Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SWATH-MS based protein quantification for diagnosis in systemic lupus erythematous

ABSTRACT: The gold standard for diagnosing lupus nephritis, one of the common symptoms of systemic lupus erythematosus, is an invasive procedure, a Renal biopsy. To overcome the risk of invasive methods, we constructed a spectral library using biological samples that can be obtained non-invasively and analyzed it using the SWATH-MS method, a quantitative proteomic analysis.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Systemic Lupus Erythematosus

SUBMITTER: Jeonghun Yeom

LAB HEAD: Kyunggon Kim

PROVIDER: PXD040099 | Pride | 2023-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Urine SERPINC1/ORM1 as biomarkers for early detection of lupus nephritis in MRL-lpr mice.

Kim Young-Eun YE Lee Eun-Ju EJ Kim Kyunggon K Kim Do Hoon DH Jeong Mi Ryeong MR Yu Jiyoung J Hong Seokchan S Lee Chang-Keun CK Yoo Bin B Kim Yong-Gil YG

Frontiers in immunology 20230908

<h4>Background</h4>To evaluate the usefulness of urine SERPINC1 and ORM1 as biomarkers for early detection of lupus nephritis (LN).<h4>Methods</h4>Using proteomics, we screened for potential urine biomarkers that differentiate LN from systemic lupus erythematosus (SLE) patients without nephritis. In addition, urine levels of target biomarkers were measured by ELISA in 13- and 23-week-old MRL-lpr (murine model for LN) and MRL/MpJ mice. Histological analysis was also performed on the kidneys of 23 ...[more]

PMID: 37744355

Similar Datasets

Comparative analysis of therapeutic effects between medium cut-off and high flux dialyzers using metabolomics and proteomics

Project description:This study compared the therapeutic effects of medium cut-off (MCO) and high flux (HF) dialyzers using metabolomics and proteomics. This was a single-center prospective trial of 20 patients receiving maintenance hemodialysis (HD). A consecutive dialyzer membrane was used for 15-week study periods as follows: 1st HF dialyzer, MCO dialyzer, 2nd HF dialyzer, for 5 weeks respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to identify proteins.

2021-11-03 | PXD026907 | Pride

Proteomic profiling of canine (dog) serum and urine

Project description:Companion dog care market is annually increasing. A relationship with a dog who lives with humans gives a lot of psychological stability. Therefore, companion dog's health is important to the owner. It would be of great help if a non-invasive method could monitor health through bodily fluids (urine, serum). In addition to this, it is principal to discover and verify protein biomarkers that can detect the presence or absence of disease. Despite the growing application of proteomics in biomarker research using canine serum or urine, there is no spectral assay library publicly available. Here, we set up spectral assay libraries for canine serum and urine samples using 24 midpH-fractionated samples to enable deep proteome coverage. The canine serum assay library includes 4,749 protein groups and 25,228 peptides and urine assay library contains 1,132 protein groups and 5,483 peptides.

2023-09-04 | PXD038645 | Pride

Proteomic profiling of canine (dog) serum and urine

2023-04-05 | PXD034770 | Pride

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model

Project description:Deposition of amyloid beta (Aβ) and hyperphosphorylated tau along with glial cell-mediated neuroinflammation are prominent pathogenic hallmarks of Alzheimer’s disease (AD). In recent years, impairment of autophagy has been found to be another important feature contributing to AD progression. Therefore, the potential of the autophagy activator spermidine, a small body-endogenous polyamine often used as dietary supplement, was assessed on Aβ pathology and glial cell-mediated neuroinflammation. Oral treatment of the amyloid prone AD-like APPPS1 mice with spermidine reduced neurotoxic soluble Aβ and decreased AD-associated neuroinflammation. A subsequent proteome analysis of isolated microglia confirmed the anti-inflammatory and revealed cytoskeletal effects of spermidine in APPPS1 mice. Our data highlight that the autophagy activator spermidine holds the potential to enhance Aβ degradation and to counteract microglia-mediated neuroinflammation in AD pathology.

2022-07-04 | PXD034638 | Pride

Spatiotemporal proteomics of hormone treated mice (urine across time, prostate tissue)

Project description:Benign prostatic hyperplasia and related lower urinary tract symptoms remain common, costly, and impactful issues for aging males. Etiology and pathogenesis are multifactorial and include steroid hormone changes and inflammation. Noninvasive markers could one day inform personalized medicine, but interindividual variation and lack of healthy age-matched controls hamper research. Experimental models are appealing for insight into disease mechanisms. Here, we present a spatiotemporal proteomics study in a mouse model of hormone-induced urinary dysfunction. Urine samples were collected noninvasively across time: before, during, and after disease onset. Microcomputed tomography analysis implicated the prostate as a spatially relevant contributor to bladder outlet obstruction. Prostates were collected after disease onset and compared with control mice. Notable changes in urine include proteins representing oxidative stress defense and acute phase inflammatory response processes. In the prostate, hormone treatment led to perturbations related to oxidative stress response and H2O2 metabolism. Several protein changes coincided in both urine and prostate tissue, including Ctsb, Qsox1, and Gpx3. This study supports the concept of noninvasive urinary biomarkers for prostate disease diagnostics. Oxidative stress and acute phase inflammatory processes were identified as key consequences of hormone-induced bladder outlet obstruction. Future research into antioxidants and anti-inflammatories in prostate disease appears promising.

2021-09-08 | PXD014416 | Pride

Cellular and culture medium proteomes from umbilical cord mesenchymal stem cell and human umbilical vein endothelial cells

Project description:Application of umbilical cord mesenchymal stem cell-derived conditioned media (HUCMSC-CM) to treat severe, progressive PAH. Serial infusions of HUCMSC-CM resulted in marked clinical and hemodynamic improvement after 6 months, and showed no adverse events. Differential expression analysis between conditioned media and cells was used to identify molecular processes with a putative role in treatment benefit.

2022-11-29 | PXD032234 | Pride

Intact Glycopeptide Analysis of Human Urine

Project description:Identification of intact glycopeptides in pooled healthy human urine samples

2024-02-21 | PXD038923 | Pride

The human host response to monkeypox infection: a proteomic case series study

Project description:The rapid rise of Monkeypox (MPX) cases outside previously endemic areas prompt for a better understanding of the disease. We studied the plasma proteome of a group of MPX patients with a similar infection history and clinical manifestation typical for the current outbreak. We report that MPX is associated with a strong plasma proteomic response among nutritional and acute phase response proteins. Moreover, we report a correlation between plasma proteins and disease severity. Contrasting the MPX host response with that of COVID-19, we find a range of similarities, but also important differences. For instance, CFHR1 is induced in COVID-19, but suppressed in MPX, reflecting the different role of the complement system in the two infectious diseases. The partial overlap in response proteins, however, allowed us to explore repurposing of a COVID-19 biomarker panel assay, which resulted in successful patient classification. Hence, our results provide a first proteomic characterization of the MPX human host response, and we reveal a thus far untapped potential for accelerating the response to disease outbreaks through the repurposing of biomarker assays.

2022-09-22 | PXD036074 | Pride

Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia

Project description:Current techniques to diagnose and/or monitor critically ill neonates with bronchopulmonary dysplasia (BPD) require invasive sampling of body fluids, which can affect the health status of these frail neonate. We tested our hypotheses 1) it is feasible to use early urine samples from extremely low gestational age newborns at risk for bronchopulmonary dysplasia for proteomics, and 2) urine proteomics can confirm previously identified proteins and biomarkers associated with BPD without invasive sample collection. We developed a robust high throughput urine proteomics methodology that requires only 50 microliters of urine. We validated the methodology on urine collected within 72 hours of birth. Urine samples were collected from extremely low gestational age newborns (ELGANS) (gestational age (26 + 1.2) weeks) admitted to a single Neonatal Intensive Care Unit(NICU); half of whom eventually developed BPD, while the other half served as controls. Our high throughput urine proteomics approach clearly identified several BPD-associated changes in the urine proteome recapitulating expected blood proteome changes. Interestingly, sixteen identified urinary proteins are known targets of drugs approved by the Food and Drug Administration (FDA). Urine proteomics can be used for prediction of BPD risk. In addition to identifying numerous proteins implicated in BPD pathophysiology, previously found in invasively collected blood, tracheal aspirate, and broncho-alveolar lavage, urine proteomics also suggested novel potential therapeutic targets. Ease of access to urine for sequential proteomic evaluations could also allow for longitudinal monitoring of disease progression and impact of therapeutic intervention.

2022-04-04 | PXD028895 | Pride

Candida glabrata transcription profile when grown under Niacin starvation or in human urine

Project description:The transcription profile of Candida glabrata grown under two different Niacin limitation conditions were determined. Condition 1 is comparing log phase C. glabrata cells (O.D. 0.5-0.6) grown in synthetic medium containing 0.016 uM versus 3.25 uM nicotinic acid (NA), a common form of Niacin. The NA concentration of 3.25 uM is the standard concentration in synthetic complete (SC) medium. Condition 2 is comparing log phase C. glabrata cells (O.D. 0.4-0.6) grown in 3 individual human urine samples (supplemented with 2% glucose) versus in SC medium. Keywords: transcriptional profiling by microarray GSM151863, GSM151869 are dye-swap experiment #1 and GSM151880, GSM151881 are dye-swap experiment #2 for Niacin limitation condition 1. GSM151934, GSM152116 are dye-swap experiment #1, GSM152118, GSM152119 are dye-swap experiment #2 and GSM152130, GSM152131 are dye-swap experiment #3 for Niacin limitation condition 2.

2010-06-05 | E-GEOD-6582 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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