Summary of Study ST002048

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 PR001295. The data can be accessed directly via it's Project DOI: 10.21228/M8B13G 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 IDST002048
Study TitleEffects of Zika virus infection on the metabolome of pregnant women: a longitudinal study
Study Typeuntargeted NMR analysis
Study SummaryZika virus (ZIKV) is a mosquito-borne +ssRNA virus that can cause abnormal development in human fetal central neuron system and even lead to stillbirth. Despite the popularity of studies in this area recently, there is currently still no sufficient treatment for it. Knowledge on how ZIKV infection impact human metabolisms is still lacking. Untargeted metabolomics can profile the overall change in metabolites after infection, thus provide hypothesis for specific investigations. We here performed a Nuclear Magnetic Resonance spectroscopy (NMR)-based untargeted case-control metabolomics study on urine of ZIKV-infected pregnant women. We collected samples monthly from the first trimester till up to 6 months of ZIKV-infected and non-infected individuals and modelled the longitudinal data. We identified 3-aminoisobutyrate and trigonelline with significantly higher levels in the ZIKV-infected patients, while 11 metabolites (fucose, 2-hydroxyglutarate, N-acetyl-glutamine, dimethylamine, 4-hydroxyphenethyl alcohol, creatinine, lactate, threonine, histidine, pseudouridine, and 1-methylnicotinamide) had significantly lower levels. We also identified 2 metabolites, including glucose and 1-methylnicotinamide, where the trends over time of the intensity levels between the two groups were significantly different. These metabolites suggested further study on tryptophan, NAD+, pyrimidine, and glucose metabolisms. These metabolomic changes may lead us to a better understanding of mechanisms that cause poor fetal outcomes as well as effects of virus infection on human pregnancy.
Institute
University of Georgia
DepartmentBiochemistry and Molecular Biology and Complex Carbohydrate Research Center
LaboratoryEdison Lab
Last NameZhang
First NameSicong
Address315 Riverbend Road, Complex Carbohydrate Research Center, Athens, Georgia, 30602, USA
Email499753121@qq.com
Phone7067151662
Submit Date2022-01-03
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2024-07-01
Release Version1
Sicong Zhang Sicong Zhang
https://dx.doi.org/10.21228/M8B13G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001295
Project DOI:doi: 10.21228/M8B13G
Project Title:Effects of Zika virus infection on the metabolome of pregnant women: a longitudinal study
Project Type:untargeted NMR analysis
Project Summary:Zika virus (ZIKV) is a mosquito-borne +ssRNA virus that can cause abnormal development in human fetal central neuron system and even lead to stillbirth. Despite the popularity of studies in this area recently, there is currently still no sufficient treatment for it. Knowledge on how ZIKV infection impact human metabolisms is still lacking. Untargeted metabolomics can profile the overall change in metabolites after infection, thus provide hypothesis for specific investigations. We here performed a Nuclear Magnetic Resonance spectroscopy (NMR)-based untargeted case-control metabolomics study on urine of ZIKV-infected pregnant women. We collected samples monthly from the first trimester till up to 6 months of ZIKV-infected and non-infected individuals and modelled the longitudinal data. We identified 3-aminoisobutyrate and trigonelline with significantly higher levels in the ZIKV-infected patients, while 11 metabolites (fucose, 2-hydroxyglutarate, N-acetyl-glutamine, dimethylamine, 4-hydroxyphenethyl alcohol, creatinine, lactate, threonine, histidine, pseudouridine, and 1-methylnicotinamide) had significantly lower levels. We also identified 2 metabolites, including glucose and 1-methylnicotinamide, where the trends over time of the intensity levels between the two groups were significantly different. These metabolites suggested further study on tryptophan, NAD+, pyrimidine, and glucose metabolisms. These metabolomic changes may lead us to a better understanding of mechanisms that cause poor fetal outcomes as well as effects of virus infection on human pregnancy.
Institute:University of Georgia
Last Name:Zhang
First Name:Sicong
Address:315 Riverbend Road, Complex Carbohydrate Research Center, Athens, Georgia, 30602, USA
Email:499753121@qq.com
Phone:7067151662

Subject:

Subject ID:SU002130
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:15-37
Gender:Female
Human Inclusion Criteria:pregnant, at the first trimester

Factors:

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

mb_sample_id local_sample_id Group Urine timepoint
SA1926165003440777after ZIKV+ 2
SA1926175003443229after ZIKV+ 2
SA1926185003434607after ZIKV+ 2
SA1926195003440740after ZIKV+ 2
SA1926205003449159after ZIKV+ 3
SA1926215003440039after ZIKV+ 3
SA1926225003449126after ZIKV+ 3
SA1926235003434815after ZIKV+ 3
SA1926245003448852after ZIKV+ 5
SA1926255003444020after ZIKV+ 5
SA1926265003450182after ZIKV+ 5
SA1926275003446601after ZIKV+ 6
SA1926285003442675after ZIKV+ 6
SA1926295003451109before ZIKV+ 1
SA1926305003445344before ZIKV+ 2
SA1926315003437811before ZIKV+ 3
SA1926325003438940before ZIKV+ 4
SA1925125003447415External Control -
SA1925135003443754External Control -
SA1925145003435352External Control -
SA1925155003448455External Control -
SA1925165003449036External Control -
SA1925175003436137External Control -
SA1925185003444543External Control -
SA1925195003434865External Control -
SA1925205003448809External Control -
SA1925215003441259Pooled Control -
SA1925225003435204Pooled Control -
SA1925235003451861Pooled Control -
SA1925245003439802Pooled Control -
SA1925255003451417Pooled Control -
SA1925265003434563Pooled Control -
SA1925275003440314Pooled Control -
SA1925285003443030Pooled Control -
SA1925305003445453ZIKV+ 1
SA1925315003442972ZIKV+ 1
SA1925325003452643ZIKV+ 1
SA1925335003445995ZIKV+ 1
SA1925345003443609ZIKV+ 1
SA1925355003437343ZIKV+ 1
SA1925495003449413ZIKV- -1
SA1925505003452535ZIKV- -1
SA1925515003439519ZIKV- -1
SA1925525003437233ZIKV- -1
SA1925535003448281ZIKV- -1
SA1925545003445389ZIKV- -1
SA1925555003443371ZIKV- -1
SA1925565003445901ZIKV- -1
SA1925575003450367ZIKV- -1
SA1925585003445462ZIKV- -1
SA1925365003441973ZIKV+ 2
SA1925375003450840ZIKV+ 2
SA1925385003449264ZIKV+ 2
SA1925395003441787ZIKV+ 2
SA1925595003437978ZIKV- -2
SA1925605003447293ZIKV- -2
SA1925615003438082ZIKV- -2
SA1925625003448941ZIKV- -2
SA1925635003443548ZIKV- -2
SA1925645003445178ZIKV- -2
SA1925655003445191ZIKV- -2
SA1925665003446147ZIKV- -2
SA1925675003449380ZIKV- -2
SA1925685003449278ZIKV- -2
SA1925695003431831ZIKV- -2
SA1925705003440438ZIKV- -2
SA1925295003437107ZIKV+ -3
SA1925405003450379ZIKV+ 3
SA1925415003437690ZIKV+ 3
SA1925425003437998ZIKV+ 3
SA1925715003449124ZIKV- -3
SA1925725003445059ZIKV- -3
SA1925735003434787ZIKV- -3
SA1925745003444858ZIKV- -3
SA1925755003448610ZIKV- -3
SA1925765003446949ZIKV- -3
SA1925775003444621ZIKV- -3
SA1925785003449100ZIKV- -3
SA1925795003438827ZIKV- -3
SA1925805003437938ZIKV- -3
SA1925815003444975ZIKV- -3
SA1925435003436209ZIKV+ 4
SA1925445003445650ZIKV+ 4
SA1925455003448998ZIKV+ 4
SA1925825003445758ZIKV- -4
SA1925835003445524ZIKV- -4
SA1925845003434416ZIKV- -4
SA1925855003438797ZIKV- -4
SA1925865003445859ZIKV- -4
SA1925875003449902ZIKV- -4
SA1925885003440026ZIKV- -4
SA1925895003448928ZIKV- -4
SA1925905003443073ZIKV- -4
SA1925915003438135ZIKV- -4
SA1925465003434424ZIKV+ 5
SA1925475003446677ZIKV+ 5
SA1925925003452543ZIKV- -5
SA1925935003441599ZIKV- -5
SA1925945003438995ZIKV- -5
SA1925955003443656ZIKV- -5
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Collection:

Collection ID:CO002123
Collection Summary:At each visit, women were given a physical examination and blood, urine, saliva, and vaginal fluid samples were collected as per ZIP study protocols (see attachment). In between monthly visits, women would also collect a urine sample at home to be brought to the next monthly visit or collected at a biweekly visit to the clinic.
Collection Protocol Filename:Lebov_Study_protocol.pdf
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002142
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP002136
Sampleprep Summary:In brief, each sample was centrifuged at 3500g and then 540µl of supernatant was added by 60µl NMR buffer (1.5M KH2PO4 in D2O with a final concentration of 0.33 mM DSS, pH = 7.4). After this, we centrifuged the sample again at 4000g and transferred 590 µl supernatant to the 5mm NMR tubes in racks of 96 tubes (Bruker Biospin, USA).
Sampleprep Protocol Filename:zika_01_sz_urine_extraction.pdf

Analysis:

Analysis ID:AN003335
Laboratory Name:Edison Lab
Analysis Type:NMR
Results File:Zika_binned_mw.txt
Units:(relative)

NMR:

NMR ID:NM000227
Analysis ID:AN003335
Instrument Name:Bruker 600MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:D2O
Standard Concentration:0.33 mM
Spectrometer Frequency:600 MHz
NMR Probe:CryoProbe
NMR Solvent:1.5M KH2PO4 in D2O with a final concentration of 0.33 mM DSS, pH = 7.4
NMR Tube Size:5 mm
Shimming Method:topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:18.06
Power Level:-7.45 dB
Receiver Gain:90.5
Offset Frequency:2820.68
Presaturation Power Level:41.4 dB
Chemical Shift Ref Cpd:DSS
Temperature:27
Number Of Scans:128
Dummy Scans:4
Acquisition Time:2.72 s
Relaxation Delay:4
Spectral Width:20.0276 ppm
Num Data Points Acquired:65382
Real Data Points:65536
Line Broadening:0.3
Chemical Shift Ref Std:DSS
Binned Increment:Manual
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