Summary of Study ST003780

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 PR002358. The data can be accessed directly via it's Project DOI: 10.21228/M8TZ68 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003780
Study TitleDengue Virus infection in infants: serum metabolomics profiling for biomarker discovery
Study SummaryDengue is an acute febrile illness transmitted by mosquitoes infected with the dengue virus (DENV), considered one of the leading causes of morbidity and mortality globally.The study of metabolites in the serum of infected patients aims to identify biomarkers for a better understanding of the pathophysiological mechanisms and the development of diagnostic tools.For this study, serum samples from 40 children between 0 and 17 years old, treated at the Dr. Roberto Gilbert Children’s Hospital in Guayaquil, were included. The samples were subjected to molecular diagnosis by RT-PCR and divided into two groups: Dengue (N=25) and healthy controls (N=15). Serum metabolites were extracted following the Glasgow Polyomics protocol. The metabolites were analyzed by ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), and the resulting data were analyzed by multivariate statistics using partial least squares discriminant analysis (PLS-DA). The metabolite masses with biomarker potential were attributed to molecules using the Lipid Maps platform. As a result, PLS-DA showed a separation between the two groups and identified 14 metabolites with higher importance values in the projection of these variables (VIP>2), responsible for the separation considering the top 5 components of the PLS-DA. Relative concentrations of 3 metabolites were found to be higher in dengue patients, while 11 were more abundant in the control group. These metabolites belong to different lipid classes, such as fatty acids, sphingolipids, glycerolipids, sterols, and glycerophospholipids.
Institute
Escuela Superior Politécnica del Litoral (ESPOL)
DepartmentFacultad Ciencias de la Vida
LaboratoryLaboratorio para investigaciones biomédicas
Last NameB. Cordeiro
First NameFernanda
Addresskm 30.5 Via Perimetral, Campus Gustavo Galindo
Emailfbertuc@espol.edu.ec
Phone+593984594225
Submit Date2024-09-09
Num Groups2
Total Subjects40
Num Males18
Num Females22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-09-09
Release Version1
Fernanda B. Cordeiro Fernanda B. Cordeiro
https://dx.doi.org/10.21228/M8TZ68
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002358
Project DOI:doi: 10.21228/M8TZ68
Project Title:Dengue Virus infection in infants: serum metabolomics profiling for biomarker discovery
Project Type:LC-MS exploratory metabolomics
Project Summary:For this study, serum samples from 40 children between 0 and 17 years old were included. The samples were subjected to molecular diagnosis by RT-PCR and divided into two groups: Dengue (N=25) and healthy controls (N=15). Serum metabolites were extracted following the Glasgow Polyomics protocol. The metabolites were analyzed by ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), and the resulting data were analyzed by multivariate statistics using partial least squares discriminant analysis (PLS-DA).
Institute:Escuela Superior Politécnica del Litoral (ESPOL)
Department:Facultad Ciencias de la Vida
Laboratory:Laboratorio para investigaciones biomédicas
Last Name:B. Cordeiro
First Name:Fernanda
Address:km 30.5 Via Perimetral, Campus Gustavo Galindo
Email:fbertuc@espol.edu.ec
Phone:+593984594225
Contributors:Ricardo E Correa Fierro, Noroska Gabriela Mogollón Salazar, Washington Cárdenas, Evencio Joel Medina-Villamizar, Jefferson Pastuña-Fasso, Melanie Ochoa-Ocampo, Giovanna Morán-Marcillo, Melanie Cedeño-Zambrano, Mary Ernestina Regato Arrata, Mildred Zambrano, Joyce Andrade, Juan Chang

Subject:

Subject ID:SU003914
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:0 - 16
Gender:Male and female
Human Inclusion Criteria:Dengue mono-infected individuals vs. age paired healthy controls

Factors:

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

mb_sample_id local_sample_id Sample source Sex Disease cohort
SA410044QCC_3Pool Control NA CONTROL
SA410045QCC_16Pool Control NA CONTROL
SA410046QCC_15Pool Control NA CONTROL
SA410047QCC_14Pool Control NA CONTROL
SA410048QCC_13Pool Control NA CONTROL
SA410049QCC_12Pool Control NA CONTROL
SA410050QCC_11Pool Control NA CONTROL
SA410051QCC_10Pool Control NA CONTROL
SA410052QCC_9Pool Control NA CONTROL
SA410053QCC_8Pool Control NA CONTROL
SA410054QCC_7Pool Control NA CONTROL
SA410055QCC_6Pool Control NA CONTROL
SA410056QCC_5Pool Control NA CONTROL
SA410057QCC_4Pool Control NA CONTROL
SA410058QCC_0Pool Control NA CONTROL
SA410059QCC_2Pool Control NA CONTROL
SA410060QCC_1Pool Control NA CONTROL
SA410061QCD_4Pool DENV NA DENV
SA410062QCD_8Pool DENV NA DENV
SA410063QCD_2Pool DENV NA DENV
SA410064QCD_1Pool DENV NA DENV
SA410065QCD_9Pool DENV NA DENV
SA410066QCD_6Pool DENV NA DENV
SA410067QCD_0Pool DENV NA DENV
SA410068QCD_5Pool DENV NA DENV
SA410069QCD_3Pool DENV NA DENV
SA410070QCD_10Pool DENV NA DENV
SA410071QCD_11Pool DENV NA DENV
SA410072QCD_12Pool DENV NA DENV
SA410073QCD_13Pool DENV NA DENV
SA410074QCD_14Pool DENV NA DENV
SA410075QCD_15Pool DENV NA DENV
SA410076QCD_16Pool DENV NA DENV
SA410077QCD_7Pool DENV NA DENV
SA41007865_1Serum Female CONTROL
SA41007965_2Serum Female CONTROL
SA41008065_3Serum Female CONTROL
SA41008121_2Serum Female CONTROL
SA41008275_1Serum Female CONTROL
SA41008375_2Serum Female CONTROL
SA41008475_3Serum Female CONTROL
SA41008584_1Serum Female CONTROL
SA41008621_3Serum Female CONTROL
SA41008797_1Serum Female CONTROL
SA41008897_2Serum Female CONTROL
SA41008997_3Serum Female CONTROL
SA41009084_3Serum Female CONTROL
SA41009184_2Serum Female CONTROL
SA41009241_2Serum Female CONTROL
SA41009329_3Serum Female CONTROL
SA41009429_1Serum Female CONTROL
SA41009539_1Serum Female CONTROL
SA41009639_2Serum Female CONTROL
SA41009739_3Serum Female CONTROL
SA41009821_1Serum Female CONTROL
SA41009944_1Serum Female CONTROL
SA41010044_2Serum Female CONTROL
SA41010141_1Serum Female CONTROL
SA41010229_2Serum Female CONTROL
SA41010341_3Serum Female CONTROL
SA41010444_3Serum Female CONTROL
SA41010530_2Serum Female DENV
SA410106115_3Serum Female DENV
SA410107115_2Serum Female DENV
SA41010847_1Serum Female DENV
SA410109132_1Serum Female DENV
SA410110115_1Serum Female DENV
SA41011130_3Serum Female DENV
SA41011247_2Serum Female DENV
SA410113105_3Serum Female DENV
SA410114105_2Serum Female DENV
SA41011530_1Serum Female DENV
SA410116136_2Serum Female DENV
SA410117132_2Serum Female DENV
SA410118157_1Serum Female DENV
SA4101192_1Serum Female DENV
SA410120158_3Serum Female DENV
SA410121158_2Serum Female DENV
SA410122158_1Serum Female DENV
SA410123157_3Serum Female DENV
SA410124157_2Serum Female DENV
SA410125155_3Serum Female DENV
SA410126132_3Serum Female DENV
SA410127155_2Serum Female DENV
SA410128155_1Serum Female DENV
SA4101292_2Serum Female DENV
SA4101302_3Serum Female DENV
SA410131136_3Serum Female DENV
SA410132136_1Serum Female DENV
SA410133105_1Serum Female DENV
SA41013473_2Serum Female DENV
SA41013516_1Serum Female DENV
SA41013616_3Serum Female DENV
SA41013747_3Serum Female DENV
SA41013845_3Serum Female DENV
SA41013945_2Serum Female DENV
SA41014073_1Serum Female DENV
SA41014145_1Serum Female DENV
SA41014273_3Serum Female DENV
SA41014316_2Serum Female DENV
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Collection:

Collection ID:CO003907
Collection Summary:Patients with fever above 38.5° C and at least one of the following symptoms: headache, retro-orbital pain, myalgia, arthralgia, nausea, vomiting and rash. Clinical staff nurse or treating physician performed a single venipuncture and filled two study blood tubes at the same time as samples are collected for clinical testing, using a vacutainer: a tube for whole blood and plasma collection with 3.2% sodium citrate and a sterile non-additives tube, both with approximately 4 mL. Serum and plasma fractions were obtained by centrifugation and distributed in aliquots on 1.5mL micro-centrifuge tubes for long-time storage at -80°C. Healthy individuals without any sign or symptom of arboviral infection were also recruited as a Control group. Personal information and data from interviews during patient enrollment were codified to guarantee anonymous processing. Nucleic acid amplification tests were performed in three blood fractions: whole blood, plasma and serum to discriminate between arboviral infections with overlapping symptoms (Dengue, Zika and Chikungunya). Dengue mono-infection was confirmed by Reverse-Transcription Polymerase Chain Reaction (RT-PCR) using the SuperScript III Platinum One Step RT-PCR Kit (Invitrogen; CA). A two-step heminested protocol targeting the C-prM region of the POLY gene, common to all 4 serotypes allowed molecular diagnosis. The Infected DENV group consists of 25 individuals and a Healthy group CONTROL with 15 individuals, both groups with participants under 16 years
Sample Type:Blood (serum)
Collection Method:Peripheral venipuncture
Collection Location:Guayaquil, Guayas, Ecuador
Storage Conditions:Described in summary
Collection Vials:Sterile non-additive tubes.
Storage Vials:1.5 mL microcentrifuge sterile tubes.
Additives:None

Treatment:

Treatment ID:TR003923
Treatment Summary:No treatment. Sera samples selected from a cohort of DENV and CONTROL groups were randomized and assigned a new codification prior to metabolic extraction. After thawing serum for 15 to 30 min at room temperature, samples were gently homogenized by inverting the original tube 5 times. Using sterile filtered tips and a pipettor, 25 uL were aliquoted to a fresh 1.5mL microcentrifuge tube. Liquid-liquid metabolite extraction requires the addition of 1mL of solvent mixture in a (1:3:1) ratio of HPLC grade Chloroform/Methanol/Water as described in Glasgow Polyomics guidelines for serum preparation. Samples were vigorously mixed and centrifuged in a 4°C chilled centrifuge at 13000 g for 3 minutes. This extraction allows protein and cellular residues to precipitate, isolating the metabolites of interest in the supernatant. Metabolites were concentrated by speed-vacuum centrifugation of 300uL from the previous step. Two pools of metabolite extract from both groups were obtained and treated as Quality Control in DENV (QCD) and CONTROL groups (QCC). Dried samples were resuspended with 200uL of Ultrapure distilled water + 0.1% formic acid and transferred to micro vials on a 4°C chilled autosampler.

Sample Preparation:

Sampleprep ID:SP003920
Sampleprep Summary:Metabolites were concentrated by speed-vacuum centrifugation of 300uL from the previous step. Two pools of metabolite extract from both groups were obtained and treated as Quality Control in DENV (QCD) and CONTROL groups (QCC). Dried samples were resuspended with 200uL of Ultrapure distilled water + 0.1% formic acid and transferred to micro vials on a 4°C chilled autosampler.
Processing Storage Conditions:4℃
Extraction Method:Liquid-liquid metabolite extraction requires the addition of 1mL of solvent mixture in a (1:3:1) ratio of HPLC grade Chloroform/Methanol/Water as described in Glasgow Polyomics guidelines for serum preparation
Extract Storage:4℃

Combined analysis:

Analysis ID AN006208
Chromatography ID CH004709
MS ID MS005912
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity I-Class
Column Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Xevo G2 QTOF
Ion Mode POSITIVE
Units Peak intentsity

Chromatography:

Chromatography ID:CH004709
Instrument Name:Waters Acquity I-Class
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:50
Flow Gradient:80% A and 20% B for 1 minute, followed by a linear transition to 50% A and 50% B for the next minute. Subsequently, the gradient was adjusted to 35% A and 65% B for 2 minutes. Next, the gradient was inverted, employing 20% A and 80% B for 3 minutes. The gradient was further modified to 3% A and 97% B for the next 10 minutes. Finally, the initial conditions were restored for column washing for 1 minute.
Flow Rate:0.5 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile;0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005912
Analysis ID:AN006208
Instrument Name:Waters Xevo G2 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:For mass spectrometry, electrospray ionization (ESI) source was used in positive mode, and data were acquired in full scan. The capillary voltage was set at 0.5 kV, with a cone gas flow rate of 30 L/h and a desolvation gas flow rate of 900 L/h. The source temperature was maintained at 120 °C, while the desolvation temperature was set at 450 °C. Both the sampling cone and source compensation were adjusted to 40 and 80 V, respectively. Scan rate of 1 s and covering a mass range of m/z 100 to 1200 Da was used in full scan mode. To ensure data quality, MS data was obtained from the QC samples from dengue and control groups. The QC samples were injected into the LC–MS instrument sixteen times along the analytical block to condition and equilibrate the system. Data from QC samples were used to graph the retention time drift and as a reference for data processing. To assess the quality of the experiment, Principal Component Analysis (PCA) was performed including QCC and QCD pools presenting the expected nested grouping of the samples to their identified class groups in the cluster analysis (Supplementary Figure 1). The raw data from LC-MS (*.raw) was converted to *.mzML format using ProteoWizard (19) Then, the *.mzML files were processed in MS-DIAL ver. 4.9.221218 (http://prime.psc.riken.jp/) considering peak detection, alignment, gap filling, and blank filtering (maximum sample intensity/average blank intensity ratio > 7) according to parameters shown in Supplementary Table 1. The MS-DIAL feature list table *.txt was exported for statistical analysis. Prior to statistical analysis, we preprocessed the MS-DIAL-exported data to obtain high-quality data. The data preprocessing was implemented in R 4.2.2 using “notame” package (https://github.com/antonvsdata/notame). Preprocessing included drift correction by smoothed cubic spline, batch correction by mean/median difference of QCs, and data imputation by the random forest algorithm. The detailed method is available at the GitHub repository (https://github.com/IKIAM-NPLab/Dengue_metabolomics).
Ion Mode:POSITIVE
Capillary Voltage:0.5 kV
Fragment Voltage:NA
Fragmentation Method:NA
Source Temperature:120
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450
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