Summary of Study ST001662

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001067. The data can be accessed directly via it's Project DOI: 10.21228/M8S69H This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001662
Study TitleLC-MS Metabolomics of Urine Reveals Distinct Profiles for Low- and High-Grade Bladder Cancer
Study SummaryBladder cancer (BC) is among the most frequent malignancies worldwide. Novel non-invasive markers are needed to diagnose and stage BC with more accuracy than invasive procedures such as cystoscopy. Our aim was to discover novel urine metabolomic profiles to diagnose and stage non-muscle invasive (NMIBC) and muscle-invasive (MIBC) patients using ultra-performance liquid chromatography analysis (UPLC)-based metabolomics. We prospectively recruited 64 BC patients (19 TaG1, 11 TaG3, 20 T1G3, 12 T2G3, 1 T2G2, 1 T3G3) and 20 age- and sex-matched healthy volunteers without evidence of renal or bladder condition confirmed by ultrasound, from whom we collected a first morning urine sample (before surgery in patients). We conducted a UPLC-quadrupole-time-of-flight mass spectrometry (UPLC-Q-ToF MS) untargeted metabolomic analysis in all urine samples. We selected the discriminant variables between groups with a supervised orthogonal-least-squares discriminant analysis (OPLS-DA) analysis and we identified them by querying their exact mass against those presented in online databases through a mediator platform. Subsequently, we confirmed the dysregulated metabolites when chemical standards were commercially available. We compared all clinical groups of patients with controls and we identified dysregulated metabolites in every comparison. Of these, we confirmed p-cresol glucuronide as potential diagnostic biomarker, and potential staging tool for NMIBC patients. Among NMIBC patients, we identified p-coumaric acid as a potential staging biomarker for milder NMIBC stages (TaG1). Additionally, we confirmed spermine and adenosine as potential staging biomarkers for MIBC. This is the first study conducted in urine samples of most stages of NMIBC and MIBC and healthy controls to identify non-invasive biomarkers. Once confirmed, these may improve BC management thus reducing the use of current harmful diagnostic techniques.
Institute
Health Research Institute Hospital La Fe
LaboratoryAnalytical Unit
Last NameRoca Marugán
First NameMarta
AddressAvenida Fernando Abril Martorell 106, Torre A, Valencia, Valencia, 46026, Spain
Emailmarta_roca@iislafe.es
Phone680888576
Submit Date2021-01-21
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailGC-MS
Release Date2021-08-16
Release Version1
Marta Roca Marugán Marta Roca Marugán
https://dx.doi.org/10.21228/M8S69H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001067
Project DOI:doi: 10.21228/M8S69H
Project Title:Urinary LCMS metabolimc study in bladder cancer
Project Summary:Bladder cancer (BC) is among the most frequent malignancies worldwide. Novel non-invasive markers are needed to diagnose and stage BC with more accuracy than invasive procedures such as cystoscopy. Our aim was to discover novel urine metabolomic profiles to diagnose and stage non-muscle invasive (NMIBC) and muscle-invasive (MIBC) patients using ultra-performance liquid chromatography analysis (UPLC)-based metabolomics. We prospectively recruited 64 BC patients (19 TaG1, 11 TaG3, 20 T1G3, 12 T2G3, 1 T2G2, 1 T3G3) and 20 age- and sex-matched healthy volunteers without evidence of renal or bladder condition confirmed by ultrasound, from whom we collected a first morning urine sample (before surgery in patients). We conducted a UPLC-quadrupole-time-of-flight mass spectrometry (UPLC-Q-ToF MS) untargeted metabolomic analysis in all urine samples. We selected the discriminant variables between groups with a supervised orthogonal-least-squares discriminant analysis (OPLS-DA) analysis and we identified them by querying their exact mass against those presented in online databases through a mediator platform. Subsequently, we confirmed the dysregulated metabolites when chemical standards were commercially available. We compared all clinical groups of patients with controls and we identified dysregulated metabolites in every comparison. Of these, we confirmed p-cresol glucuronide as potential diagnostic biomarker, and potential staging tool for NMIBC patients. Among NMIBC patients, we identified p-coumaric acid as a potential staging biomarker for milder NMIBC stages (TaG1). Additionally, we confirmed spermine and adenosine as potential staging biomarkers for MIBC. This is the first study conducted in urine samples of most stages of NMIBC and MIBC and healthy controls to identify non-invasive biomarkers. Once confirmed, these may improve BC management thus reducing the use of current harmful diagnostic techniques.
Institute:Health Research Institute Hospital La Fe
Laboratory:Analytical Unit
Last Name:Roca Marugán
First Name:Marta
Address:Avenida Fernando Abril Martorell 106, Torre A, Valencia, Valencia, 46026, Spain
Email:marta_roca@iislafe.es
Phone:680888576

Subject:

Subject ID:SU001739
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Pooled

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Disease Type of tumor
SA152084mv08618_87.mzXMLControl Control
SA152085mv08618_37.mzXMLControl Control
SA152086mv08618_78.mzXMLControl Control
SA152087mv08618_55.mzXMLControl Control
SA152088mv08618_57.mzXMLControl Control
SA152089mv08618_86.mzXMLControl Control
SA152090mv08618_80.mzXMLControl Control
SA152091mv08618_81.mzXMLControl Control
SA152092mv08618_75.mzXMLControl Control
SA152093mv08618_64.mzXMLControl Control
SA152094mv08618_48.mzXMLControl Control
SA152095mv08618_12.mzXMLControl Control
SA152096mv08618_32.mzXMLControl Control
SA152097mv08618_45.mzXMLControl Control
SA152098mv08618_13.mzXMLControl Control
SA152099mv08618_98.mzXMLControl Control
SA152100mv08618_17.mzXMLControl Control
SA152101mv08618_93.mzXMLControl Control
SA152102mv08618_43.mzXMLControl Control
SA152103mv08618_65.mzXMLControl Control
SA152104mv08618_40.mzXMLQC QC
SA152105mv08618_72.mzXMLQC QC
SA152106mv08618_50.mzXMLQC QC
SA152107mv08618_83.mzXMLQC QC
SA152108mv08618_94.mzXMLQC QC
SA152109mv08618_18.mzXMLQC QC
SA152110mv08618_61.mzXMLQC QC
SA152111mv08618_29.mzXMLQC QC
SA152112mv08618_05.mzXMLQC QC
SA152113mv08618_60.mzXMLT1G3 NMIBC
SA152114mv08618_68.mzXMLT1G3 NMIBC
SA152115mv08618_58.mzXMLT1G3 NMIBC
SA152116mv08618_70.mzXMLT1G3 NMIBC
SA152117mv08618_56.mzXMLT1G3 NMIBC
SA152118mv08618_51.mzXMLT1G3 NMIBC
SA152119mv08618_63.mzXMLT1G3 NMIBC
SA152120mv08618_35.mzXMLT1G3 NMIBC
SA152121mv08618_20.mzXMLT1G3 NMIBC
SA152122mv08618_24.mzXMLT1G3 NMIBC
SA152123mv08618_19.mzXMLT1G3 NMIBC
SA152124mv08618_11.mzXMLT1G3 NMIBC
SA152125mv08618_99.mzXMLT1G3 NMIBC
SA152126mv08618_46.mzXMLT1G3 NMIBC
SA152127mv08618_33.mzXMLT1G3 NMIBC
SA152128mv08618_41.mzXMLT1G3 NMIBC
SA152129mv08618_76.mzXMLT1G3 NMIBC
SA152130mv08618_42.mzXMLT1G3 NMIBC
SA152131mv08618_62.mzXMLT1G3 NMIBC
SA152132mv08618_39.mzXMLT1G3 NMIBC
SA152133mv08618_89.mzXMLT2G3 MIBC
SA152134mv08618_88.mzXMLT2G3 MIBC
SA152135mv08618_74.mzXMLT2G3 MIBC
SA152136mv08618_54.mzXMLT2G3 MIBC
SA152137mv08618_28.mzXMLT2G3 MIBC
SA152138mv08618_15.mzXMLT2G3 MIBC
SA152139mv08618_25.mzXMLT2G3 MIBC
SA152140mv08618_22.mzXMLT2G3 MIBC
SA152141mv08618_21.mzXMLT2G3 MIBC
SA152142mv08618_36.mzXMLT2G3 MIBC
SA152143mv08618_14.mzXMLT2G3 MIBC
SA152144mv08618_16.mzXMLTAG1 NMIBC
SA152145mv08618_82.mzXMLTAG1 NMIBC
SA152146mv08618_08.mzXMLTAG1 NMIBC
SA152147mv08618_91.mzXMLTAG1 NMIBC
SA152148mv08618_85.mzXMLTAG1 NMIBC
SA152149mv08618_53.mzXMLTAG1 NMIBC
SA152150mv08618_23.mzXMLTAG1 NMIBC
SA152151mv08618_52.mzXMLTAG1 NMIBC
SA152152mv08618_09.mzXMLTAG1 NMIBC
SA152153mv08618_31.mzXMLTAG1 NMIBC
SA152154mv08618_44.mzXMLTAG1 NMIBC
SA152155mv08618_71.mzXMLTAG1 NMIBC
SA152156mv08618_47.mzXMLTAG1 NMIBC
SA152157mv08618_96.mzXMLTAG1 NMIBC
SA152158mv08618_38.mzXMLTAG1 NMIBC
SA152159mv08618_97.mzXMLTAG1 NMIBC
SA152160mv08618_77.mzXMLTAG1 NMIBC
SA152161mv08618_90.mzXMLTAG1 NMIBC
SA152162mv08618_79.mzXMLTAG1 NMIBC
SA152163mv08618_95.mzXMLTAG3 NMIBC
SA152164mv08618_27.mzXMLTAG3 NMIBC
SA152165mv08618_49.mzXMLTAG3 NMIBC
SA152166mv08618_67.mzXMLTAG3 NMIBC
SA152167mv08618_66.mzXMLTAG3 NMIBC
SA152168mv08618_69.mzXMLTAG3 NMIBC
SA152169mv08618_73.mzXMLTAG3 NMIBC
SA152170mv08618_26.mzXMLTAG3 NMIBC
SA152171mv08618_59.mzXMLTAG3 NMIBC
SA152172mv08618_34.mzXMLTAG3 NMIBC
SA152173mv08618_84.mzXMLTAG3 NMIBC
Showing results 1 to 90 of 90

Collection:

Collection ID:CO001732
Collection Summary:Study subjects Sixty-four BC patients were recruited between May 2016 and April 2018 at La Fe University and Polytechnic Hospital (Valencia, Spain). Twenty age- and sex-matched healthy volunteers (control group) who underwent an ultrasound scan to rule out the presence of urological malignancies or other alterations were also recruited. Patients and controls were clinically followed-up until May 2020. Pre-operative clinical staging was performed through physical examination, urine cytology and CT scans of the chest, abdomen and pelvis (in case of invasive bladder cancer). The tumor histological classification was done according to grade in the WHO 1973 and 2004 classifications. Demographic and clinical data were collected. The exclusion criteria were lack of informed consent, absence of histological confirmation and presence of other malignancies. Informed consent was obtained from all participants according to protocols approved by the ethics review board at La Fe University and Polytechnic Hospital. The study was performed according to the declaration of Helsinki, as amended in Edinburgh in 2000. Urine collection A first morning urine sample of 25-50 ml was collected in sterile containers from all participants. Urine was kept at 4 ºC until processing and centrifuged at 805 x g for 5 min at 4 ºC to remove cellular debris. Supernatant was aliquoted and frozen at -80 ºC until analyzed. The concentration of creatinine in each urine sample was measured by clinical laboratory standardized methods.
Sample Type:Urine

Treatment:

Treatment ID:TR001752
Treatment Summary:A first morning urine sample of 25-50 ml was collected in sterile containers from all participants. Urine was kept at 4 ºC until processing and centrifuged at 805 x g for 5 min at 4 ºC to remove cellular debris. Supernatant was aliquoted and frozen at -80 ºC until analyzed. The concentration of creatinine in each urine sample was measured by clinical laboratory standardized methods

Sample Preparation:

Sampleprep ID:SP001745
Sampleprep Summary:Sample treatment was performed according to a previous study 22. Briefly, after centrifugation, 40 µl of urine cleaned supernatant were transferred to a 96 well-plate for LC-MS (liquid chromatography-mass spectrometry) analysis and diluted by adding 50 µl of H2O (0.1 % v/v HCOOH). Each sample was spiked with 10 µl of 20 µM IS solution containing phenylalanine-d5, caffeine-d9, leukine enkephaline and reserpine in H2O:CH3OH (1:1, 0.1% v/v HCOOH). Blank samples were prepared by replacing urine by ultrapure H2O. A quality control (QC) sample was prepared by mixing 10 µl from each urine sample.

Combined analysis:

Analysis ID AN002713
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 6550
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type EI
MS instrument type QTOF
MS instrument name Agilent 6550 QTOF
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH002002
Chromatography Summary:The metabolomic analysis was carried out using an Ultra-Performance Liquid Chromatography (UPLC) system coupled to an iFunnel Q-ToF (quadrupole-time-of-flight) Agilent 6550 mass spectrometer (Agilent Technologies, CA, USA) using an UPLC BEH C18 (100 x 2.1 mm, 1.7 µm, Waters, Wexford, Ireland) column from Waters (Wexford, Ireland). Autosampler and column temperatures were set to 4 °C and 40 °C, respectively, and the injection volume was 5 µl. Mobile phase A and mobile phase B consisted of H2O and acetonitrile, both containing 0.1% of formic acid. A gradient elution was performed at a flow rate of 400 µl min-1 along 14 min as follows: initial conditions of 98% of mobile phase A was maintained for 1 min, and then decreased until 75% in 2 min, 50% in 3 min and 5% in 3 more min. 95% of mobile phase B was held for 3 min and then, a 0.55 min gradient was used to return to the initial conditions, which were held for 2.5 min to totally column recovery.
Instrument Name:Agilent 6550
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:40
Flow Gradient:initial conditions of 98% of mobile phase A was maintained for 1 min, and then decreased until 75% in 2 min, 50% in 3 min and 5% in 3 more min. 95% of mobile phase B was held for 3 min and then, a 0.55 min gradient was used to return to the initial conditions, which were held for 2.5 min to totally column recovery
Flow Rate:400ul/min
Solvent A:100% water; 0.1% formic acid
Solvent B:acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002510
Analysis ID:AN002713
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:EI
MS Comments:Full scan MS data from 50 to 1700 m/z with a scan frequency of 6 Hz was collected both in positive (ESI+) and negative (ESI-) electrospray ionization modes. The following electrospray ionization parameters were used: gas temperature, 200 °C; drying gas, 14 l min-1; nebulizer, 60 psi; sheath gas temperature, 350 °C; sheath gas flow, 11 l min-1. Urine samples were randomly injected in the chromatographic system in order to avoid intra-batch variability, as well as to enhance quality and reproducibility. QC sample was analyzed every 7 injections to monitor and correct changes in the instrument response. QC sample was also repeatedly analysed under auto MS/MS and All-ion (MSE) fragmentation modes to provide useful information of fragment ions for identification purposes. Sample stability and analytical drift were investigated through IS intensities. Blank analysis was performed at the end of the sequence and used to identify artefacts from sampling, preparation of samples and analysis.
Ion Mode:POSITIVE
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