Summary of Study ST001241

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	ST001241
Study Title	Global Metabolic Analysis Trisomy 21 - Cohort 3, Plasma
Study Summary	Global metabolic analysis of plasma 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:	SU001309
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
SA090110	nHTP_5neg_D21_1-70-6PY4	D21
SA090111	nHTP_5neg_D21_1-71-6RUQ	D21
SA090112	nHTP_5neg_D21_1-69-7PTF	D21
SA090113	nHTP_5neg_D21_1-67-6MX8	D21
SA090114	nHTP_5neg_D21_1-65-7VN0	D21
SA090115	nHTP_5neg_D21_1-72-4PGJ	D21
SA090116	nHTP_5neg_D21_1-74-7KCK	D21
SA090117	nHTP_5neg_D21_1-78-6ULA	D21
SA090118	nHTP_5neg_D21_1-79-4UE4	D21
SA090119	nHTP_5neg_D21_1-77-9AYB	D21
SA090120	nHTP_5neg_D21_1-76-3XMZ	D21
SA090121	nHTP_5neg_D21_1-60-0YGG	D21
SA090122	nHTP_5neg_D21_1-73-1BX5	D21
SA090123	nHTP_5neg_D21_1-52-6YZK	D21
SA090124	nHTP_5neg_D21_1-7-6CNN	D21
SA090125	nHTP_5neg_D21_1-9-5BBH	D21
SA090126	nHTP_5neg_D21_1-4-8UHC	D21
SA090127	nHTP_5neg_D21_1-3-4UDC	D21
SA090128	nHTP_5neg_D21_1-2-3MZX	D21
SA090129	nHTP_5neg_D21_1-10-3TML	D21
SA090130	nHTP_5neg_D21_1-11-3UU4	D21
SA090131	nHTP_5neg_D21_1-51-2MT7	D21
SA090132	nHTP_5neg_D21_1-83-2BDX	D21
SA090133	nHTP_5neg_D21_1-47-2AMQ	D21
SA090134	nHTP_5neg_D21_1-15-0RED	D21
SA090135	nHTP_5neg_D21_1-13-2AYD	D21
SA090136	nHTP_5neg_D21_1-55-5CHY	D21
SA090137	nHTP_5neg_D21_1-84-4UWU	D21
SA090138	nHTP_5neg_D21_2-11-4ZCA	D21
SA090139	nHTP_5neg_D21_2-12-6LKL	D21
SA090140	nHTP_5neg_D21_2-10-2JAL	D21
SA090141	nHTP_5neg_D21_2-9-8HZ9	D21
SA090142	nHTP_5neg_D21_2-8-3XHT	D21
SA090143	nHTP_5neg_D21_2-13-0CYL	D21
SA090144	nHTP_5neg_D21_2-16-5MH0	D21
SA090145	nHTP_5neg_D21_1-3CMM	D21
SA090146	nHTP_5neg_D21_3-8FHC	D21
SA090147	nHTP_5neg_D21_2-20-2YMY	D21
SA090148	nHTP_5neg_D21_2-19-4VEE	D21
SA090149	nHTP_5neg_D21_2-18-0GGN	D21
SA090150	nHTP_5neg_D21_2-7-9JX3	D21
SA090151	nHTP_5neg_D21_2-6-8XWP	D21
SA090152	nHTP_5neg_D21_1-88-0HF9	D21
SA090153	nHTP_5neg_D21_1-89-7GXD	D21
SA090154	nHTP_5neg_D21_1-87-8AF8	D21
SA090155	nHTP_5neg_D21_1-86-2RHE	D21
SA090156	nHTP_5neg_D21_1-85-0KM5	D21
SA090157	nHTP_5neg_D21_1-93-1NRT	D21
SA090158	nHTP_5neg_D21_1-94-1UJ7	D21
SA090159	nHTP_5neg_D21_2-3-5KPV	D21
SA090160	nHTP_5neg_D21_2-2-5NL0	D21
SA090161	nHTP_5neg_D21_2-1-2GGN	D21
SA090162	nHTP_5neg_D21_1-95-8GZF	D21
SA090163	nHTP_5pos_D21_1-1-9BN7	D21
SA090164	nHTP_5neg_D21_1-1-9BN7	D21
SA090165	nHTP_5pos_D21_1-95-8GZF	D21
SA090166	nHTP_5pos_D21_1-94-1UJ7	D21
SA090167	nHTP_5pos_D21_2-1-2GGN	D21
SA090168	nHTP_5pos_D21_2-2-5NL0	D21
SA090169	nHTP_5pos_D21_2-3-5KPV	D21
SA090170	nHTP_5pos_D21_1-93-1NRT	D21
SA090171	nHTP_5pos_D21_1-89-7GXD	D21
SA090172	nHTP_5pos_D21_1-85-0KM5	D21
SA090173	nHTP_5pos_D21_1-84-4UWU	D21
SA090174	nHTP_5pos_D21_1-86-2RHE	D21
SA090175	nHTP_5pos_D21_1-87-8AF8	D21
SA090176	nHTP_5pos_D21_1-88-0HF9	D21
SA090177	nHTP_5pos_D21_2-6-8XWP	D21
SA090178	nHTP_5pos_D21_2-7-9JX3	D21
SA090179	nHTP_5pos_D21_2-18-0GGN	D21
SA090180	nHTP_5pos_D21_2-16-5MH0	D21
SA090181	nHTP_5pos_D21_2-19-4VEE	D21
SA090182	nHTP_5pos_D21_2-20-2YMY	D21
SA090183	nHTP_5pos_D21_1-3CMM	D21
SA090184	nHTP_5pos_D21_2-13-0CYL	D21
SA090185	nHTP_5pos_D21_2-12-6LKL	D21
SA090186	nHTP_5pos_D21_2-8-3XHT	D21
SA090187	nHTP_5pos_D21_2-9-8HZ9	D21
SA090188	nHTP_5pos_D21_2-10-2JAL	D21
SA090189	nHTP_5pos_D21_2-11-4ZCA	D21
SA090190	nHTP_5pos_D21_1-79-4UE4	D21
SA090191	nHTP_5pos_D21_1-78-6ULA	D21
SA090192	nHTP_5pos_D21_1-13-2AYD	D21
SA090193	nHTP_5pos_D21_1-11-3UU4	D21
SA090194	nHTP_5pos_D21_1-15-0RED	D21
SA090195	nHTP_5pos_D21_1-47-2AMQ	D21
SA090196	nHTP_5pos_D21_1-51-2MT7	D21
SA090197	nHTP_5pos_D21_1-10-3TML	D21
SA090198	nHTP_5pos_D21_1-9-5BBH	D21
SA090199	nHTP_5pos_D21_1-2-3MZX	D21
SA090200	nHTP_5pos_D21_1-3-4UDC	D21
SA090201	nHTP_5pos_D21_1-4-8UHC	D21
SA090202	nHTP_5pos_D21_1-7-6CNN	D21
SA090203	nHTP_5pos_D21_1-52-6YZK	D21
SA090204	nHTP_5pos_D21_1-55-5CHY	D21
SA090205	nHTP_5pos_D21_1-73-1BX5	D21
SA090206	nHTP_5pos_D21_1-72-4PGJ	D21
SA090207	nHTP_5pos_D21_1-74-7KCK	D21
SA090208	nHTP_5pos_D21_1-76-3XMZ	D21
SA090209	nHTP_5pos_D21_1-77-9AYB	D21

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Collection:

Collection ID:	CO001303
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:	Blood (plasma)

Treatment:

Treatment ID:	TR001324
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP001317
Sampleprep Summary:	For plasma analyses, a volume of 20μL of was extracted in 480μL of ice-cold methanol:acetonitrile:water (5:3:2). For CSF analyses, a volume of 20μL was extracted in 180μL and for cell-based experiments, 2 million cells were extracted in 1mL of the same ice-cold lysis solution. 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:

SP001317

Sampleprep Summary:

For plasma analyses, a volume of 20μL of was extracted in 480μL of ice-cold methanol:acetonitrile:water (5:3:2). For CSF analyses, a volume of 20μL was extracted in 180μL and for cell-based experiments, 2 million cells were extracted in 1mL of the same ice-cold lysis solution. 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	AN002061	AN002062
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:	CH001499
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
Analytical Time:	5min
Chromatography Type:	Reversed phase

Chromatography ID:	CH001500
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
Analytical Time:	5min
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001912
Analysis ID:	AN002061
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:	MS001913
Analysis ID:	AN002062
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