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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

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			Action	DRS
	200114-LN_IDA_F01.wiff	Wiff
	200114-LN_IDA_F01.wiff.scan	Wiff
	200114-LN_IDA_F02.wiff	Wiff
	200114-LN_IDA_F02.wiff.scan	Wiff
	200114-LN_IDA_F03.wiff	Wiff

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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

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Proteomic profiling of canine (dog) serum and urine

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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

Intact Glycopeptide Analysis of Human Urine

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

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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

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.

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Quantitative SWATH-Based Proteomic Profiling of Urine for the Identification of Endometrial Cancer Biomarkers in Symptomatic Women

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Urine proteome in patients with metabolic associated fatty liver disease

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