A comprehensive urine proteome database generated from patients with various renal conditions and prostate cancer

AbstractUrine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers. Surprisingly, 43% (167) of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as myoglobin, serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

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A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

Frontiers in Medicine ◽

10.3389/fmed.2021.548212 ◽

2021 ◽

Vol 8 ◽

Author(s):

Adam C. Swensen ◽

Jingtang He ◽

Alexander C. Fang ◽

Yinyin Ye ◽

Carrie D. Nicora ◽

...

Keyword(s):

Prostate Cancer ◽

Extracellular Proteins ◽

Urine Samples ◽

Protein Biomarkers ◽

Urine Protein ◽

Urine Proteome ◽

Proteome Profiling ◽

Transplant Patients ◽

Associated Proteins ◽

Proteome Database

Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

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Detection of Prostate Cancer via IR Spectroscopic Analysis of Urinary Extracellular Vesicles: A Pilot Study

Membranes ◽

10.3390/membranes11080591 ◽

2021 ◽

Vol 11 (8) ◽

pp. 591

Author(s):

Xin-Le Yap ◽

Bayden Wood ◽

Teng-Aik Ong ◽

Jasmine Lim ◽

Bey-Hing Goh ◽

...

Keyword(s):

Prostate Cancer ◽

Extracellular Vesicles ◽

Cancer Progression ◽

Prostate Cancer Screening ◽

Principal Component ◽

Urine Samples ◽

Cancer Type ◽

Marker Proteins ◽

Novel Strategy ◽

Ir Spectroscopic

Extracellular vesicles (EVs) are membranous nanoparticles naturally released from living cells which can be found in all types of body fluids. Recent studies found that cancer cells secreted EVs containing the unique set of biomolecules, which give rise to a distinctive absorbance spectrum representing its cancer type. In this study, we aimed to detect the medium EVs (200–300 nm) from the urine of prostate cancer patients using Fourier transform infrared (FTIR) spectroscopy and determine their association with cancer progression. EVs extracted from 53 urine samples from patients suspected of prostate cancer were analyzed and their FTIR spectra were preprocessed for analysis. Characterization of morphology, particle size and marker proteins confirmed that EVs were successfully isolated from urine samples. Principal component analysis (PCA) of the EV’s spectra showed the model could discriminate prostate cancer with a sensitivity of 59% and a specificity of 81%. The area under curve (AUC) of FTIR PCA model for prostate cancer detection in the cases with 4–20 ng/mL PSA was 0.7, while the AUC for PSA alone was 0.437, suggesting the analysis of urinary EVs described in this study may offer a novel strategy for the development of a noninvasive additional test for prostate cancer screening.

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Comparison of several methods for semiquantitative determination of urinary protein.

Clinical Chemistry ◽

10.1093/clinchem/23.5.876 ◽

1977 ◽

Vol 23 (5) ◽

pp. 876-879 ◽

Cited By ~ 42

Author(s):

W L Gyure

Keyword(s):

Serum Albumin ◽

Salt Concentration ◽

Urine Samples ◽

Urine Protein ◽

Sulfosalicylic Acid ◽

Green Method ◽

Semiquantitative Determination ◽

Acid Method ◽

Bromcresol Green

Abstract Two types of urine protein dipsticks and the sulfosalicylic acid method were compared for their accuracy and specificity, with use of urine samples supplemented with various proteins. Dipsticks yield accurate results when the protein under consideration is restricted to albumin; the sulfosalicylic acid method accurately determines many kinds of proteins in addition to albumin. Detergents affect each of the methods, but changes in salt concentration only affect results by dipstick procedures. Dipsticks, which are based on the protein-error principle for indicators, are subject to some of the conditions that apply to the bromcresol green method for serum albumin determination.

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Detection of Human Polyomaviruses in Urine from Bone Marrow Transplant Patients: Comparison of Electron Microscopy with PCR

Clinical Chemistry ◽

10.1373/clinchem.2003.024539 ◽

2004 ◽

Vol 50 (2) ◽

pp. 306-312 ◽

Cited By ~ 24

Author(s):

Stefan S Biel ◽

Andreas Nitsche ◽

Andreas Kurth ◽

Wolfgang Siegert ◽

Muhsin Özel ◽

...

Keyword(s):

Electron Microscopy ◽

Bone Marrow ◽

Real Time ◽

Bone Marrow Transplant ◽

Real Time Pcr ◽

Marrow Transplant ◽

Test System ◽

Urine Samples ◽

Clinical Samples ◽

Transplant Patients

Abstract Background: We studied electron microscopy (EM) as an appropriate test system for the detection of polyomavirus in urine samples from bone marrow transplant patients. Methods: We evaluated direct EM, ultracentrifugation (UC) before EM, and solid-phase immuno-EM (SPIEM). The diagnostic accuracy of EM was studied by comparison with a real-time PCR assay on 531 clinical samples. Results: The detection rate of EM was increased by UC and SPIEM. On 531 clinical urine samples, the diagnostic sensitivity of EM was 47% (70 of 149) with a specificity of 100%. We observed a linear relationship between viral genome concentration and the proportion of urine samples positive by EM, with a 50% probability for a positive EM result for urine samples with a polyomavirus concentration of 106 genome-equivalents (GE)/mL; the probability of a positive EM result was 0% for urine samples with <103 GE/mL and 100% for urine samples containing 109 GE/mL. Conclusions: UC/EM is rapid and highly specific for polyomavirus in urine. Unlike real-time PCR, EM has low sensitivity and cannot quantify the viral load.

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Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

10.1101/675348 ◽

2019 ◽

Cited By ~ 1

Author(s):

Rui Sun ◽

Christie Hunter ◽

Chen Chen ◽

Weigang Ge ◽

Nick Morrice ◽

...

Keyword(s):

Prostate Cancer ◽

Biomarker Discovery ◽

Single Shot ◽

Protein Biomarkers ◽

Differential Abundance ◽

Tissue Samples ◽

Peptide Precursors ◽

High Consistency ◽

Method R ◽

Acquisition Method

ABSTRACTWe report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 15-min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration and OpenSWATH software for data analysis.We applied the method to a cohort 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).Overall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.

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Comparison of Extracellular Proteins from Virulent and Avirulent Vibrio parahaemolyticus Strains to Identify Potential Virulence Factors

Journal of Food Protection ◽

10.4315/0362-028x.jfp-19-188 ◽

2019 ◽

Vol 83 (1) ◽

pp. 155-162

Author(s):

YU HE ◽

SHUAI WANG ◽

XIANTING YIN ◽

FENGJIAO SUN ◽

BIN HE ◽

...

Keyword(s):

Foodborne Pathogens ◽

Vibrio Parahaemolyticus ◽

Stress Protein ◽

Extracellular Proteins ◽

Trigger Factor ◽

Uncharacterized Protein ◽

Adverse Conditions ◽

Semialdehyde Dehydrogenase ◽

Associated Proteins ◽

Related Proteins

ABSTRACT Vibrio parahaemolyticus is a leading seafood-borne pathogen that causes gastroenteritis, septicemia, and serious wound infections due to the actions of virulence-associated proteins. We compared the extracellular proteins of nonvirulent JHY20 and virulent ATCC 33847 V. parahaemolyticus reference strains. Eighteen extracellular proteins were identified from secretory profiles, and 11 (68.75%) of the 16 proteins in ATCC 33847 are associated with virulence and/or protection against adverse conditions: trigger factor, chaperone SurA, aspartate–semialdehyde dehydrogenase, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, glutamate 5-kinase, alanine dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, outer membrane protein OmpV, ribosome-associated inhibitor A, chaperone protein Skp, and universal stress protein. Two nontoxic-related proteins, amino acid ABC transporter substrate-binding protein and an uncharacterized protein, were identified in JHY20. The results provide a theoretical basis for supporting safety risk assessment of aquatic foods, illuminate the pathogenic mechanisms of V. parahaemolyticus, and assist the identification of novel vaccine candidates for foodborne pathogens. HIGHLIGHTS

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Methodology for the at-home collection of urine samples for prostate cancer detection

BioTechniques ◽

10.2144/btn-2019-0092 ◽

2020 ◽

Vol 68 (2) ◽

pp. 65-71 ◽

Cited By ~ 3

Author(s):

Martyn Webb ◽

Kate Manley ◽

Mireia Olivan ◽

Ingrid Guldvik ◽

Malgorzata Palczynska ◽

...

Keyword(s):

Prostate Cancer ◽

Cancer Detection ◽

Large Scale ◽

Digital Rectal Examination ◽

Urine Samples ◽

Rt Pcr ◽

Rectal Examination ◽

Diagnosis And Prognosis ◽

Gene Transcripts ◽

At Home

Urine from patients with prostate cancer (PCa) contains gene transcripts that have been used for PCa diagnosis and prognosis. Historically, patient urine samples have been collected after a digital rectal examination of the prostate, which was thought necessary to boost the levels of prostatic secretions in the urine. We herein describe methodology that allows urine to be collected by patients at home and then posted to a laboratory for analysis. RNA yields and quality were comparable to those for post digital rectal examination urine, and there was improved sensitivity for the detection of TMPRSS2:ERG transcripts by RT-PCR. The At-Home collection protocol has opened up the potential to perform large-scale PCa studies without the inconvenience, cost, discomfort and expense of patients having to visit the clinic.

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