Summary of Study ST004033

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 PR002525. The data can be accessed directly via it's Project DOI: 10.21228/M8884N 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 IDST004033
Study TitleA pilot metabolomics study across the continuum of interstitial lung disease fibrosis severity
Study TypeCross-sectional
Study SummaryInterstitial lung diseases (ILDs) include a variety of inflammatory and fibrotic pulmonary conditions. This study employs high-resolution metabolomics (HRM) to explore plasma metabolites and pathways across ILD phenotypes, including non-fibrotic ILD, idiopathic pulmonary fibrosis (IPF), and non-IPF fibrotic ILD. The study used 80 plasma samples for HRM, and involved linear trend and group-wise analyses of metabolites altered in ILD phenotypes. We utilized limma one-way ANOVA and mummichog algorithms to identify differences in metabolites and pathways across ILD groups. Then, we focused on metabolites within critical pathways, indicated by high pathway overlap sizes and low p-values, for further analysis. Targeted HRM identified putrescine, hydroxyproline, prolyl-hydroxyproline, aspartate, and glutamate with significant linear increases in more fibrotic ILD phenotypes, suggesting their role in ILD fibrogenesis. Untargeted HRM highlighted pathway alterations in lysine, vitamin D3, tyrosine, and urea cycle metabolism, all associated with pulmonary fibrosis. In addition, methylparaben level had a significantly increasing linear trend and was higher in the IPF than fibrotic and non-ILD groups. This study highlights the importance of specific amino acids, metabolic pathways, and xenobiotics in the progression of pulmonary fibrosis.
Institute
Emory University
DepartmentDivision of Pulmonary, Allergy, Critical Care and Sleep Medicine
LaboratoryDean Jones and Young-Mi Go
Last NameZhan
First NameJiada
Address615 Michael St
Emailjzha832@emory.edu
Phone7656378399
Submit Date2025-06-22
Num Groups4
Total Subjects80
Num Males33
Num Females47
Publicationshttps://pubmed.ncbi.nlm.nih.gov/39424430/
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-07-25
Release Version1
Jiada Zhan Jiada Zhan
https://dx.doi.org/10.21228/M8884N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002525
Project DOI:doi: 10.21228/M8884N
Project Title:A pilot metabolomics study across the continuum of interstitial lung disease fibrosis severity
Project Summary:Interstitial lung diseases (ILDs) include a variety of inflammatory and fibrotic pulmonary conditions. This study employs high-resolution metabolomics (HRM) to explore plasma metabolites and pathways across ILD phenotypes, including non-fibrotic ILD, idiopathic pulmonary fibrosis (IPF), and non-IPF fibrotic ILD.
Institute:Emory University
Department:Division of Pulmonary, Allergy, Critical Care and Sleep Medicine
Laboratory:Dean Jones and Young-Mi Go
Last Name:Zhan
First Name:Jiada
Address:615 Michael St
Email:jzha832@emory.edu
Phone:7656378399
Funding Source:NIH
Publications:https://pubmed.ncbi.nlm.nih.gov/39424430/

Subject:

Subject ID:SU004179
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:42-76
Gender:Male and female
Human Race:White, Black, Asian
Human Smoking Status:28 Ever Smoker
Human Inclusion Criteria:Patients were eligible for the study if they were greater than 18 years old and determined to have pulmonary fibrosis and/or rare lung disease, including various NF-ILD, F-ILD and IPF. Individuals evaluated in the pulmonary clinic without pulmonary fibrosis and/or rare lung disease were enrolled as disease control (Non-ILD).
Human Exclusion Criteria:Patients who could not provide informed consent or were pregnant or breastfeeding were excluded.

Factors:

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

mb_sample_id local_sample_id Sample source Diagnosis Fibrosis_present ILD_group
SA465522JZ_220715_M512_211blood Anti-synthetase syndrome No NF_ILD
SA465523JZ_220715_M512_213blood Anti-synthetase syndrome No NF_ILD
SA465524JZ_220715_M512_215blood Anti-synthetase syndrome No NF_ILD
SA465525JZ_220707_M512_213blood Anti-synthetase syndrome Yes F_ILD
SA465526JZ_220715_M512_247blood Anti-synthetase syndrome Yes F_ILD
SA465527JZ_220715_M512_249blood Anti-synthetase syndrome Yes F_ILD
SA465528JZ_220707_M512_199blood Anti-synthetase syndrome Yes F_ILD
SA465529JZ_220707_M512_211blood Anti-synthetase syndrome Yes F_ILD
SA465530JZ_220707_M512_215blood Anti-synthetase syndrome Yes F_ILD
SA465531JZ_220707_M512_207blood Anti-synthetase syndrome Yes F_ILD
SA465532JZ_220715_M512_067blood Anti-synthetase syndrome Yes F_ILD
SA465533JZ_220715_M512_069blood Anti-synthetase syndrome Yes F_ILD
SA465534JZ_220715_M512_071blood Anti-synthetase syndrome Yes F_ILD
SA465535JZ_220707_M512_269blood Anti-synthetase syndrome Yes F_ILD
SA465536JZ_220707_M512_267blood Anti-synthetase syndrome Yes F_ILD
SA465537JZ_220707_M512_265blood Anti-synthetase syndrome Yes F_ILD
SA465538JZ_220707_M512_203blood Anti-synthetase syndrome Yes F_ILD
SA465539JZ_220707_M512_201blood Anti-synthetase syndrome Yes F_ILD
SA465540JZ_220707_M512_205blood Anti-synthetase syndrome Yes F_ILD
SA465541JZ_220715_M512_251blood Anti-synthetase syndrome Yes F_ILD
SA465542JZ_220707_M512_209blood Anti-synthetase syndrome Yes F_ILD
SA465543JZ_220715_M512_029blood Anti-synthetase syndrome Yes F_ILD
SA465544JZ_220707_M512_151blood Anti-synthetase syndrome Yes F_ILD
SA465545JZ_220707_M512_251blood Anti-synthetase syndrome Yes F_ILD
SA465546JZ_220707_M512_153blood Anti-synthetase syndrome Yes F_ILD
SA465547JZ_220707_M512_155blood Anti-synthetase syndrome Yes F_ILD
SA465548JZ_220707_M512_249blood Anti-synthetase syndrome Yes F_ILD
SA465549JZ_220707_M512_247blood Anti-synthetase syndrome Yes F_ILD
SA465550JZ_220715_M512_025blood Anti-synthetase syndrome Yes F_ILD
SA465551JZ_220715_M512_027blood Anti-synthetase syndrome Yes F_ILD
SA465552JZ_220715_M512_179blood Bronchiectasis Yes F_ILD
SA465553JZ_220707_M512_173blood Bronchiectasis Yes F_ILD
SA465554JZ_220707_M512_169blood Bronchiectasis Yes F_ILD
SA465555JZ_220707_M512_171blood Bronchiectasis Yes F_ILD
SA465556JZ_220715_M512_175blood Bronchiectasis Yes F_ILD
SA465557JZ_220715_M512_177blood Bronchiectasis Yes F_ILD
SA465558JZ_220715_M512_239blood CPFE Yes F_ILD
SA465559JZ_220715_M512_237blood CPFE Yes F_ILD
SA465560JZ_220715_M512_235blood CPFE Yes F_ILD
SA465561JZ_220715_M512_157blood CTD related ILD No NF_ILD
SA465562JZ_220715_M512_159blood CTD related ILD No NF_ILD
SA465563JZ_220715_M512_161blood CTD related ILD No NF_ILD
SA465564JZ_220715_M512_075blood CTD related ILD Yes F_ILD
SA465565JZ_220715_M512_145blood CTD related ILD Yes F_ILD
SA465566JZ_220715_M512_023blood CTD related ILD Yes F_ILD
SA465567JZ_220715_M512_021blood CTD related ILD Yes F_ILD
SA465568JZ_220715_M512_019blood CTD related ILD Yes F_ILD
SA465569JZ_220707_M512_187blood CTD related ILD Yes F_ILD
SA465570JZ_220707_M512_189blood CTD related ILD Yes F_ILD
SA465571JZ_220707_M512_191blood CTD related ILD Yes F_ILD
SA465572JZ_220715_M512_241blood CTD related ILD Yes F_ILD
SA465573JZ_220707_M512_117blood CTD related ILD Yes F_ILD
SA465574JZ_220707_M512_119blood CTD related ILD Yes F_ILD
SA465575JZ_220715_M512_221blood CTD related ILD Yes F_ILD
SA465576JZ_220715_M512_147blood CTD related ILD Yes F_ILD
SA465577JZ_220715_M512_077blood CTD related ILD Yes F_ILD
SA465578JZ_220715_M512_149blood CTD related ILD Yes F_ILD
SA465579JZ_220715_M512_219blood CTD related ILD Yes F_ILD
SA465580JZ_220715_M512_217blood CTD related ILD Yes F_ILD
SA465581JZ_220715_M512_243blood CTD related ILD Yes F_ILD
SA465582JZ_220715_M512_245blood CTD related ILD Yes F_ILD
SA465583JZ_220715_M512_097blood CTD related ILD Yes F_ILD
SA465584JZ_220715_M512_101blood CTD related ILD Yes F_ILD
SA465585JZ_220707_M512_097blood CTD related ILD Yes F_ILD
SA465586JZ_220707_M512_099blood CTD related ILD Yes F_ILD
SA465587JZ_220707_M512_101blood CTD related ILD Yes F_ILD
SA465588JZ_220715_M512_099blood CTD related ILD Yes F_ILD
SA465589JZ_220715_M512_073blood CTD related ILD Yes F_ILD
SA465590JZ_220707_M512_115blood CTD related ILD Yes F_ILD
SA465591JZ_220715_M512_091blood CTD related ILD Yes F_ILD
SA465592JZ_220707_M512_049blood CTD related ILD Yes F_ILD
SA465593JZ_220707_M512_053blood CTD related ILD Yes F_ILD
SA465594JZ_220715_M512_093blood CTD related ILD Yes F_ILD
SA465595JZ_220715_M512_095blood CTD related ILD Yes F_ILD
SA465596JZ_220715_M512_257blood CTD related ILD Yes F_ILD
SA465597JZ_220715_M512_255blood CTD related ILD Yes F_ILD
SA465598JZ_220715_M512_253blood CTD related ILD Yes F_ILD
SA465599JZ_220715_M512_263blood CTD related ILD Yes F_ILD
SA465600JZ_220715_M512_261blood CTD related ILD Yes F_ILD
SA465601JZ_220707_M512_167blood CTD related ILD Yes F_ILD
SA465602JZ_220715_M512_259blood CTD related ILD Yes F_ILD
SA465603JZ_220707_M512_165blood CTD related ILD Yes F_ILD
SA465604JZ_220707_M512_163blood CTD related ILD Yes F_ILD
SA465605JZ_220707_M512_051blood CTD related ILD Yes F_ILD
SA465606JZ_220715_M512_201blood Cystic Lung Disease No NF_ILD
SA465607JZ_220715_M512_203blood Cystic Lung Disease No NF_ILD
SA465608JZ_220715_M512_199blood Cystic Lung Disease No NF_ILD
SA465609JZ_220707_M512_029blood Hypersensitivity Pneumonitis Yes F_ILD
SA465610JZ_220707_M512_025blood Hypersensitivity Pneumonitis Yes F_ILD
SA465611JZ_220707_M512_113blood Hypersensitivity Pneumonitis Yes F_ILD
SA465612JZ_220715_M512_181blood Hypersensitivity Pneumonitis Yes F_ILD
SA465613JZ_220715_M512_183blood Hypersensitivity Pneumonitis Yes F_ILD
SA465614JZ_220715_M512_185blood Hypersensitivity Pneumonitis Yes F_ILD
SA465615JZ_220707_M512_111blood Hypersensitivity Pneumonitis Yes F_ILD
SA465616JZ_220707_M512_109blood Hypersensitivity Pneumonitis Yes F_ILD
SA465617JZ_220707_M512_027blood Hypersensitivity Pneumonitis Yes F_ILD
SA465618JZ_220715_M512_197blood Hypersensitivity Pneumonitis Yes F_ILD
SA465619JZ_220707_M512_061blood Hypersensitivity Pneumonitis Yes F_ILD
SA465620JZ_220707_M512_063blood Hypersensitivity Pneumonitis Yes F_ILD
SA465621JZ_220715_M512_195blood Hypersensitivity Pneumonitis Yes F_ILD
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Collection:

Collection ID:CO004172
Collection Summary:Whole blood samples were obtained from patients during the clinical visit and then separated into plasma, which was stored at −80°C until future analyses.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004188
Treatment Summary:Observational study. Samples were received frozen in aliquouts of <250uL. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section.

Sample Preparation:

Sampleprep ID:SP004185
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods(Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80 degrees C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 microliters was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 microliters of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 microliters of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, urine was equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (14,000 rpm at 4 degrees C for 10 min). The resulting supernatant (100 microliters) was removed, added to a low volume autosampler vial and maintained at 4 degrees C until analysis (<22 h).
Sampleprep Protocol ID:HRM_SP_082016_01
Sampleprep Protocol Filename:HRM_plasma_sample_preparation_082016_01.pdf
Processing Storage Conditions:On ice

Chromatography:

Chromatography ID:CH005067
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10- port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 μL of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge BEH Amide (50 x 2.1mm,2.5um)
Column Temperature:60
Flow Gradient:Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min.
Flow Rate:Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min.
Solvent A:100% Water
Solvent B:100% Acetonitrile
Chromatography Type:HILIC
Solvent C:100% water; 2% formic acid

Analysis:

Analysis ID:AN006670
Analysis Type:MS
Chromatography ID:CH005067
Num Factors:15
Num Metabolites:14
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004033_AN006670_Results.txt
Units:intensity
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