Summary of Study ST002442

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 PR001573. The data can be accessed directly via it's Project DOI: 10.21228/M8CD9V 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 ID	ST002442
Study Title	Alterations in CSF Urea Occur in Late Manifest Stage Huntington Disease
Study Type	untargeted metabolomics analysis
Study Summary	Huntington Disease (HD) is a neurodegenerative disorder caused by expanded cytosine-adenine-guanine (CAG) repeats in the Huntingtin gene, resulting in the production of mutant huntingtin proteins (mHTT). Previous research has identified urea as a key metabolite elevated in HD animal models and post-mortem tissues of HD patients. The exact timing of these elevations in urea and the molecular mechanism(s) responsible for these disturbances remain unknown. To better understand the pathophysiologic mechanisms responsible for elevations in urea in HD, we completed a global metabolomic profile of cerebrospinal fluid (CSF) from individuals who were at several stages of disease: pre-manifest (PRE), manifest (MAN), and late-manifest (LATE) HD participants compared to controls. We found approximately 500 metabolites were significantly altered in pre-manifest participants compared to controls, although no significant difference in CSF urea or urea metabolites. Interestingly, CSF urea was only significantly elevated in LATE participants compared to controls. There were no changes in the urea metabolites, citrulline, ornithine and arginine throughout disease; however, we did observe changes in acetate, creatinine, 4-acetamidobutanoate and 4-aminobutyraldehyde which are indirect modifiers of urea. Overall, our study confirms that elevations in urea do occur in HD, albeit later in disease and that these changes may reflect more central impairments to cellular energy metabolism yet to be explored.
Institute	Vanderbilt University
Department	Chemistry
Laboratory	Center for Innovative Technology
Last Name	CODREANU
First Name	SIMONA
Address	1234 STEVENSON CENTER LANE
Email	SIMONA.CODREANU@VANDERBILT.EDU
Phone	6158758422
Submit Date	2023-01-12
Num Groups	4
Total Subjects	60
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-01-25
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001573
Project DOI:	doi: 10.21228/M8CD9V
Project Title:	Alterations in CSF Urea Occur in Late Manifest Stage Huntington Disease
Project Type:	Untargeted Metabolomics analysis
Project Summary:	Huntington Disease (HD) is a neurodegenerative disorder caused by expanded cytosine-adenine-guanine (CAG) repeats in the Huntingtin gene, resulting in the production of mutant huntingtin proteins (mHTT). Previous research has identified urea as a key metabolite elevated in HD animal models and post-mortem tissues of HD patients. The exact timing of these elevations in urea and the molecular mechanism(s) responsible for these disturbances remain unknown. To better understand the pathophysiologic mechanisms responsible for elevations in urea in HD, we completed a global metabolomic profile of cerebrospinal fluid (CSF) from individuals who were at several stages of disease: pre-manifest (PRE), manifest (MAN), and late-manifest (LATE) HD participants compared to controls. We found approximately 500 metabolites were significantly altered in pre-manifest participants compared to controls, although no significant difference in CSF urea or urea metabolites. Interestingly, CSF urea was only significantly elevated in LATE participants compared to controls. There were no changes in the urea metabolites, citrulline, ornithine and arginine throughout disease; however, we did observe changes in acetate, creatinine, 4-acetamidobutanoate and 4-aminobutyraldehyde which are indirect modifiers of urea. Overall, our study confirms that elevations in urea do occur in HD, albeit later in disease and that these changes may reflect more central impairments to cellular energy metabolism yet to be explored.
Institute:	Vanderbilt University
Department:	Chemistry
Laboratory:	Center for Innovative Technology
Last Name:	CODREANU
First Name:	SIMONA
Address:	1234 STEVENSON CENTER LANE
Email:	SIMONA.CODREANU@VANDERBILT.EDU
Phone:	6158758422

Subject:

Subject ID:	SU002531
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Genotype	sex	age
SA244189	SC_20201109_HILICp_FMS_CSF_E04_C_1_1	CONTROL	f	47
SA244190	SC_20201109_HILICp_FMS_CSF_E11_C_1_2	CONTROL	f	47
SA244191	SC_20201109_HILICp_FMS_CSF_G04_C_1_1	CONTROL	f	53
SA244192	SC_20201109_HILICp_FMS_CSF_G06_C_1_1	CONTROL	f	53
SA244193	SC_20201109_HILICp_FMS_CSF_F01_C_1_2	CONTROL	f	53
SA244194	SC_20201109_HILICp_FMS_CSF_G07_C_1_2	CONTROL	f	54
SA244195	SC_20201109_HILICp_FMS_CSF_D10_C_1_1	CONTROL	f	58
SA244196	SC_20201109_HILICp_FMS_CSF_E12_C_1_2	CONTROL	f	59
SA244197	SC_20201109_HILICp_FMS_CSF_G09_C_1_2	CONTROL	f	61
SA244198	SC_20201109_HILICp_FMS_CSF_G11_C_1_1	CONTROL	f	61
SA244199	SC_20201109_HILICp_FMS_CSF_D01_C_1_1	CONTROL	m	28
SA244200	SC_20201109_HILICp_FMS_CSF_D08_C_1_2	CONTROL	m	28
SA244201	SC_20201109_HILICp_FMS_CSF_C07_C_1_1	CONTROL	m	32
SA244202	SC_20201109_HILICp_FMS_CSF_D09_C_1_2	CONTROL	m	32
SA244203	SC_20201109_HILICp_FMS_CSF_F04_C_1_1	CONTROL	m	35
SA244204	SC_20201109_HILICp_FMS_CSF_F05_C_1_2	CONTROL	m	36
SA244205	SC_20201109_HILICp_FMS_CSF_D06_C_1_2	CONTROL	m	44
SA244206	SC_20201109_HILICp_FMS_CSF_D02_C_1_1	CONTROL	m	44
SA244207	SC_20201109_HILICp_FMS_CSF_F12_C_1_2	CONTROL	m	51
SA244208	SC_20201109_HILICp_FMS_CSF_F06_C_1_1	CONTROL	m	51
SA244209	SC_20201109_HILICp_FMS_CSF_F10_C_1_1	CONTROL	m	54
SA244210	SC_20201109_HILICp_FMS_CSF_G03_C_1_2	CONTROL	m	54
SA244211	SC_20201109_HILICp_FMS_CSF_G05_C_1_2	CONTROL	m	57
SA244212	SC_20201109_HILICp_FMS_CSF_G01_C_1_1	CONTROL	m	57
SA244213	SC_20201109_HILICp_FMS_CSF_F07_HD_3	EARLY MANIFEST	f	41
SA244214	SC_20201109_HILICp_FMS_CSF_H01_HD_3	EARLY MANIFEST	f	47
SA244215	SC_20201109_HILICp_FMS_CSF_B10_HD_3	EARLY MANIFEST	f	48
SA244216	SC_20201109_HILICp_FMS_CSF_G12_HD_3	EARLY MANIFEST	f	50
SA244217	SC_20201109_HILICp_FMS_CSF_F03_HD_3	EARLY MANIFEST	f	52
SA244218	SC_20201109_HILICp_FMS_CSF_A02_HD_3	EARLY MANIFEST	f	57
SA244219	SC_20201109_HILICp_FMS_CSF_G02_HD_3	EARLY MANIFEST	f	59
SA244220	SC_20201109_HILICp_FMS_CSF_F09_HD_3	EARLY MANIFEST	f	59
SA244221	SC_20201109_HILICp_FMS_CSF_H04_HD_3	EARLY MANIFEST	f	60
SA244222	SC_20201109_HILICp_FMS_CSF_A07_HD_3	EARLY MANIFEST	m	35
SA244223	SC_20201109_HILICp_FMS_CSF_C04_HD_3	EARLY MANIFEST	m	39
SA244224	SC_20201109_HILICp_FMS_CSF_D05_HD_3	EARLY MANIFEST	m	41
SA244225	SC_20201109_HILICp_FMS_CSF_G08_HD_3	EARLY MANIFEST	m	46
SA244226	SC_20201109_HILICp_FMS_CSF_A05_HD_3	EARLY MANIFEST	m	49
SA244227	SC_20201109_HILICp_FMS_CSF_A08_HD_3	EARLY MANIFEST	m	56
SA244228	SC_20201109_HILICp_FMS_CSF_C09_HD_3	EARLY MANIFEST	m	59
SA244229	SC_20201109_HILICp_FMS_CSF_A01_HD_4	LATE MANIFEST	f	38
SA244230	SC_20201109_HILICp_FMS_CSF_C02_HD_4	LATE MANIFEST	f	47
SA244231	SC_20201109_HILICp_FMS_CSF_C06_HD_4	LATE MANIFEST	f	55
SA244232	SC_20201109_HILICp_FMS_CSF_C03_HD_4	LATE MANIFEST	f	57
SA244233	SC_20201109_HILICp_FMS_CSF_B01_HD_4	LATE MANIFEST	f	58
SA244234	SC_20201109_HILICp_FMS_CSF_B11_HD_4	LATE MANIFEST	f	65
SA244235	SC_20201109_HILICp_FMS_CSF_E09_HD_4	LATE MANIFEST	f	72
SA244236	SC_20201109_HILICp_FMS_CSF_A10_HD_4	LATE MANIFEST	m	46
SA244237	SC_20201109_HILICp_FMS_CSF_D04_HD_4	LATE MANIFEST	m	47
SA244238	SC_20201109_HILICp_FMS_CSF_D03_HD_4	LATE MANIFEST	m	51
SA244239	SC_20201109_HILICp_FMS_CSF_A06_HD_4	LATE MANIFEST	m	58
SA244240	SC_20201109_HILICp_FMS_CSF_F08_HD_4	LATE MANIFEST	m	60
SA244241	SC_20201109_HILICp_FMS_CSF_A11_HD_4	LATE MANIFEST	m	60
SA244242	SC_20201109_HILICp_FMS_CSF_E07_HD_4	LATE MANIFEST	m	63
SA244243	SC_20201109_HILICp_FMS_CSF_A09_HD_4	LATE MANIFEST	m	66
SA244244	SC_20201109_HILICp_FMS_CSF_D07_HD_4	LATE MANIFEST	m	69
SA244245	SC_20201109_HILICp_FMS_CSF_H03_HD_2_2	PRE-MANIFEST	f	26
SA244246	SC_20201109_HILICp_FMS_CSF_G10_HD_2_1	PRE-MANIFEST	f	26
SA244247	SC_20201109_HILICp_FMS_CSF_B09_HD_2_2	PRE-MANIFEST	f	30
SA244248	SC_20201109_HILICp_FMS_CSF_B03_HD_2_1	PRE-MANIFEST	f	30
SA244249	SC_20201109_HILICp_FMS_CSF_C01_HD_2_2	PRE-MANIFEST	f	33
SA244250	SC_20201109_HILICp_FMS_CSF_C05_HD_2_1	PRE-MANIFEST	f	33
SA244251	SC_20201109_HILICp_FMS_CSF_B04_HD_2_1	PRE-MANIFEST	f	33
SA244252	SC_20201109_HILICp_FMS_CSF_C08_HD_2_2	PRE-MANIFEST	f	33
SA244253	SC_20201109_HILICp_FMS_CSF_B02_HD_2_1	PRE-MANIFEST	f	36
SA244254	SC_20201109_HILICp_FMS_CSF_B08_HD_2_2	PRE-MANIFEST	f	36
SA244255	SC_20201109_HILICp_FMS_CSF_H02_HD_2_1	PRE-MANIFEST	f	40
SA244256	SC_20201109_HILICp_FMS_CSF_C12_HD_2_2	PRE-MANIFEST	f	40
SA244257	SC_20201109_HILICp_FMS_CSF_F11_HD_2_1	PRE-MANIFEST	f	42
SA244258	SC_20201109_HILICp_FMS_CSF_F02_HD_2_2	PRE-MANIFEST	f	42
SA244259	SC_20201109_HILICp_FMS_CSF_E03_HD_2_1	PRE-MANIFEST	f	43
SA244260	SC_20201109_HILICp_FMS_CSF_E10_HD_2_2	PRE-MANIFEST	f	43
SA244261	SC_20201109_HILICp_FMS_CSF_B05_HD_2_1	PRE-MANIFEST	m	29
SA244262	SC_20201109_HILICp_FMS_CSF_B06_HD_2_2	PRE-MANIFEST	m	29
SA244263	SC_20201109_HILICp_FMS_CSF_E06_HD_2_2	PRE-MANIFEST	m	30
SA244264	SC_20201109_HILICp_FMS_CSF_E01_HD_2_1	PRE-MANIFEST	m	30
SA244265	SC_20201109_HILICp_FMS_CSF_E08_HD_2_1	PRE-MANIFEST	m	31
SA244266	SC_20201109_HILICp_FMS_CSF_A04_HD_2_2	PRE-MANIFEST	m	31
SA244267	SC_20201109_HILICp_FMS_CSF_B12_HD_2_2	PRE-MANIFEST	m	35
SA244268	SC_20201109_HILICp_FMS_CSF_B07_HD_2_1	PRE-MANIFEST	m	35
SA244269	SC_20201109_HILICp_FMS_CSF_C11_HD_2_1	PRE-MANIFEST	m	36
SA244270	SC_20201109_HILICp_FMS_CSF_C10_HD_2_2	PRE-MANIFEST	m	37
SA244271	SC_20201109_HILICp_FMS_CSF_D12_HD_2_2	PRE-MANIFEST	m	42
SA244272	SC_20201109_HILICp_FMS_CSF_D11_HD_2_1	PRE-MANIFEST	m	42
SA244273	SC_20201109_HILICp_FMS_CSF_A03_HD_2_1	PRE-MANIFEST	m	48
SA244274	SC_20201109_HILICp_FMS_CSF_E02_HD_2_1	PRE-MANIFEST	m	48
SA244275	SC_20201109_HILICp_FMS_CSF_A12_HD_2_2	PRE-MANIFEST	m	48
SA244276	SC_20201109_HILICp_FMS_CSF_E05_HD_2_2	PRE-MANIFEST	m	48

Showing results 1 to 88 of 88

Showing results 1 to 88 of 88

Collection:

Collection ID:	CO002524
Collection Summary:	CSF samples were collected from 60 participants as part of the CHDI HD-Clarity study. There were 16 PRE, 16 MAN, 16 LATE HD participants and 12 control participants. Disease stage was determined using the diagnostic confidence level (DCL), length of CAG expansion and burden of pathology calculated from (CAG expansion – 35.5) x Age. Control participants were individuals without a known history of Huntington Disease (HD). All HD participants have a CAG expansion of > 40. PRE participants were not motor manifest as indicated by a DCL of <4 and a burden of pathology of > 250. MAN participants had a DCL =4 and a total functional capacity (TFC) between 7-13. The LATE group had all the above criteria for MAN and a TFC score between 0-6. Repeat CSF and blood samples collected 4-8 weeks after a baseline (BL) visit are provided for all control and PRE participants. Participants’ age and gender are reported here. Three participants (2 PRE, 1 MAN) were taking supplemental vitamins; however, their metal levels were similar to those in their corresponding participant group and thus, the data from these participants are included. Basic demographics like age and gender were reported previously in addition to participants' scores on a battery of cognitive, behavioral and motor assessments including the symbol digit modality test (SDMT), Stroop Word Reading (SWR), total functional capacity (TFC), total motor score (TMS) and the recently developed cUHDRS.
Collection Protocol Filename:	Sample_Collection.pdf
Sample Type:	CSF
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002543
Treatment Summary:	No treatment

Sample Preparation:

Sampleprep ID:	SP002537
Sampleprep Summary:	CSF samples collected were flash frozen and stored at -80°C until analyzed via Liquid ChromatographyHigh Resolution Mass Spectrometry (LC-HRMS and LC-HRMS/MS)-based metabolomics in the Vanderbilt Center for Innovative Technology (CIT) using previously described methods (cite). Briefly, equal volumes (100 µL) of previously frozen CSF was diluted with 100 µL ice-cold lysis buffer (1:1:2, Acetonitrile:MeOH:Ammonium Bicarbonate 0.1M, pH 8.0, LC-MS grade). Addition of isotopically labeled phenylalanine-D8 and biotin-D2 were added to individual samples prior to protein precipitation by addition of 800 µL of ice-cold methanol. Following overnight incubation at -80°C, precipitated proteins were pelleted by centrifugation at 10,000 rpm for 10 min and metabolite extracts were dried down in vacuo and stored at -80°C until reconstitution prior to MS analysis.

Sampleprep ID:

SP002537

Sampleprep Summary:

CSF samples collected were flash frozen and stored at -80°C until analyzed via Liquid ChromatographyHigh Resolution Mass Spectrometry (LC-HRMS and LC-HRMS/MS)-based metabolomics in the Vanderbilt Center for Innovative Technology (CIT) using previously described methods (cite). Briefly, equal volumes (100 µL) of previously frozen CSF was diluted with 100 µL ice-cold lysis buffer (1:1:2, Acetonitrile:MeOH:Ammonium Bicarbonate 0.1M, pH 8.0, LC-MS grade). Addition of isotopically labeled phenylalanine-D8 and biotin-D2 were added to individual samples prior to protein precipitation by addition of 800 µL of ice-cold methanol. Following overnight incubation at -80°C, precipitated proteins were pelleted by centrifugation at 10,000 rpm for 10 min and metabolite extracts were dried down in vacuo and stored at -80°C until reconstitution prior to MS analysis.

Combined analysis:

Analysis ID	AN003979
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Vanquish
Column	Waters ACQUITY UPLC BEH HILIC (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE
Units	time_m/z

Chromatography:

Chromatography ID:	CH002942
Chromatography Summary:	CSF extracts (5uL injection volume) were separated on an ACQUITY UPLC BEH Amide HILIC 1.7μm, 2.1 × 100 mm column (Waters Corporation, Milford, MA) held at 30°C as previously described (cite). Briefly, liquid chromatography was performed at 200 µL min−1 using solvent A (5 mM ammonium formate in 90% water, 10% acetonitrile and 0.1% formic acid) and solvent B (5 mM ammonium formate in 90% acetonitrile, 10% water and 0.1% formic acid) with a gradient length of 30 min.
Methods Filename:	Metabolomics_Analyses.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC BEH HILIC (100 x 2.1mm,1.7um)
Column Temperature:	30
Flow Gradient:	30 min
Flow Rate:	0.20mL/min
Solvent A:	90% water, 10% acetonitrile, 5mM Ammonium Formate, 0.1%FA
Solvent B:	10% water, 90% acetonitrile, 5mM Ammonium Formate, 0.1%FA
Chromatography Type:	HILIC

MS:

MS ID:	MS003713
Analysis ID:	AN003979
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full MS analyses were acquired over the mass-to-charge ratio (m/z) range of 70-1,050 in positive ion mode. Full mass scan was acquired at 120,000 resolution with a scan rate of 3.5 Hz, automatic gain control (AGC) target of 1x106, and maximum ion injection time of 100 ms, and MS/MS spectra were collected at 15,000 resolution, AGC target of 2x105 ions, with a maximum ion injection time of 100 ms
Ion Mode:	POSITIVE
Analysis Protocol File:	Metabolomics_Analyses.pdf