Summary of Study ST002350

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 PR001064. The data can be accessed directly via it's Project DOI: 10.21228/M85H6W 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 IDST002350
Study TitleIdentify putative volatile biomarkers of Valley fever using a murine lung infection model
Study TypeUntargeted metabolomics
Study SummaryCoccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections, to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host-pathogen interactions, we infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira via intranasal inoculation. We collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid phase microextraction (SPME) and two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated to cytokine abundances and clustered mice by disease severity. These 36 VOCs were also able to separate mice with a moderate to high disease severity by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect Coccidioidal infection and provide clinically relevant information on disease severity.
Institute
Arizona State University
DepartmentSchool of Life Sciences
LaboratoryBean Laboratory
Last NameBean
First NameHeather
AddressPO Box 874501
EmailHeather.D.Bean@asu.edu
Phone4807273395
Submit Date2022-09-30
Raw Data AvailableYes
Raw Data File Type(s)smp
Analysis Type DetailGC-MS
Release Date2023-01-02
Release Version1
Heather Bean Heather Bean
https://dx.doi.org/10.21228/M85H6W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001064
Project DOI:doi: 10.21228/M85H6W
Project Title:Volatile Biomarkers for a Valley Fever Breath Test
Project Type:GCxGC-TOFMS metabolomics
Project Summary:Coccidioidomycosis, or valley fever, is prevalent in AZ, with more than 12,000 new human infections diagnosed every year. In highly endemic areas, e.g., Phoenix and Tucson, up to 30% of community-acquired pneumonia may be caused by Valley fever, and cases are on the rise. The current diagnostics for Valley fever are severely lacking due to invasiveness (biopsy) and poor sensitivity (serology), strongly contributing to an unacceptable 23-day median time-to-diagnosis. There is a critical need for sensitive and non-invasive diagnostics for identifying Valley fever lung infections. Our long-term goal is to substantially shorten the time-to-diagnosis for Valley fever through the development of sensitive and specific breath-based diagnostics for coccidioidomycosis lung infections. The overall objective of this application is to identify and validate putative volatile biomarkers of Coccidioides infections via metabolomics analyses of in vitro cultures, mouse model lung infections, and lung specimens from humans with Valley fever. At the completion of the proposed study, we expect to have identified and validated a panel of 10-15 volatile biomarkers for the sensitive and specific detection of valley fever in lung specimens.
Institute:Arizona State University
Department:School of Life Sciences
Laboratory:Bean Laboratory
Last Name:Bean
First Name:Heather
Address:PO Box 874501, Tempe, AZ, 85287, USA
Email:Heather.D.Bean@asu.edu
Phone:480-727-3395
Funding Source:Arizona Biomedical Research Centre New Investigator Award to HDB

Subject:

Subject ID:SU002439
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:6-8 weeks
Gender:Female
Animal Animal Supplier:The Jackson Laboratory, Bar Harbor, ME

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Subject_ID treatment
SA235762KI_1alkane standard NA
SA235763KI mix_1alkane standard NA
SA235764KI_2alkane standard NA
SA235713RS_M2-3_1C. immitis Fungi
SA235714RS_M3-2_1C. immitis Fungi
SA235715RS_M3-3_1C. immitis Fungi
SA235716RS_M2-2_1C. immitis Fungi
SA235717RS_M2-1_1C. immitis Fungi
SA235718RS_M1-2_1C. immitis Fungi
SA235719RS_M1-3_1C. immitis Fungi
SA235720RS_M4-1_1C. immitis Fungi
SA235721RS_M4-2_1C. immitis Fungi
SA235722RS_M6-2_1C. immitis Fungi
SA235723RS_M6-3_1C. immitis Fungi
SA235724RS_M6-1_1C. immitis Fungi
SA235725RS_M5-2_1C. immitis Fungi
SA235726RS_M4-3_1C. immitis Fungi
SA235727RS_M5-1_1C. immitis Fungi
SA235728RS_M1-1_1C. immitis Fungi
SA235729RS_M3-1_1C. immitis Fungi
SA235730SIL_M2-2_1C. posadasii Fungi
SA235731SIL_M2-3_1C. posadasii Fungi
SA235732SIL_M3-1_1C. posadasii Fungi
SA235733SIL_M2-1_1C. posadasii Fungi
SA235734SIL_M1-3_1C. posadasii Fungi
SA235735SIL_M1-1_1C. posadasii Fungi
SA235736SIL_M1-2_1C. posadasii Fungi
SA235737SIL_M3-2_1C. posadasii Fungi
SA235738SIL_M3-3_1C. posadasii Fungi
SA235739SIL_M5-3_1C. posadasii Fungi
SA235740SIL_M6-1_1C. posadasii Fungi
SA235741SIL_M5-2_1C. posadasii Fungi
SA235742SIL_M5-1_1C. posadasii Fungi
SA235743SIL_M4-1_1C. posadasii Fungi
SA235744SIL_M4-2_1C. posadasii Fungi
SA235745SIL_M6-2_1C. posadasii Fungi
SA235746SIL_M6-3_1C. posadasii Fungi
SA235747Blank_20Empty run NA
SA235748Blank_8Empty run NA
SA235749Blank_14Empty run NA
SA235765Grob_1grob mix NA
SA235766Grob_3grob mix NA
SA235767Grob_2grob mix NA
SA235750PBS_M1-2_1PBS Mouse NA
SA235751PBS_M1-1_1PBS Mouse NA
SA235752PBS_M1-3_1PBS Mouse NA
SA235753PBS_M3-2_1PBS Mouse PBS
SA235754PBS_M3-1_1PBS Mouse PBS
SA235755PBS_M3-3_1PBS Mouse PBS
SA235756PBS_M4-3_1PBS Mouse PBS
SA235757PBS_M4-2_1PBS Mouse PBS
SA235758PBS_M2-3_1PBS Mouse PBS
SA235759PBS_M2-2_1PBS Mouse PBS
SA235760PBS_M2-1_1PBS Mouse PBS
SA235761PBS_M4-1_1PBS Mouse PBS
Showing results 1 to 55 of 55

Collection:

Collection ID:CO002432
Collection Summary:Female C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME) 6-8 weeks of age were used for these studies. Mice were housed according to NIH guidelines for housing and care in a biosafety level 3 animal laboratory. All procedures were approved by the Institutional Animal Care and Use Committee (protocol number 16-011) of Northern Arizona University. The Coccidioides isolates used in this study were the type strains C. immitis strain RS (ATCC® catalog no. NR-48942; NCBI accession no. AAEC00000000.3) and C. posadasii strain Silveira (ATCC® catalog no. NR-48944; NCBI accession no. ABAI00000000.2). Mice were anesthetized with ketamine/xylene (80/8 mg/kg) and intranasally inoculated with 100 arthroconidia of C. immitis strain RS (n=6) or C. posadasii strain Silveira (n=6) suspended in 30 μL phosphate-buffered saline (PBS), as described previously (22, 58). Control mice were inoculated with PBS alone (n=4). The mice were sacrificed at day 10 post-inoculation. The lungs were rinsed with 2 mL of PBS to collect bronchoalveolar lavage fluid (BALF), which were filtered with 0.22 μm Ultrafree® - MC centrifugal filter devices with Durapore® membrane (MilliporeSigma, Burlington, MA). One milliliter of each BALF sample was stored at –80°C for volatilomics analysis. Halt™ Protease Inhibitor Cocktail (10 μL/mL) was added to the remainder of each BALF sample for cytokine analysis. Spleen and brain were homogenized in 1 ml of sterile PBS followed by culture of 10-fold dilutions of each tissue on 2X GYE agar (2% glucose (VWR™, USA), 1% yeast extract (BD™, Franklin Lakes, New Jersey, USA, and 1.5% bacteriological agar (Difco, USA)) to assess fungal dissemination.
Sample Type:Bronchoalveolar lavage

Treatment:

Treatment ID:TR002451
Treatment Summary:Mice were anesthetized with ketamine/xylene (80/8 mg/kg) and intranasally inoculated with 100 arthroconidia of C. immitis strain RS (n=6) or C. posadasii strain Silveira (n=6) suspended in 30 μL phosphate-buffered saline (PBS), as described previously (22, 58). Control mice were inoculated with PBS alone (n=4). The mice were sacrificed at day 10 post-inoculation. The lungs were rinsed with 2 mL of PBS to collect bronchoalveolar lavage fluid (BALF), which were filtered with 0.22 μm Ultrafree® - MC centrifugal filter devices with Durapore® membrane (MilliporeSigma, Burlington, MA). One milliliter of each BALF sample was stored at –80°C for volatilomics analysis. Halt™ Protease Inhibitor Cocktail (10 μL/mL) was added to the remainder of each BALF sample for cytokine analysis. Spleen and brain were homogenized in 1 ml of sterile PBS followed by culture of 10-fold dilutions of each tissue on 2X GYE agar (2% glucose (VWR™, USA), 1% yeast extract (BD™, Franklin Lakes, New Jersey, USA, and 1.5% bacteriological agar (Difco, USA)) to assess fungal dissemination.

Sample Preparation:

Sampleprep ID:SP002445
Sampleprep Summary:The BALF samples were allowed to thaw at 4°C overnight, and then split into technical triplicates of 200 μL that were transferred and sealed into sterilized 2mL GC headspace vials with Supelco® PTFE/silicone septum magnetic screw caps (Sigma-Aldrich®, St. Louis, MO). Samples were randomized for analysis. Volatile metabolites sampling was performed by solid phase microextraction (SPME) using a Gerstel® MPS Robotic Pro MultiPurpose autosampler directed by Maestro® software (Gerstel®, Inc., Linthicum, MD). Sample extraction and injection parameters are provided in Table S3 (see Autosampler Method). Volatile metabolite analysis was performed by two-dimensional gas chromatography−time-of-flight mass spectrometry (GC×GC–TOFMS) using a LECO® Pegasus® 4D and Agilent® 7890B GC (LECO® Corp., St. Joseph, MI). Chromatographic, mass spectrometric, and peak detection parameters are provided in Table S3 (see GC×GC Method and Mass Spectrometry Method). An external alkane standards mixture (C8 – C20; Sigma-Aldrich®) was sampled multiple times for calculating retention indices (RI). The injection, chromatographic, and mass spectrometric methods for analyzing the alkane standards were the same as for the samples.
Extraction Method:Solid-phase microextraction (SPME)

Combined analysis:

Analysis ID AN003836
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Column 1: Rxi-624Sil MS,(60m × 0.25mm × 1.4um); 2: Stabilwax,(1m × 0.25mm × 0.5um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus 4D GCxGC TOF
Ion Mode POSITIVE
Units Peak areas

Chromatography:

Chromatography ID:CH002840
Instrument Name:Agilent 7890B
Column Name:Column 1: Rxi-624Sil MS,(60m × 0.25mm × 1.4um); 2: Stabilwax,(1m × 0.25mm × 0.5um)
Chromatography Type:GC

MS:

MS ID:MS003578
Analysis ID:AN003836
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:See attached protocol
Ion Mode:POSITIVE
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