Summary of Study ST003917

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 PR002450. The data can be accessed directly via it's Project DOI: 10.21228/M8Z84V This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST003917
Study Title	Gut Microbial Bile and Amino Acid Metabolism Associate with Peanut Oral Immunotherapy Failure
Study Summary	Fecal microbiota perturbation and metabolic dysfunction, including increased concentrations of metabolites that promote cardinal features of allergic inflammation, are characteristic of allergic disease. To determine whether the distinct fecal microbiota compositions associated with POIT outcomes exhibited divergent metabolic profiles, untargeted metabolomic analyses were performed on a subset (see Methods section) of participants who provided fecal samples with sufficient remaining material for analysis at all three key visits: baseline, end of treatment, and end of avoidance (n=58 participants [POIT=43, Placebo=15], 174 fecal samples)
Institute	University of California, San Francisco
Department	Department of Medicine
Laboratory	Susan Lynch
Last Name	Mustafa
First Name	Ozcam
Address	513 Parnassus Avenue s363
Email	mustafa.ozcam@ucsf.edu
Phone	415-476-6784
Submit Date	2025-05-11
Total Subjects	58
Publications	https://www.medrxiv.org/content/10.1101/2024.07.15.24309840v1
Analysis Type Detail	LC-MS
Release Date	2025-06-02
Release Version	1

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Project:

Project ID:	PR002450
Project DOI:	doi: 10.21228/M8Z84V
Project Title:	Gut Microbial Bile and Amino Acid Metabolism Associate with Peanut Oral Immunotherapy Failure
Project Summary:	Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Longitudinal analysis of fecal microbiomes of children (n=90) in a double-blind, placebo-controlled POIT trial (NCT01867671) revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids (BAs) present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific BA profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues – a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.
Institute:	University of California, San Francisco
Last Name:	Ozcam
First Name:	Mustafa
Address:	513 Parnassus S363
Email:	m.ozcam19@gmail.com
Phone:	3023575858
Funding Source:	NIAID, NIH
Publications:	https://www.medrxiv.org/content/10.1101/2024.07.15.24309840v1

Subject:

Subject ID:	SU004052
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	1-4 Years
Gender:	Male and female
Human Trial Type:	Clinical
Human Inclusion Criteria:	Peanut Allergy

Factors:

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

mb_sample_id	local_sample_id	Age_at_screening (years)	Sex	Visit	Treatment	Tolerance_Outcome	Remission	Desensitized
SA443655	UCSF-09341	1.1	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443656	UCSF-09197	1.1	Male	Baseline	Placebo	D+R+	Yes	Yes
SA443657	UCSF-09340	1.1	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443658	UCSF-09195	1.1	Male	End of Avoidance	Placebo	D+R+	Yes	Yes
SA443659	UCSF-09339	1.1	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443660	UCSF-09196	1.1	Male	End of Treatment	Placebo	D+R+	Yes	Yes
SA443661	UCSF-09356	1.4	Female	Baseline	Peanut OIT	D+R-	No	Yes
SA443662	UCSF-09354	1.4	Female	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443663	UCSF-09355	1.4	Female	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443664	UCSF-09365	1.4	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443665	UCSF-09364	1.4	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443666	UCSF-09363	1.4	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443667	UCSF-09260	1.5	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443668	UCSF-09258	1.5	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443669	UCSF-09259	1.5	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443670	UCSF-09198	1.9	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443671	UCSF-09291	1.9	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443672	UCSF-09200	1.9	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443673	UCSF-09294	1.9	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443674	UCSF-09199	1.9	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443675	UCSF-09292	1.9	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443676	UCSF-09206	2.1	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443677	UCSF-09205	2.1	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443678	UCSF-09203	2.1	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443679	UCSF-09319	2.2	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443680	UCSF-09215	2.2	Male	Baseline	Placebo	D-R-	No	No
SA443681	UCSF-09317	2.2	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443682	UCSF-09214	2.2	Male	End of Avoidance	Placebo	D-R-	No	No
SA443683	UCSF-09318	2.2	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443684	UCSF-09213	2.2	Male	End of Treatment	Placebo	D-R-	No	No
SA443685	UCSF-09261	2.3	Female	Baseline	Placebo	D-R-	No	No
SA443686	UCSF-09262	2.3	Female	End of Avoidance	Placebo	D-R-	No	No
SA443687	UCSF-09263	2.3	Female	End of Treatment	Placebo	D-R-	No	No
SA443688	UCSF-09277	2.3	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443689	UCSF-09344	2.3	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443690	UCSF-09268	2.3	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443691	UCSF-09276	2.3	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443692	UCSF-09343	2.3	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443693	UCSF-09266	2.3	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443694	UCSF-09264	2.3	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443695	UCSF-09275	2.3	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443696	UCSF-09342	2.3	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443697	UCSF-09288	2.4	Female	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443698	UCSF-09237	2.4	Female	Baseline	Placebo	D-R-	No	No
SA443699	UCSF-09289	2.4	Female	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443700	UCSF-09234	2.4	Female	End of Avoidance	Placebo	D-R-	No	No
SA443701	UCSF-09290	2.4	Female	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443702	UCSF-09235	2.4	Female	End of Treatment	Placebo	D-R-	No	No
SA443703	UCSF-09324	2.6	Female	Baseline	Placebo	D-R-	No	No
SA443704	UCSF-09323	2.6	Female	End of Avoidance	Placebo	D-R-	No	No
SA443705	UCSF-09321	2.6	Female	End of Treatment	Placebo	D-R-	No	No
SA443709	UCSF-09257	2.6	Male	Baseline	Peanut OIT	D-R-	No	No
SA443706	UCSF-09225	2.6	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443707	UCSF-09208	2.6	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443708	UCSF-09325	2.6	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443713	UCSF-09255	2.6	Male	End of Avoidance	Peanut OIT	D-R-	No	No
SA443710	UCSF-09322	2.6	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443711	UCSF-09207	2.6	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443712	UCSF-09226	2.6	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443717	UCSF-09253	2.6	Male	End of Treatment	Peanut OIT	D-R-	No	No
SA443714	UCSF-09227	2.6	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443715	UCSF-09209	2.6	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443716	UCSF-09320	2.6	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443718	UCSF-09338	2.7	Female	Baseline	Placebo	D-R-	No	No
SA443719	UCSF-09336	2.7	Female	End of Avoidance	Placebo	D-R-	No	No
SA443720	UCSF-09337	2.7	Female	End of Treatment	Placebo	D-R-	No	No
SA443721	UCSF-09316	2.8	Male	Baseline	Placebo	D-R-	No	No
SA443722	UCSF-09315	2.8	Male	End of Avoidance	Placebo	D-R-	No	No
SA443723	UCSF-09314	2.8	Male	End of Treatment	Placebo	D-R-	No	No
SA443724	UCSF-09201	3.1	Female	Baseline	Peanut OIT	D+R-	No	Yes
SA443725	UCSF-09204	3.1	Female	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443726	UCSF-09202	3.1	Female	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443729	UCSF-09233	3.1	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443727	UCSF-09329	3.1	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443728	UCSF-09236	3.1	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443730	UCSF-09243	3.1	Male	Baseline	Placebo	D-R-	No	No
SA443733	UCSF-09231	3.1	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443731	UCSF-09330	3.1	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443732	UCSF-09239	3.1	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443734	UCSF-09241	3.1	Male	End of Avoidance	Placebo	D-R-	No	No
SA443737	UCSF-09232	3.1	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443735	UCSF-09238	3.1	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443736	UCSF-09331	3.1	Male	End of Treatment	Peanut OIT	D+R+	Yes	Yes
SA443738	UCSF-09242	3.1	Male	End of Treatment	Placebo	D-R-	No	No
SA443739	UCSF-09284	3.2	Female	Baseline	Placebo	D-R-	No	No
SA443740	UCSF-09280	3.2	Female	End of Avoidance	Placebo	D-R-	No	No
SA443741	UCSF-09281	3.2	Female	End of Treatment	Placebo	D-R-	No	No
SA443742	UCSF-09229	3.2	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443743	UCSF-09228	3.2	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443744	UCSF-09230	3.2	Male	End of Treatment	Peanut OIT	D+R-	No	Yes
SA443747	UCSF-09218	3.3	Male	Baseline	Peanut OIT	D-R-	No	No
SA443746	UCSF-09240	3.3	Male	Baseline	Peanut OIT	D+R-	No	Yes
SA443745	UCSF-09332	3.3	Male	Baseline	Peanut OIT	D+R+	Yes	Yes
SA443748	UCSF-09347	3.3	Male	Baseline	Placebo	D-R-	No	No
SA443749	UCSF-09267	3.3	Male	Baseline	Placebo	D-R-	No	No
SA443752	UCSF-09217	3.3	Male	End of Avoidance	Peanut OIT	D-R-	No	No
SA443751	UCSF-09250	3.3	Male	End of Avoidance	Peanut OIT	D+R-	No	Yes
SA443750	UCSF-09310	3.3	Male	End of Avoidance	Peanut OIT	D+R+	Yes	Yes
SA443753	UCSF-09345	3.3	Male	End of Avoidance	Placebo	D-R-	No	No
SA443754	UCSF-09265	3.3	Male	End of Avoidance	Placebo	D-R-	No	No

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Collection:

Collection ID:	CO004045
Collection Summary:	Stool samples were collected by participants at home and stored at clinical collection sites at -80 °C. D+R+: Desensitized and remission, D+R-: Desensitized but no remission, D-R-: Not desensitized and no remission. X.SampleIDs are provided as they match with metagenomics data submitted to SRA so that users can integrate metagenommics and metabolomics datasets if desired.
Sample Type:	Stool
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004061
Treatment Summary:	Participants were screened with standardised procedures for SPT, DBPCFCs, and immune assays, as defined in the protocol (Jones et. al. 2022, Lancet, doi: 10.1016/S0140-6736(21)02390-4. appendix pp 3–10). Eligible participants were randomly assigned to receive peanut oral immunotherapy or placebo for daily oral dosing. We used lightly roasted, partly defatted (12% fat) peanut flour (Golden Peanut Company, Blakely, GA, USA) and oat flour placebo (Arrowhead Mills, Melville, NY, USA) for oral immunotherapy, manufactured at the University of North Carolina Good Manufacturing Practice facility under quality-controlled protocols.22 The oral immunotherapy protocol consisted of four phases: first, an initial dose escalation (0·1 mg to 6·0 mg); second, a build-up every 2 weeks to a maximal target dose of 2000 mg peanut daily (week 0 to about week 30), with a minimum dose of 250 mg reached after three attempts of build-up required to continue to daily maintenance; third, daily maintenance (weeks 30–134); and fourth, oral immunotherapy discontinuation (weeks 134–160). Dosing was modified, per protocol, for dose-related symptoms and illness. Adherence with the study product dosing was monitored by daily diaries and drug accountability logs. During all phases of the trial, participants were instructed to avoid dietary peanut consumption. DBPCFCs were done up to a cumulative dose of 500 mg of peanut at study entry and up to a cumulative dose of 5000 mg of peanut at the end of dosing (week 134) and avoidance (week 160). Per protocol, participants progressed to week 160, independent of the DBPCFC outcome at week 134. Participants who passed the DBPCFC at week 134 were categorised as desensitised, and those who passed the DBPCFC at week 160 were categorised as being in remission (defined in the protocol as tolerant but revised to remission for clarity in this manuscript). For those passing the week 160 DBPCFC, an 8000 mg open-label feeding of peanut butter was conducted to confirm tolerability. details can be found at Jones et al. (2022) Lancet. Efficacy and safety of oral immunotherapy in children aged 1–3 years with peanut allergy (the Immune Tolerance Network IMPACT trial): a randomised placebo-controlled study https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02390-4/abstract

Treatment ID:

TR004061

Treatment Summary:

Participants were screened with standardised procedures for SPT, DBPCFCs, and immune assays, as defined in the protocol (Jones et. al. 2022, Lancet, doi: 10.1016/S0140-6736(21)02390-4. appendix pp 3–10). Eligible participants were randomly assigned to receive peanut oral immunotherapy or placebo for daily oral dosing. We used lightly roasted, partly defatted (12% fat) peanut flour (Golden Peanut Company, Blakely, GA, USA) and oat flour placebo (Arrowhead Mills, Melville, NY, USA) for oral immunotherapy, manufactured at the University of North Carolina Good Manufacturing Practice facility under quality-controlled protocols.22 The oral immunotherapy protocol consisted of four phases: first, an initial dose escalation (0·1 mg to 6·0 mg); second, a build-up every 2 weeks to a maximal target dose of 2000 mg peanut daily (week 0 to about week 30), with a minimum dose of 250 mg reached after three attempts of build-up required to continue to daily maintenance; third, daily maintenance (weeks 30–134); and fourth, oral immunotherapy discontinuation (weeks 134–160). Dosing was modified, per protocol, for dose-related symptoms and illness. Adherence with the study product dosing was monitored by daily diaries and drug accountability logs. During all phases of the trial, participants were instructed to avoid dietary peanut consumption. DBPCFCs were done up to a cumulative dose of 500 mg of peanut at study entry and up to a cumulative dose of 5000 mg of peanut at the end of dosing (week 134) and avoidance (week 160). Per protocol, participants progressed to week 160, independent of the DBPCFC outcome at week 134. Participants who passed the DBPCFC at week 134 were categorised as desensitised, and those who passed the DBPCFC at week 160 were categorised as being in remission (defined in the protocol as tolerant but revised to remission for clarity in this manuscript). For those passing the week 160 DBPCFC, an 8000 mg open-label feeding of peanut butter was conducted to confirm tolerability. details can be found at Jones et al. (2022) Lancet. Efficacy and safety of oral immunotherapy in children aged 1–3 years with peanut allergy (the Immune Tolerance Network IMPACT trial): a randomised placebo-controlled study https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02390-4/abstract

Sample Preparation:

Sampleprep ID:	SP004058
Sampleprep Summary:	Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.
Sampleprep Protocol Filename:	UCSF-0303-21MD_Final_Report.pdf

Chromatography:

Chromatography ID:	CH004878
Chromatography Summary:	Low pH polar (LC/MS Pos early)
Methods Filename:	UCSF-0303-21MD_Final_Report.pdf
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:	100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:	Reversed phase

Chromatography ID:	CH004879
Chromatography Summary:	Low pH Lipophilic (LC/MS Pos late)
Methods Filename:	UCSF-0303-21MD_Final_Report.pdf
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:	0.60 mL/min
Solvent A:	100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:	50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:	Reversed phase

Chromatography ID:	CH004880
Chromatography Summary:	High pH (LC/MS Neg)
Methods Filename:	UCSF-0303-21MD_Final_Report.pdf
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 6.5 mM ammonium bicarbonate, pH 8
Solvent B:	95% methanol/5% water; 6.5 mM ammonium bicarbonate
Chromatography Type:	Reversed phase

Chromatography ID:	CH004881
Chromatography Summary:	HILIC (LC/MS Polar Neg)
Methods Filename:	UCSF-0303-21MD_Final_Report.pdf
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:	40-50
Flow Gradient:	Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:	0.50 mL/min
Solvent A:	15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH)
Solvent B:	50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH)
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006430
Analysis Type:	MS
Analysis Protocol File:	UCSF-0303-21MD_Final_Report.pdf
Chromatography ID:	CH004878
Num Factors:	135
Num Metabolites:	403
Units:	Peak area

Analysis ID:	AN006431
Analysis Type:	MS
Analysis Protocol File:	UCSF-0303-21MD_Final_Report.pdf
Chromatography ID:	CH004879
Num Factors:	135
Num Metabolites:	163
Units:	Peak area

Analysis ID:	AN006432
Analysis Type:	MS
Analysis Protocol File:	UCSF-0303-21MD_Final_Report.pdf
Chromatography ID:	CH004880
Num Factors:	135
Num Metabolites:	824
Units:	Peak area

Analysis ID:	AN006433
Analysis Type:	MS
Analysis Protocol File:	UCSF-0303-21MD_Final_Report.pdf
Chromatography ID:	CH004881
Num Factors:	135
Num Metabolites:	140
Units:	Peak area