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urine proteomics

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https://www.readbyqxmd.com/read/27915473/urine-proteomics-in-the-era-of-mass-spectrometry
#1
REVIEW
Ashley Beasley-Green
With the technological advances of mass spectrometry (MS)-based platforms, clinical proteomics is one of the most rapidly growing areas in biomedical research. Urine proteomics has become a popular subdiscipline of clinical proteomics because it is an ideal source for the discovery of noninvasive disease biomarkers. The urine proteome offers a comprehensive view of the local and systemic physiology since the proteome is primarily composed of proteins/peptides from the kidneys and plasma. The emergence of MS-based proteomic platforms as prominent bioanalytical tools in clinical applications has enhanced the identification of protein-based urinary biomarkers...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27914711/proteomic-based-research-strategy-identified-laminin-subunit-alpha-2-as-a-potential-urinary-specific-biomarker-for-the-medullary-sponge-kidney-disease
#2
Antonia Fabris, Maurizio Bruschi, Laura Santucci, Giovanni Candiano, Simona Granata, Alessandra Dalla Gassa, Nadia Antonucci, Andrea Petretto, Gian Marco Ghiggeri, Giovanni Gambaro, Antonio Lupo, Gianluigi Zaza
Medullary sponge kidney (MSK) disease, a rare kidney malformation featuring recurrent renal stones and nephrocalcinosis, continues to be diagnosed using expensive and time-consuming clinical/instrumental tests (mainly urography). Currently, no molecular diagnostic biomarkers are available. To identify such we employed a proteomic-based research strategy utilizing urine from 22 patients with MSK and 22 patients affected by idiopathic calcium nephrolithiasis (ICN) as controls. Notably, two patients with ICN presented cysts...
November 30, 2016: Kidney International
https://www.readbyqxmd.com/read/27903615/urine-proteome-specific-for-eye-damage-can-predict-kidney-damage-in-patients-with-type-2-diabetes-a-case-control-and-a-5-3-year-prospective-cohort-study
#3
Jin-Kui Yang, Ying-Ying Wang, Chang Liu, Ting-Ting Shi, Jing Lu, Xi Cao, Fang-Yuan Yang, Jian-Ping Feng, Chen Chen, Li-Nong Ji, Aimin Xu
OBJECTIVE: The predictive value of microalbuminuria (MAU) for kidney damage is limited in type 2 diabetes (T2D). We studied whether a urine proteome specific for sight-threatening proliferative diabetic retinopathy (PDR) is an indicator to predict chronic renal insufficiency (CRI) in patients with T2D. RESEARCH DESIGN AND METHODS: A shotgun urine proteomic analysis was performed in patients with MAU and PDR (case subjects) and in patients with MAU and a duration of T2D for >10 years but with without any degree of retinopathy (control subjects)...
November 30, 2016: Diabetes Care
https://www.readbyqxmd.com/read/27860107/quantitative-method-to-investigate-the-balance-between-metabolism-and-proteome-biomass-starting-from-glycine
#4
Haiwei Gu, Patrick A Carroll, Jianhai Du, Jiangjiang Zhu, Fausto Carnevale Neto, Robert N Eisenman, Daniel Raftery
The balance between metabolism and biomass is very important in biological systems; however, to date there has been no quantitative method to characterize the balance. In this methodological study, we propose to use the distribution of amino acids in different domains to investigate this balance. It is well known that endogenous or exogenous amino acids in a biological system are either metabolized or incorporated into free amino acids (FAAs) or proteome amino acids (PAAs). Using glycine (Gly) as an example, we demonstrate a novel method to accurately determine the amounts of amino acids in various domains using serum, urine, and cell samples...
November 15, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27847095/proteomic-analysis-and-translational-perspective-of-hepatocellular-carcinoma-identification-of-diagnostic-protein-biomarkers-by-an-onco-proteogenomics-approach
#5
REVIEW
Shyh-Horng Chiou, King-Teh Lee
Hepatocellular carcinoma (HCC) has been ranked as the third leading cause of cancer-related mortality worldwide. Typically, patients are already in advanced stages of liver cirrhosis at the time of HCC diagnosis. Because HCC is often detected at a late stage and is highly aggressive, noninvasive biomarkers are urgently needed for early diagnosis. Recent advances in gene-expression profiling technologies have enabled molecular classification of HCC into defined subclasses that provide a firm basis for further study of potential mechanisms and biomarkers underlying the development of HCC...
November 2016: Kaohsiung Journal of Medical Sciences
https://www.readbyqxmd.com/read/27843374/potential-serum-and-urine-biomarkers-in-patients-with-lupus-nephritis-and-the-unsolved-problems
#6
REVIEW
Song-Chou Hsieh, Chang-Youh Tsai, Chia-Li Yu
Lupus nephritis (LN) is one of the most frequent and serious complications in the patients with systemic lupus erythematosus. Autoimmune-mediated inflammation in both renal glomerular and tubulointerstitial tissues is the major pathological finding of LN. In clinical practice, the elevated anti-dsDNA antibody titer concomitant with reduced complement C3 and C4 levels has become the predictive and disease-activity surrogate biomarkers in LN. However, more and more evidences suggest that autoantibodies other than anti-dsDNA antibodies, such as anti-nucleosome, anti-C1q, anti-C3b, anti-cardiolipin, anti-endothelial cell, anti-ribonuclear proteins, and anti-glomerular matrix (anti-actinin) antibodies, may also involve in LN...
2016: Open Access Rheumatology: Research and Reviews
https://www.readbyqxmd.com/read/27834300/the-surmetagit-study-design-and-rationale-for-a-prospective-pan-omics-examination-of-the-gastrointestinal-response-to-roux-en-y-gastric-bypass-surgery
#7
Priscila Sala, Giliane Belarmino, Natasha Mendonça Machado, Camila Siqueira Cardinelli, Karina Al Assal, Mariane Marques Silva, Danielle Cristina Fonseca, Robson Kiyoshi Ishida, Marco Aurélio Santo, Eduardo Guimarães Hourneaux de Moura, Paulo Sakai, Ismael Francisco Mota Siqueira Guarda, Ismael Dale Cotrim Guerreiro da Silva, Agatha Sacramento Rodrigues, Carlos Alberto de Bragança Pereira, Steven Heymsfield, Joel Doré, Raquel Susana Matos de Miranda Torrinhas, Daniel Giannella-Neto, Dan Linetzky Waitzberg
OBJECTIVE: To describe the protocol of the SURgically induced Metabolic effects on the Human GastroIntestinal Tract (SURMetaGIT) study, a clinical pan-omics study exploring the gastrointestinal tract as a central organ driving remission of type 2 diabetes mellitus (T2DM) after Roux-en-Y gastric bypass (RYGB). The main points considered in the study's design and challenges faced in its application are detailed. METHODS: This observational, longitudinal, prospective study involved collection of gastrointestinal biopsy specimens, faeces, urine, and blood from 25 obese women with T2DM who were candidates for RYGB (20 patients for omics assessment and 5 for omics validation)...
November 10, 2016: Journal of International Medical Research
https://www.readbyqxmd.com/read/27799660/toward-noninvasive-diagnosis-of-iga-nephropathy-a-pilot-urinary-metabolomic-and-proteomic-study
#8
Michaela Neprasova, Dita Maixnerova, Jan Novak, Colin Reily, Bruce A Julian, Jan Boron, Petr Novotny, Miloslav Suchanek, Vladimir Tesar, Petr Kacer
IgA nephropathy is diagnosed by renal biopsy, an invasive procedure with a risk of significant complications. Noninvasive approaches are needed for possible diagnostic purposes and especially for monitoring disease activity or responses to treatment. In this pilot project, we assessed the utility of urine samples as source of biomarkers of IgA nephropathy. We used spot urine specimens from 19 healthy controls, 11 patients with IgA nephropathy, and 8 renal-disease controls collected on day of renal biopsy. Urine samples were analyzed using untargeted metabolomic and targeted proteomic analyses by several experimental techniques: liquid chromatography coupled with mass spectrometry, immunomagnetic isolation of target proteins coupled with quantitation by mass spectrometry, and protein arrays...
2016: Disease Markers
https://www.readbyqxmd.com/read/27796656/proteomic-analysis-reveals-downregulation-of-housekeeping-proteins-in-the-diabetic-vascular-proteome
#9
Josua Dwinovan, Alexander D Colella, Nusha Chegeni, Timothy K Chataway, Elke M Sokoya
AIMS: Type 2 diabetes (T2D) increases the risk of death associated with cardiovascular complications. However, a complete understanding of protein changes within the diabetic vasculature is still lacking. METHODS: Herein, we utilized mass spectrometry to perform vascular and urinary proteome analysis using a rat model of high-fat feeding and low-dose streptozotocin to simulate late-stage T2D. The purpose of this study was to identify aortic and urine proteins that are differentially expressed in normal and T2D rats...
October 28, 2016: Acta Diabetologica
https://www.readbyqxmd.com/read/27780262/the-specific-%C3%AE-1-adrenergic-receptor-antagonist-prazosin-influences-the-urine-proteome
#10
Mindi Zhao, Jianqiang Wu, Youhe Gao
Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible impact of α1-adrenergic receptor on urine proteome, this study investigated effects of the specific inhibitor prazosin on the urine proteome in a rat model by using tandem mass tagging and two-dimensional liquid chromatography-tandem mass spectrometry...
2016: PloS One
https://www.readbyqxmd.com/read/27731382/urinary-interleukin-6-as-a-predictor-of-radiographic-progression-in-rheumatoid-arthritis-a-3-year-evaluation
#11
Yune-Jung Park, Seung-Ah Yoo, Ga-Ram Kim, Chul-Soo Cho, Wan-Uk Kim
Previously, we demonstrated that the urine proteome signature of patients with rheumatoid arthritis (RA) reflects inflammation-related cellular processes. Here, we measured interleukin (IL)-6, IL-8, and chemokine ligand 2 (CCL2) concentrations in the urine of RA patients and prospectively investigated their role in predicting RA activity and prognosis. One hundred seventy-three RA patients and 62 non-RA controls were recruited. Urinary IL-6, CCL2, and IL-8 levels were elevated in RA patients and correlated well with disease activity...
October 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27716443/a-discrete-cluster-of-urinary-biomarkers-discriminates-between-active-systemic-lupus-erythematosus-patients-with-and-without-glomerulonephritis
#12
Carolina Landolt-Marticorena, Stephenie D Prokopec, Stacey Morrison, Babak Noamani, Dennisse Bonilla, Heather Reich, James Scholey, Carmen Avila-Casado, Paul R Fortin, Paul C Boutros, Joan Wither
BACKGROUND: Management of lupus nephritis (LN) would be greatly aided by the discovery of biomarkers that accurately reflect changes in disease activity. Here, we used a proteomics approach to identify potential urinary biomarkers associated with LN. METHODS: Urine was obtained from 60 LN patients with paired renal biopsies, 25 active non-LN SLE patients, and 24 healthy controls. Using Luminex, 128 analytes were quantified and normalized to urinary creatinine levels...
October 4, 2016: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/27711093/in-the-search-of-novel-urine-biomarkers-for-the-early-diagnosis-of-prostate-cancer-intracellular-or-secreted-proteins-as-the-target-group-where-and-how-to-search-for-possible-biomarkers-useful-in-the-everyday-clinical-practice
#13
Amalia Katafigioti, Ioannis Katafigiotis, Stavros Sfoungaristos, Christos Alamanis, Konstantinos Stravodimos, Ioannis Anastasiou, Eleni Roumelioti, Mordechai Duvdevani, Constantinos Constantinides
OBJECTIVE: To search which category of proteins can be detected in urine in order to examine subsequently its ability to improve our accuracy for the diagnosis of Prostate Cancer (PCa) as biomarkers in clinical useful fluids like urine and serum. Material and method(s): Urine samples of 127 patients were obtained after a vigorous transrectal prostatic massage to both lobes. The patients were considered to have a high risk for PCa according to their PSA (> 4 ng/ml), their digital rectal examination (DRE) (positive for suspicious prostatic lesions) or to their abnormal PSA kinetics (PSA velocity (PSAV > 0...
October 5, 2016: Archivio Italiano di Urologia, Andrologia
https://www.readbyqxmd.com/read/27686150/proteome-profiling-of-urinary-exosomes-identifies-alpha-1-antitrypsin-and-h2b1k-as-diagnostic-and-prognostic-biomarkers-for-urothelial-carcinoma
#14
Shih-Yi Lin, Chao-Hsiang Chang, His-Chin Wu, Ching-Chan Lin, Kai-Po Chang, Chi-Rei Yang, Chi-Ping Huang, Wu-Huei Hsu, Chiz-Tzung Chang, Chao-Jung Chen
MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96...
September 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27664330/exosomal-proteins-as-prostate-cancer-biomarkers-in-urine-from-mass-spectrometry-discovery-to-immunoassay-based-validation
#15
Ling Wang, Tore Skotland, Viktor Berge, Kirsten Sandvig, Alicia Llorente
Exosomes have recently appeared as a novel source of non-invasive cancer biomarkers since tumor-specific molecules can be found in exosomes isolated from biological fluids. We have previously analyzed the proteome of urinary exosomes by mass spectrometry, and identified proteins differentially expressed in prostate cancer patients compared to healthy males. Since mass spectrometry is so far not commonly used in clinical laboratories, we have here investigated whether antibody-based methods such as Western blot or ELISA can be used to validate the use of the identified proteins as prostate cancer biomarkers...
September 21, 2016: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27634439/biomarkers-for-early-diagnosis-of-acute-kidney-injury-current-progress-and-clinical-prospects
#16
Hongfeng Huang, Jingyi Zhou, Jianghua Chen
Acute kidney injury (AKI) is one of the most common complications in critically ill patients, resulting in high morbidity and mortality. AKI usually occurs after major surgery, severe infection or drug-induced nephrotoxicity and is associated with prolonged hospital stays, increased costs and adverse clinical outcomes. The diagnosis of AKI is currently based on decreased glomerular filtration rate (GFR) and urine output, and increased serum creatinine. Novel biomarkers are required for early identification of patients with AKI to allow timely therapy and improve patient outcomes...
September 9, 2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27609515/biochemical-foundations-of-health-and-energy-conservation-in-hibernating-free-ranging-subadult-brown-bear-ursus-arctos
#17
Karen Gjesing Welinder, Rasmus Hansen, Michael Toft Overgaard, Malene Brohus, Mads Sønderkær, Martin von Bergen, Ulrike Rolle-Kampczyk, Wolfgang Otto, Tomas L Lindahl, Karin Arinell, Alina L Evans, Jon E Swenson, Inge G Revsbech, Ole Frøbert
Brown bears (Ursus arctos) hibernate for 5-7 months without eating, drinking, urinating, and defecating at a metabolic rate of only 25% of the summer activity rate. Nonetheless, they emerge healthy and alert in spring. We quantified the biochemical adaptations for hibernation by comparing the proteome, metabolome, and hematological features of blood from hibernating and active free-ranging subadult brown bears with a focus on conservation of health and energy. We found that total plasma protein concentration increased during hibernation, even though the concentrations of most individual plasma proteins decreased, as did the white blood cell types...
October 21, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27603418/vitamin-d-binding-protein-is-a-potential-urinary-biomarker-of-irbesartan-treatment-response-in-patients-with-iga-nephropathy
#18
Jiashun Zeng, Qiong Wen, Rong Rong, Fengxian Huang, Qiongqiong Yang, Xueqing Tang, Feng He, Naya Huang, Xueqing Yu
AIMS: The purpose of this study was to identify predictive markers of irbesartan (an angiotensin receptor blocker) treatment response in immunoglobulin A nephropathy (IgAN) patients. METHODS: Urine samples were collected both before and after irbesartan treatment in IgAN patients and compared with urine from healthy volunteers. The total urinary protein produced in 24 h was measured to determine therapeutic response. The urinary proteome was evaluated by two-dimensional gel electrophoresis coupled with MALDI-TOF-MS/MS analysis...
September 7, 2016: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/27590860/comparative-proteomics-in-alkaptonuria-provides-insights-into-inflammation-and-oxidative-stress
#19
Daniela Braconi, Giulia Bernardini, Alessandro Paffetti, Lia Millucci, Michela Geminiani, Marcella Laschi, Bruno Frediani, Barbara Marzocchi, Annalisa Santucci
Alkaptonuria (AKU) is an ultra-rare inborn error of metabolism associated with a defective catabolism of phenylalanine and tyrosine leading to increased systemic levels of homogentisic acid (HGA). Excess HGA is partly excreted in the urine, partly accumulated within the body and deposited onto connective tissues under the form of an ochronotic pigment, leading to a range of clinical manifestations. No clear genotype/phenotype correlation was found in AKU, and today there is the urgent need to identify biomarkers able to monitor AKU progression and evaluate response to treatment...
August 30, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27589965/peptickddb-peptide-and-protein-centric-database-for-the-investigation-of-genesis-and-progression-of-chronic-kidney-disease
#20
Magdalena Krochmal, Marco Fernandes, Szymon Filip, Claudia Pontillo, Holger Husi, Jerome Zoidakis, Harald Mischak, Antonia Vlahou, Joachim Jankowski
The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated...
2016: Database: the Journal of Biological Databases and Curation
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