS), the core proteins of proteoglycans, and other glycosylated matrisomal proteins in GBM subtypes vs. control human brain tissue samples. We scrutinized the proteomics data to acquire in-depth site-specific glycoproteomic profiles of the GBM subtypes that will assist in identifying specific glycosylation changes in GBM. We observed an increase in CS 6-O sulfation and a decrease in HS 6-O sulfation, accompanied by an increase in unsulfated CS and HS disaccharides in GBM vs. control samples. Several core matrisome proteins, including proteoglycans (decorin, biglycan, agrin, prolargin, glypican-1, CSPG4), tenascin, fibronectin, hyaluronan link protein 1 and 2, laminins, and collagens, were differentially regulated in GBM vs. controls. Interestingly, a higher degree of collagen hydroxyprolination was also observed for GBM vs. controls. Further, two proteoglycans, CSPG4 and agrin, were significantly lower, about 6–fold for IDH-mutant compared to the WT GBM samples. Differential regulation of O-glycopeptides for proteoglycans, including brevican, neurocan, and versican, was observed for GBM subtypes vs. controls. Moreover, an increase in levels of glycosyltransferase and glycosidase enzymes was observed for GBM when compared to control samples. We also report distinct protein, peptide, and glycopeptide features for GBM subtypes comparisons. Taken together, our study informs understanding of the alterations to key matrisomal molecules that occur during GBM development.