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urine proteomics

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https://www.readbyqxmd.com/read/28211531/proteomic-analysis-of-urinary-extracellular-vesicles-from-high-gleason-score-prostate-cancer
#1
Kazutoshi Fujita, Hideaki Kume, Kyosuke Matsuzaki, Atsunari Kawashima, Takeshi Ujike, Akira Nagahara, Motohide Uemura, Yasushi Miyagawa, Takeshi Tomonaga, Norio Nonomura
Extracellular vesicles (EVs) are microvesicles secreted from various cell types. We aimed to discover a new biomarker for high Gleason score (GS) prostate cancer (PCa) in urinary EVs via quantitative proteomics. EVs were isolated from urine after massage from 18 men (negative biopsy [n = 6], GS 6 PCa [n = 6], or GS 8-9 PCa [n = 6]). EV proteins were labeled with iTRAQ and analyzed by LC-MS/MS. We identified 4710 proteins and quantified 3528 proteins in the urinary EVs. Eleven proteins increased in patients with PCa compared to those with negative biopsy (ratio >1...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28188435/marked-increase-in-urinary-excretion-of-apolipoproteins-in-children-with-nephrolithiasis-associated-with-hypercalciuria
#2
Larisa Kovacevic, Hong Lu, Joseph A Caruso, Tuhina Govil-Dalela, Ronald Thomas, Yegappan Lakshmanan
BACKGROUND: Using a proteomic approach, we aimed to identify and compare the urinary excretion of proteins involved in lipid transport and metabolism in children with kidney stones and hypercalciuria (CAL), hypocitraturia (CIT), and normal metabolic work-up (NM), and in healthy controls (HCs). Additionally, we aimed to confirm these results using ELISA, and to examine the relationship between the urinary excretion of selected proteins with demographic, dietary, blood, and urinary parameters...
February 10, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28159781/insights-into-diabetic-kidney-disease-using-urinary-proteomics-and-bioinformatics
#3
Julie A D Van, James W Scholey, Ana Konvalinka
A number of proteomic and peptidomic analyses of urine from diabetic subjects have been published in the quest for a biomarker that predicts progression of nephropathy. Less attention has been paid to the relationships between urinary proteins and the underlying biological processes revealed by the analyses. In this review, we focus on the biological processes identified by studying urinary proteins and protein-protein interactions at each stage of diabetic nephropathy to provide an overview of the events underlying progression of kidney disease reflected in the urine...
February 3, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28158993/comparative-differential-proteomic-analysis-of-minimal-change-disease-and-focal-segmental-glomerulosclerosis
#4
Vanessa Pérez, Dolores López, Ester Boixadera, Meritxell Ibernón, Anna Espinal, Josep Bonet, Ramón Romero
BACKGROUND: Minimal change disease (MCD) and primary focal segmental glomerulosclerosis (FSGS) are glomerular diseases characterized by nephrotic syndrome. Their diagnosis requires a renal biopsy, but it is an invasive procedure with potential complications. In a small biopsy sample, where only normal glomeruli are observed, FSGS cannot be differentiated from MCD. The correct diagnosis is crucial to an effective treatment, as MCD is normally responsive to steroid therapy, whereas FSGS is usually resistant...
February 3, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28149930/ten-years-of-proteomics-in-bladder-cancer-progress-and-future-directions
#5
REVIEW
Maria Frantzi, Antonia Vlahou
Research efforts targeting the identification of bladder cancer biomarkers have been extensive during the past decade. Investigations have been performed at the genome, transcriptome, proteome, and metabolome levels and outputs have started appearing including the sketching of disease molecular subtypes. Proteins are directly linked to cell phenotype hence they accumulate special interest as both biomarkers and therapeutic targets. Multiple technical challenges exist, of the main, being the protein concentration vast dynamic range and presence of proteins in modified forms...
January 27, 2017: Bladder Cancer
https://www.readbyqxmd.com/read/28146445/risk-of-cholangiocarcinoma-in-patients-with-primary-sclerosing-cholangitis-diagnosis-and-surveillance
#6
Hanno Ehlken, Roman Zenouzi, Christoph Schramm
PURPOSE OF REVIEW: Primary sclerosing cholangitis (PSC) is associated with an increased risk of hepatobiliary and extrahepatic malignancy. Particularly the risk of cholangiocarcinoma (CCA) is greatly increased. To provide potentially curative treatments for affected patients an early diagnosis of CCA is crucial. We here review the current advances with respect to CCA diagnosis and surveillance and discuss a rational approach on how to perform surveillance of CCA in PSC patients. RECENT FINDINGS: Given the shortcomings of the current modalities for the surveillance and diagnosis of CCA in PSC, recent studies have focused on novel biomarkers for CCA...
March 2017: Current Opinion in Gastroenterology
https://www.readbyqxmd.com/read/28129394/characterization-of-early-phase-neutrophil-extracellular-traps-in-urinary-tract-infections
#7
Yanbao Yu, Keehwan Kwon, Tamara Tsitrin, Shiferaw Bekele, Patricia Sikorski, Karen E Nelson, Rembert Pieper
Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28109429/body-fluid-degradomics-and-characterization-of-basic-n-terminome
#8
F Sabino, O Hermes, U Auf dem Keller
Rapid improvements in instrumentation and data analysis make mass spectrometry-based proteomics the method of choice for global characterization of proteomes and discovery of protein-based biomarkers. On the contrary to tissue biopsies, body fluids-e.g., blood, wound fluid, urine, and saliva-are noninvasive and easy to collect and process. However, they are very complex and present high dynamic ranges of protein concentrations, rendering direct shotgun proteomics analysis as inefficient for identification of low-abundance proteins in these specimens...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109170/comparative-proteomic-analysis-of-urine-and-laser-microdissected-glomeruli-in-iga-nephropathy
#9
Xiaoyuan Ning, Zhong Yin, Zuoxiang Li, Jiayun Xu, Linna Wang, Wanjun Shen, Yang Lu, Guangyan Cai, Xueguang Zhang, Xiangmei Chen
The purpose of the present study was to identify the differential proteins that synchronously change in urine and glomeruli and could be used to monitor glomerular lesions of IgA nephropathy (IgAN). The proteomes of urine and glomeruli from 4 IgAN patients who were graded III/IV according to the grading system of Lee et al were compared to the urine proteomes of 4 healthy volunteers and the glomeruli proteomes of adjacent normal tissue from 4 patients with renal tumors, respectively. Western blot, enzyme-linked immunosorbent assay and immunofluorescence assay were applied to verify the results of the proteomic analysis...
January 21, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28107998/multiplex-and-accurate-quantification-of-acute-kidney-injury-biomarker-candidates-in-urine-using-protein-standard-absolute-quantification-psaq-and-targeted-proteomics
#10
Benoît Gilquin, Mathilde Louwagie, Michel Jaquinod, Alexandre Cez, Guillaume Picard, Leila El Kholy, Brigitte Surin, Jérôme Garin, Myriam Ferro, Thomas Kofman, Caroline Barau, Emmanuelle Plaisier, Pierre Ronco, Virginie Brun
There is a need for multiplex, specific and quantitative methods to speed-up the development of acute kidney injury biomarkers and allow a more specific diagnosis. Targeted proteomic analysis combined with stable isotope dilution has recently emerged as a powerful option for the parallelized evaluation of candidate biomarkers. This article presents the development of a targeted proteomic assay to quantify 4 acute kidney injury biomarker candidates in urine samples. The proteins included in the assessed panel consisted of myo-inositol oxygenase (MIOX), phosphoenolpyruvate carboxykinase 1 (PCK1), neutrophil gelatinase-associated lipocalin (NGAL) and liver fatty acid-binding protein (L-FABP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28099838/osteoarthritis-year-in-review-2016-biomarkers-biochemical-markers
#11
REVIEW
A Mobasheri, A-C Bay-Jensen, W E van Spil, J Larkin, M C Levesque
PURPOSE: The aim of this "Year in Review" article is to summarize and discuss the implications of biochemical marker related articles published between the Osteoarthritis Research Society International (OARSI) 2015 Congress in Seattle and the OARSI 2016 Congress in Amsterdam. METHODS: The PubMed/MEDLINE bibliographic database was searched using the combined keywords: 'biomarker' and 'osteoarthritis'. The PubMed/MEDLINE literature search was conducted using the Advanced Search Builder function (http://www...
February 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28087010/breaking-the-ice-urine-proteomics-of-medullary-sponge-kidney-disease
#12
Somchai Chutipongtanate
Urinary proteomics is a promising tool for biomarker investigation, particularly in complex kidney diseases. Fabris and colleagues report that urinary laminin subunit alpha-2 is a potential diagnostic marker of medullary sponge kidney (MSK) disease by using a label-free quantitative proteomics platform and a clinically compatible enzyme-linked immunosorbent assay. The neglected issue of stone pathogenesis was also evidenced. This commentary discusses several considerations in biomarker validation, and how urinary proteomics breaks new ground in MSK research...
February 2017: Kidney International
https://www.readbyqxmd.com/read/28067231/multiomics-reveal-non-alcoholic-fatty-liver-disease-in-rats-following-chronic-exposure-to-an-ultra-low-dose-of-roundup-herbicide
#13
Robin Mesnage, George Renney, Gilles-Eric Séralini, Malcolm Ward, Michael N Antoniou
The impairment of liver function by low environmentally relevant doses of glyphosate-based herbicides (GBH) is still a debatable and unresolved matter. Previously we have shown that rats administered for 2 years with 0.1 ppb (50 ng/L glyphosate equivalent dilution; 4 ng/kg body weight/day daily intake) of a Roundup GBH formulation showed signs of enhanced liver injury as indicated by anatomorphological, blood/urine biochemical changes and transcriptome profiling. Here we present a multiomic study combining metabolome and proteome liver analyses to obtain further insight into the Roundup-induced pathology...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28064163/predicting-albuminuria-response-to-spironolactone-treatment-with-urinary-proteomics-in-patients-with-type-2-diabetes-and-hypertension
#14
Morten Lindhardt, Frederik Persson, Christina Oxlund, Ib A Jacobsen, Petra Zürbig, Harald Mischak, Peter Rossing, Hiddo J L Heerspink
BACKGROUND: The mineralocorticoid receptor antagonist spironolactone significantly reduces albuminuria in patients with diabetes. Prior studies have shown large between-patient variability in albuminuria treatment response. We previously developed and validated a urinary proteomic classifier that predicts onset and progression of chronic kidney disease. Here, we tested whether the proteomic classifier based on 273 urinary peptides (CKD273) predicts albuminuria response to spironolactone treatment...
January 7, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28042331/comprehensive-metaproteomic-analyses-of-urine-in-the-presence-and-absence-of-neutrophil-associated-inflammation-in-the-urinary-tract
#15
Yanbao Yu, Patricia Sikorski, Madeline Smith, Cynthia Bowman-Gholston, Nicolas Cacciabeve, Karen E Nelson, Rembert Pieper
Inflammation in the urinary tract results in a urinary proteome characterized by a high dynamic range of protein concentrations and high variability in protein content. This proteome encompasses plasma proteins not resorbed by renal tubular uptake, renal secretion products, proteins of immune cells and erythrocytes derived from trans-urothelial migration and vascular leakage, respectively, and exfoliating urothelial and squamous epithelial cells. We examined how such proteins partition into soluble urine (SU) and urinary pellet (UP) fractions by analyzing 33 urine specimens 12 of which were associated with a urinary tract infection (UTI)...
2017: Theranostics
https://www.readbyqxmd.com/read/28031956/noninvasive-metabolic-profiling-for-painless-diagnosis-of-human-diseases-and-disorders
#16
REVIEW
Mainak Mal
Metabolic profiling provides a powerful diagnostic tool complementary to genomics and proteomics. The pain, discomfort and probable iatrogenic injury associated with invasive or minimally invasive diagnostic methods, render them unsuitable in terms of patient compliance and participation. Metabolic profiling of biomatrices like urine, breath, saliva, sweat and feces, which can be collected in a painless manner, could be used for noninvasive diagnosis. This review article covers the noninvasive metabolic profiling studies that have exhibited diagnostic potential for diseases and disorders...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/28011229/differential-colony-size-cell-length-and-cellular-proteome-of-escherichia-coli-isolated-from-urine-vs-stone-nidus-of-kidney-stone-patients
#17
Ratree Tavichakorntrakool, Patcharee Boonsiri, Vitoon Prasongwatana, Aroonlug Lulitanond, Chaisiri Wongkham, Visith Thongboonkerd
BACKGROUND: Escherichia coli is associated with kidney stone disease, as a cause or an effect (secondary or recurrent urinary tract infection, UTI). Defining phenotypic or functional differences between E. coli inside stone nidus (ECS, associated with infection-induced stone) and outside the stone (i.e. from urine) (ECU, represented secondary infection) would be helpful to better understand bacterial involvement in this disease. METHODS: ECS and ECU were isolated from 100 stone formers and subjected to antimicrobial susceptibility test, ERIC-PCR genotyping, determination of biofilm formation, bacterial colony size on agar plate and cell length in broth, 2-DE, nanoLC-MS/MS, protein network analysis, and pyruvate dehydrogenase (PDH) activity assay...
December 21, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28009970/combined-serum-and-eps-urine-proteomic-analysis-using-itraq-technology-for-discovery-of-potential-prostate-cancer-biomarkers
#18
Mo Zhang, Lizhu Chen, Zhengwei Yuan, Zeyu Yang, Yue Li, Liping Shan, Bo Yin, Xiang Fei, Jianing Miao, Yongsheng Song
Prostate cancer (PCa) is one of the most common malignant tumors and a major cause of cancer-related death for men worldwide. The aim of our study was to identify potential non-invasive serum and expressed prostatic secretion (EPS)-urine biomarkers for accurate diagnosis of PCa. Here, we performed a combined isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis to compare protein profiles using pooled serum and EPS-urine samples from 4 groups of patients: benign prostate hyperplasia (BPH), high grade prostatic intraepithelial neoplasia (HGPIN), localized PCa and metastatic PCa...
November 2016: Discovery Medicine
https://www.readbyqxmd.com/read/28004973/beta-2-glycoprotein-1-and-alpha-1-antitrypsin-as-urinary-markers-of-renal-cancer-in-von-hippel-lindau-patients
#19
Giorgia Mandili, Agata Notarpietro, Amina Khadjavi, Marco Allasia, Antonino Battaglia, Barbara Lucatello, Bruno Frea, Francesco Turrini, Francesco Novelli, Giuliana Giribaldi, Paolo Destefanis
CONTEXT: Von Hippel-Lindau disease (VHLD) is a rare inherited neoplastic syndrome. Among all the VHLD-associated tumors, clear cell renal cell carcinoma (ccRCC) is the major cause of death. OBJECTIVE: The aim of this paper is the discovery of new non-invasive biomarker for the monitoring of VHLD patients. MATERIALS AND METHODS: We compared the urinary proteome of VHLD patients, ccRCC patients and healthy volunteers. RESULTS: Among all differentially expressed proteins, alpha-1-antitrypsin (A1AT) and APOH (beta-2-glycoprotein-1) are strongly over-abundant only in the urine of VHLD patients with a history of ccRCC...
December 22, 2016: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/27997253/the-progress-and-potential-of-proteomic-biomarkers-for-type-1-diabetes-in-children
#20
Robert Moulder, Santosh Dilip Bhosale, Riitta Lahesmaa, David Robinson Goodlett
Although it is possible to identify the genetic risk for type 1 diabetes (T1D), it is not possible to predict who will develop the disease. New biomarkers are needed that would help understand the mechanisms of disease onset and when to administer targeted therapies and interventions. Areas covered: An overview is presented of international study efforts towards understanding the cause of T1D, including the collection of several extensive temporal sample series that follow the development of T1D in at risk children...
January 2017: Expert Review of Proteomics
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