Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative Glycoproteomic Profiling Identifies Distinct N‑glycosylation Signatures in Renal Biopsies from Healthy Kidney Donors and Diabetic Kidney Disease Patients

ABSTRACT: Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease (ESRD) worldwide, but site-specific N-glycosylation signatures underlying DKD renal damage remain poorly characterized. Unlike previous studies relying on suboptimal control tissues, we utilized intact healthy kidney donor (HKD) cortical biopsies as physiologically accurate references. We applied an optimized quantitative glycoproteomic pipeline combining homogenization and non-contact ultrasonic-assisted protein extraction, ZIC-HILIC enrichment, and EThcD-sceHCD-MS/MS to profile intact N-glycopeptides (IGPs) from 20 DKD patients and 20 HKD controls. We identified 1,186 significant differentially expressed IGPs and 111 altered N-glycans derived from 294 glycoproteins in DKD renal tissues (adjusted p < 0.05, FC > 1.5 or < 0.67).

ORGANISM(S): Homo Sapiens

SUBMITTER: Yong Zhang

PROVIDER: PXD081593 | iProX | Fri Jul 24 00:00:00 GMT+01:00 2026

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Systems analysis of plasma IgG intact N-glycopeptides from pa-tients with chronic kidney diseases via combined electron-transfer/higher-energy collisional dissociation and stepped colli-sion energy/higher-energy collisional dissociation mass spectrom-etry within half an hour

Project description:Immunoglobulin G (IgG) molecules modulate an immune response. However, site-specific N-glycosylation signatures of plasma IgG in patients with chronic kidney disease (CKD) remain unclear. This study aimed to propose a novel method to explore the N-glycosylation pattern of IgG and to compare it with reported methods. We separated human plasma IgG from 58 healthy controls (HC) and 111 patients with CKD. Purified IgG molecules were digested by trypsin. Tryptic peptides with-out enrichment were analyzed using a combination of electron-transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) mass spectrometry (EThcD-sceHCD-MS/MS). This resulted in higher spectral quality, more informative fragment ions, higher Byonic score, and nearly twice the depth of intact N-glycopeptide identification than sceHCD or EThcD alone. Site-specific N-glycosylation mapping revealed that intact N-glycopeptides were differentially expressed in HC and CKD patients; thus, it can be a diagnostic tool. This study provides a method for the determination of glycosylation patterns in CKD and a framework for understanding the role of IgG in the pathophysiology of CKD.

2021-11-25 | PXD027174 | Pride

Oxidative modifications of urinary proteins increase kidney stone risk

Project description:Clinical and animal studies have demonstrated the increasing evidence of oxidative stress in kidney stone disease. Recent findings have shown that the interactions between calcium oxalate (CaOx) crystals and renal tubular cells can promote many cellular events such as cell proliferation, cell death, cellular injury, mitochondrial dysfunction and inflammatory cascade. All of these cellular events are associated with oxidative stress and overproduction of free radicals and reactive oxygen species (ROS) such as superoxide and hydrogen peroxide in renal tubular cells. However, almost all of these references have shown that oxidative stress occurs after the causative crystals have been deposited in the kidney or exposed to renal tubular cells, whereas its primary role as the etiology remained unclear. In this study, we examined effects of oxidative modifications of urinary proteins on CaOx stone formation processes. Urinary proteins were modified by performic oxidation and the presence of oxidatively modified urinary proteins was verified, quantified and characterized by Oxyblot assay and tandem mass spectrometry (nanoLC-ESI-LTQ-Orbitrap-MS/MS). Subsequently, activities of oxidatively modified urinary proteins on CaOx stone formation processes were examined.

2021-11-03 | PXD019360 | Pride

Pressure Cycling Technology-Based Quantitative Glycoproteomics Reveals Distinctive N‑glycosylation Patterns in Human Kidney Tissues with Minor Glomerular Abnormalities

Project description:Kidney diseases present substantial clinical challenges, with aberrant glycoprotein emerging as a key pathogenic driver. Minor glomerular abnormalities (MGAs), a category of unclassified glomerular lesions defined by subtle structural changes, are commonly detected in patients with persistent, asymptomatic, isolated proteinuria or microhematuria., yet their site-specific N-glycosylation patterns remain unelucidated. To address this gap, we applied a laboratory-developed pressure cycling technology (PCT)-based quantitative glycoproteomics workflow (GlycoPCT) to compare intact N-glycopeptides (IGPs) between distant non-neoplastic tissues (DNT; n=24) and trace renal biopsy samples from MGA patients (n=27). Integrated with high-sensitivity, high-resolution mass spectrometry (EThcD-sceHCD-MS/MS), GlycoPCT identified 672 upregulated IGPs (FC>1.5, p<0.05) and 573 downregulated IGPs (FC<0.67, p<0.05) in MGA tissues. Total fucosylation type N-glycans were significantly downregulated (p<0.05), while sialylation type N-glycans were markedly downregulated (p<0.001). Additionally, 24 glycoproteins associated with the PI3K-Akt signaling pathway (a well-documented mediator of renal injury) showed broadly N-glycosylation upregulation. Site-specific N-glycosylation analysis further revealed differential patterns in IgG subclasses and complement-related markers that distinguish MGA from DNT, offering new mechanistic insights into MGA pathogenesis. These novel glyco-signatures clarify the role of N-glycosylation in renal disease, highlight TINAGL1, IgG, IgM, and complement-related glycoproteins as potential MGA biomarkers, and validate GlycoPCT as a powerful tool for trace tissue analysis. This study lays the groundwork for translating N-glycosylation findings into clinical applications to improve MGA diagnosis and management.

2025-10-21 | PXD069708 |

Site-specific N-glycosylation Characterization of Micro Disease-related Proteins Based on EThcD-sceHCD-MS/MS

Project description:Monoclonal immunoglobulin produced by clonal plasma cells is the main cause in multiple myeloma and monoclonal gammopathy of renal significance. Because of the complicated purification method and the low stoichiometry of purified protein and glycans, site-specific N-glycosylation characterization for monoclonal immunoglobulin is still challenging. Studies reporting the N-glycosylation profiles for this monoclonal immunoglobulin have been rare until now. Therefore, in this study, we presented an integrated workflow for micro serum monoclonal IgA and IgG purification from patients with multiple myeloma in the HYDRASYS system, in-agarose-gel digestion, LC‒MS/MS analysis without intact N-glycopeptide enrichment, and compared the identification performance of different mass spectrometry dissociation methods (EThcD-sceHCD, sceHCD, EThcD and sceHCD-pd-ETD). The results showed that EThcD-sceHCD was a better choice for site-specific N-glycosylation characterization of micro in-agarose-gel immunoglobulin proteins (~2 μg) because it can cover more unique intact N-glycopeptides (37 and 50 intact N-glycopeptides from IgA1 and IgG2, respectively) and provide more high-quality spectra than sceHCD, EThcD and sceHCD-pd-ETD. We demonstrated the benefits of the alternative strategy in site-specific N-glycosylation characterizing micro disease-related proteins obtained from bands separated by electrophoresis. This work could promote the development of clinical N-glycoproteomics and related immunology.

2022-09-13 | PXD035757 | Pride

Combined Calorie and Protein Restriction in Healthy Kidney Donors Improves Kidney Outcome in Donors and Kidney Transplant Recipients

Project description:A preoperative short-term diet combining calorie and protein restriction diet given during five days before kidney donation and transplantation improves kidney outcome in live kidney donors and kidney transplant recipients, which shows that the benefits of dietary restriction on stress resistance can be induced rapidly in humans, and may be used for clinically relevant endpoints.

2020-09-04 | GSE103532 | GEO

M2-like macrophages in the injured-kidney cortex promoted kidney cancer progression via the direct pro-tumor effect and the inhibition of CD8 T cell infiltration

Project description:In this study, we aimed to evaluate the effect of M2-like macrophages in the injured kidney on kidney cancer progression. As an acute kidney injury to chronic kidney disease model, we used unilateral ischemia-reperfusion injury (uIRI). And we inoculated RenCa cells, which are murine kidney cancer cell line, into renal subcapsule 14 days after uIRI (uIRI-Can) and compared uIRI-Can to RenCa cells inoculated into sham-operated renal subcapsule (Sham-Can) 20 days after inoculation. To identify gene characteristics of M2-like macrophages that are commonly detected both in the uIRI kidney cortex and uIRI-Can, we sorted Ly6Clow macrophages from 4 groups, uIRI kidney cortex, sham kidney cortex, uIRI-Can, and Sham-Can, and conducted RNA-Seq. This study revealed the characteristic gene expression of M2-like macrophages which were commonly detected in the injured kidney cortex and kidney cancer progressed on the injured kidney. And this could be a future therapeutic target of macrophage-targeted therapy.

2022-12-06 | GSE197494 | GEO

Metabolic programming drives proximal tubule differentiation and kidney dysfunction

Project description:Renal disease development is poorly understood, mostly because the kidney is made up of more than 20 different cell types, each of them with specific function and complex interaction. Here, we used single cell RNA sequencing to resolve cell-type specific and cell fraction changes

2020-11-30 | GSE152765 | GEO

Fibrinogen is upregulated following kidney damage and protects it against ischemia-reperfusion injury

Project description:characterization of fibrinogen expression in the kidney, excretion in the urine following kidney damage and evaluating the therapeutic potential of fibrinogen in acute kidney injury. Total RNA was isolated of renal cortex and medulla from rats subjected to 20 min of bilateral ischemia followed by 6, 24 120, hr of reperfusion compared to sham rats.

2011-09-30 | E-GEOD-27274 | biostudies-arrayexpress

Gene Expression of Kidney from HSRA-S (congenital solitary kidney) and HSRA-C (two-kidney) using Rat Gene 1.1 ST Array [RaGene-1_1-st]

Project description:We recently developed a new model of renal agenesis [i.e., the heterogeneous stock derived model of unilateral renal agenesis, (HSRA)]. The HSRA model consistently exhibits unilateral renal agenesis ranging from 50-75% in each generation and is characterized by low nephron number, early kidney hypertrophy, and an inherent susceptibility to develop significant kidney injury and decline in renal function with age. Whole transcriptome analysis was evaluated at month 1 to identify early changes in genes/networks that may be involved in increased susceptibility of HSRA-S to develop kidney injury in the long-term. An n=4 per group (independent samples) were evaluated for HSRA-S (congenital solitary kidney) and HSRA-C (two-kidney). HSRA-C (two-kidney) samples were set as the control.

2014-10-07 | E-GEOD-62092 | biostudies-arrayexpress

Expression data from rejection and non-rejection kidney transplant patients

Project description:Acute renal allograft rejection is an important complication in kidney transplantation. Accurate diagnosis of rejection events is necessary for timely response and treatment. We illustrate the usefulness and biological relevance of selected multivariate approaches to detect rejection from genomic and proteomic signals. The data was used to study gene expression changes using whole genome microarray analysis of peripheral blood from subjects with acute rejection (n=20) and non-rejecting controls (n=20) to obtain insight into the molecular and biological causation of acute renal allograft rejection when combined with proteomics (iTRAQ) data for the same patients/time-points.

2014-04-26 | GSE46474 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data