Summary of Study ST001242

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 PR000830. The data can be accessed directly via it's Project DOI: 10.21228/M8D68Q 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.

Study ID	ST001242
Study Title	Global Metabolic Analysis Trisomy 21 - Cohort 3, CSF
Study Summary	global metabolic analysis of CSF from individuals with and without trisomy 21.
Institute	University of Colorado Denver
Last Name	Culp-Hill
First Name	Rachel
Address	12801 E 17th Ave L18-9403D, Aurora, Colorado, 80045, USA
Email	rachel.hill@cuanschutz.edu
Phone	303-724-5798
Submit Date	2019-08-13
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2019-08-21
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000830
Project DOI:	doi: 10.21228/M8D68Q
Project Title:	Trisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors
Project Summary:	Trisomy 21 (T21) causes Down syndrome (DS), affecting immune and neurological function by unknown mechanisms. We report here a large metabolomics study of plasma and cerebrospinal fluid showing that people with DS produce elevated levels of kynurenine and quinolinic acid, two tryptophan catabolites with potent immunosuppressive and neurotoxic properties, respectively. We demonstrate that immune cells of people with DS overexpress IDO1, the rate-limiting enzyme in the kynurenine pathway (KP) and a known interferon (IFN)-stimulated gene. Furthermore, we show positive correlations among levels of IFN-inducible cytokines and KP dysregulation. Using metabolic tracing assays, we determine that IFN stimulation causes IDO1 overexpression and kynurenine overproduction in cells with T21, dependent on overexpression of IFN receptors encoded on chromosome 21. Finally, we show a mouse model of DS carrying triplication of the IFN receptors exhibits KP dysregulation. Altogether, these results reveal a mechanism by which T21 could drive immunosuppression and neurotoxicity in DS.
Institute:	University of Colorado Denver
Laboratory:	Linda Crnic Institute, Costello Lab, D'Alessandro Lab
Last Name:	Culp-Hill
First Name:	Rachel
Address:	12801 E 17th Ave L18-9403D, Aurora, Colorado, 80045, USA
Email:	rachel.hill@cuanschutz.edu
Phone:	303-724-5798

Subject:

Subject ID:	SU001310
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Age Or Age Range:	0.5 - 76.5
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	Cohort
SA090368	SPIN_5neg_D21_68-L17-131	D21
SA090369	SPIN_5neg_D21_69-L17-170	D21
SA090370	SPIN_5neg_D21_67-L17-125	D21
SA090371	SPIN_5neg_D21_66-L17-090	D21
SA090372	SPIN_5neg_D21_65-L17-032	D21
SA090373	SPIN_5neg_D21_70-L17-207	D21
SA090374	SPIN_5neg_D21_71-L17-210	D21
SA090375	SPIN_5neg_D21_75-L17-276	D21
SA090376	SPIN_5neg_D21_74-L17-274	D21
SA090377	SPIN_5neg_D21_73-L17-246	D21
SA090378	SPIN_5neg_D21_72-L17-235	D21
SA090379	SPIN_5neg_D21_64-L16-208	D21
SA090380	SPIN_5neg_D21_62-L16-153	D21
SA090381	SPIN_5neg_D21_55-L16-048	D21
SA090382	SPIN_5neg_D21_56-L16-056	D21
SA090383	SPIN_5neg_D21_54-L16-033	D21
SA090384	SPIN_5neg_D21_53-L16-009	D21
SA090385	SPIN_5neg_D21_52-L15-195	D21
SA090386	SPIN_5neg_D21_57-L16-086	D21
SA090387	SPIN_5neg_D21_58-L16-087	D21
SA090388	SPIN_5neg_D21_76-L17-292	D21
SA090389	SPIN_5neg_D21_61-L16-146	D21
SA090390	SPIN_5neg_D21_60-L16-145	D21
SA090391	SPIN_5neg_D21_59-L16-107	D21
SA090392	SPIN_5neg_D21_63-L16-202	D21
SA090393	SPIN_5neg_D21_77-L18-020	D21
SA090394	SPIN_5neg_D21_93-L19-007	D21
SA090395	SPIN_5neg_D21_94-L19-014	D21
SA090396	SPIN_5neg_D21_92-L19-006	D21
SA090397	SPIN_5neg_D21_91-L18-342	D21
SA090398	SPIN_5neg_D21_90-L18-314	D21
SA090399	SPIN_5neg_D21_95-L19-015	D21
SA090400	SPIN_5neg_D21_96-L19-016	D21
SA090401	SPIN_5neg_D21_100-L19-114	D21
SA090402	SPIN_5neg_D21_99-L19-080	D21
SA090403	SPIN_5neg_D21_98-L19-065	D21
SA090404	SPIN_5neg_D21_97-L19-032	D21
SA090405	SPIN_5neg_D21_89-L18-303	D21
SA090406	SPIN_5neg_D21_88-L18-302	D21
SA090407	SPIN_5neg_D21_81-L18-098	D21
SA090408	SPIN_5neg_D21_80-L18-044	D21
SA090409	SPIN_5neg_D21_79-L18-028	D21
SA090410	SPIN_5neg_D21_78-L18-021	D21
SA090411	SPIN_5neg_D21_82-L18-130	D21
SA090412	SPIN_5neg_D21_83-L18-162	D21
SA090413	SPIN_5neg_D21_87-L18-238	D21
SA090414	SPIN_5neg_D21_86-L18-205	D21
SA090415	SPIN_5neg_D21_85-L18-197	D21
SA090416	SPIN_5neg_D21_84-L18-170	D21
SA090417	SPIN_5pos_D21_51-L15-181	D21
SA090418	SPIN_5neg_D21_51-L15-181	D21
SA090419	SPIN_5pos_D21_84-L18-170	D21
SA090420	SPIN_5pos_D21_83-L18-162	D21
SA090421	SPIN_5pos_D21_85-L18-197	D21
SA090422	SPIN_5pos_D21_86-L18-205	D21
SA090423	SPIN_5pos_D21_87-L18-238	D21
SA090424	SPIN_5pos_D21_82-L18-130	D21
SA090425	SPIN_5pos_D21_81-L18-098	D21
SA090426	SPIN_5pos_D21_77-L18-020	D21
SA090427	SPIN_5pos_D21_78-L18-021	D21
SA090428	SPIN_5pos_D21_79-L18-028	D21
SA090429	SPIN_5pos_D21_80-L18-044	D21
SA090430	SPIN_5pos_D21_88-L18-302	D21
SA090431	SPIN_5pos_D21_89-L18-303	D21
SA090432	SPIN_5pos_D21_96-L19-016	D21
SA090433	SPIN_5pos_D21_97-L19-032	D21
SA090434	SPIN_5pos_D21_98-L19-065	D21
SA090435	SPIN_5pos_D21_99-L19-080	D21
SA090436	SPIN_5pos_D21_95-L19-015	D21
SA090437	SPIN_5pos_D21_94-L19-014	D21
SA090438	SPIN_5pos_D21_90-L18-314	D21
SA090439	SPIN_5pos_D21_91-L18-342	D21
SA090440	SPIN_5pos_D21_92-L19-006	D21
SA090441	SPIN_5pos_D21_93-L19-007	D21
SA090442	SPIN_5pos_D21_75-L17-276	D21
SA090443	SPIN_5pos_D21_74-L17-274	D21
SA090444	SPIN_5pos_D21_58-L16-087	D21
SA090445	SPIN_5pos_D21_59-L16-107	D21
SA090446	SPIN_5pos_D21_60-L16-145	D21
SA090447	SPIN_5pos_D21_61-L16-146	D21
SA090448	SPIN_5pos_D21_57-L16-086	D21
SA090449	SPIN_5pos_D21_56-L16-056	D21
SA090450	SPIN_5pos_D21_52-L15-195	D21
SA090451	SPIN_5pos_D21_53-L16-009	D21
SA090452	SPIN_5pos_D21_54-L16-033	D21
SA090453	SPIN_5pos_D21_55-L16-048	D21
SA090454	SPIN_5pos_D21_62-L16-153	D21
SA090455	SPIN_5pos_D21_63-L16-202	D21
SA090456	SPIN_5pos_D21_70-L17-207	D21
SA090457	SPIN_5pos_D21_71-L17-210	D21
SA090458	SPIN_5pos_D21_72-L17-235	D21
SA090459	SPIN_5pos_D21_73-L17-246	D21
SA090460	SPIN_5pos_D21_69-L17-170	D21
SA090461	SPIN_5pos_D21_68-L17-131	D21
SA090462	SPIN_5pos_D21_64-L16-208	D21
SA090463	SPIN_5pos_D21_65-L17-032	D21
SA090464	SPIN_5pos_D21_66-L17-090	D21
SA090465	SPIN_5pos_D21_67-L17-125	D21
SA090466	SPIN_5pos_D21_100-L19-114	D21
SA090467	SPIN_5pos_D21_76-L17-292	D21

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Collection:

Collection ID:	CO001304
Collection Summary:	All human subjects in this study were consented according to Colorado Multiple Institutional Review Board (COMIRB)-approved protocols. Written informed consent was obtained from parents or guardians of participants under the age of 18, and assent was obtained from participants over the age of 7 who were cognitively able to assent. Deidentified plasma samples for Cohort 1 were obtained from the Translational Nexus Clinical Data Registry and Biobank (University of Colorado Anschutz Medical Campus, COMIRB 08-1276). Additional plasma and WBC samples were obtained through the Crnic’s Institute Human Trisome Project (University of Colorado Anschutz Medical Campus, COMIRB 15-2170, www.trisome.org). Plasma was collected in Vacutainer tubes (EDTA–purple capped or Lithium heparin–light green capped) and stored at -80°C. Participant medical history was collected by the respective biobanks.
Sample Type:	Cerebrospinal fluid

Treatment:

Treatment ID:	TR001325
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP001318
Sampleprep Summary:	For CSF analyses, a volume of 20μL of was extracted in 180μL of ice-cold methanol:acetonitrile:water (5:3:2). Subsequently, these solutions were vortexed for 30 minutes at 4°C. Insoluble proteins were pelleted by centrifugation (10 minutes at 4°C and 12,000 g) and supernatants were collected and stored at -80°C until analysis. For quantitative analysis of kynurenine pathway (KP) metabolites, supernatants were spun in a Speedvac until dry and resuspended in 0.1% formic acid in water as previously described (PMID: 30213797, 30143553).

Sampleprep ID:

SP001318

Sampleprep Summary:

For CSF analyses, a volume of 20μL of was extracted in 180μL of ice-cold methanol:acetonitrile:water (5:3:2). Subsequently, these solutions were vortexed for 30 minutes at 4°C. Insoluble proteins were pelleted by centrifugation (10 minutes at 4°C and 12,000 g) and supernatants were collected and stored at -80°C until analysis. For quantitative analysis of kynurenine pathway (KP) metabolites, supernatants were spun in a Speedvac until dry and resuspended in 0.1% formic acid in water as previously described (PMID: 30213797, 30143553).

Combined analysis:

Analysis ID	AN002063	AN002064
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	relative abundance	relative abundance

Chromatography:

Chromatography ID:	CH001501
Chromatography Summary:	UHPLC-MS metabolomics analyses were performed using a Vanquish UHPLC system coupled online to a Q Exactive mass spectrometer (Thermo Fisher, Bremen, Germany). 20uL of supernatant was injected for plasma and CSF samples, and 10uL of supernatant was injected for cell samples. Samples were resolved over a Kinetex C18 column (2.1x150 mm, 1.7μm; Phenomenex, Torrance, CA, USA) at 45°C using a 5-minute gradient at 450μL/minute from 5-95% B (A: water/0.1% formic acid; B: acetonitrile/0.1% formic acid) for positive mode. To monitor possible technical variability, aliquots of each of the individual samples were combined to make technical replicates, which were run after every 15 samples. Additionally, in each experiment, several lysis solution aliquots were run as blanks for artifact identification.
Methods Filename:	5MMpos_method.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Column Temperature:	45
Flow Gradient:	5-95% B
Flow Rate:	450uL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH001502
Chromatography Summary:	UHPLC-MS metabolomics analyses were performed using a Vanquish UHPLC system coupled online to a Q Exactive mass spectrometer (Thermo Fisher, Bremen, Germany). 20uL of supernatant was injected for each sample. Samples were resolved over a Kinetex C18 column (2.1x150 mm, 1.7μm; Phenomenex, Torrance, CA, USA) at 45°C using a 5-minute gradient at 450μL/minute from 0-100% B (A: 95% water/5% acetonitrile, 1mM NH4OAc; B: 95% acetonitrile/5% water, 1mM NH4OAc) for negative mode. To monitor possible technical variability, aliquots of each of the individual samples were combined to make technical replicates, which were run after every 15 samples. Additionally, in each experiment, several lysis solution aliquots were run as blanks for artifact identification.
Methods Filename:	5MMneg_method.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Column Temperature:	45
Flow Gradient:	0-100% B
Flow Rate:	450uL/min
Solvent A:	95% water/5% acetonitrile; 1 mM ammonium acetate
Solvent B:	95% acetonitrile/5% water; 1 mM ammonium acetate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001914
Analysis ID:	AN002063
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) was operated in positive ion mode using electrospray ionization, scanning in Full MS mode (1μscan) from 65 to 975 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. MS analysis and data elaboration were performed as described74,75. Calibration was performed prior to analysis using the PierceTM Positive Ion Calibration Solution (Thermo Fisher Scientific).
Ion Mode:	POSITIVE

MS ID:	MS001915
Analysis ID:	AN002064
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) was operated in negative ion mode using electrospray ionization, scanning in Full MS mode (1μscan) from 65 to 975 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. MS analysis and data elaboration were performed as described74,75. Calibration was performed prior to analysis using the PierceTM Negative Ion Calibration Solution (Thermo Fisher Scientific).
Ion Mode:	NEGATIVE