Summary of Study ST002389

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 PR001536. The data can be accessed directly via it's Project DOI: 10.21228/M8512J 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	ST002389
Study Title	Alterations in SHH signal transduction introduce a state of hypometabolism in sporadic Parkinson's disease
Study Summary	Induced pluripotent stem cells (iPSC) derived from sporadic Parkinson's disease patients and healthy control subjects were used for disease modeling. iPSC were differentiated towards midbrain dopaminergic neurons. For metabolic analysis, midbrain neuronal precursor cells were cultivated in growth medium supplemented with either 1.25 mM [U-13C]-glutamine or 21.25 mM [U-13C]-glucose. Metabolites were extracted and analyzed using GC-MS. The MetaboliteDetector software was used to analyze chromatograms, calculate mass isotopomer distributions (MIDs) and perform relative comparison of metabolite levels.
Institute	Helmholtz Centre for Environmental Research
Department	Institute of Developmental Genetics
Last Name	Schmidt
First Name	Sebastian
Address	Ingolstädter Landstraße 1, 85764 Munich, Germany
Email	sebastian.schmidt@helmholtz-muenchen.de
Phone	+4989318743660
Submit Date	2022-12-03
Num Groups	3
Total Subjects	13
Raw Data Available	Yes
Raw Data File Type(s)	bin
Analysis Type Detail	GC-MS
Release Date	2023-10-06
Release Version	1

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Project:

Project ID:	PR001536
Project DOI:	doi: 10.21228/M8512J
Project Title:	Alterations in SHH signal transduction introduce a state of hypometabolism in sporadic Parkinson's disease
Project Type:	Isotopic labeling
Project Summary:	Sporadic Parkinson’s Disease (sPD) is a progressive neurodegenerative disorder caused by multiple genetic and environmental factors with largely unknown etiology. Prominent pathological culprits include metabolic as well as mitochondrial alterations which have been identified in patients, however, their relevance at different stages of disease progression or their connection remains largely elusive. Here, human iPSCs from late-onset sPD patients were used for disease modeling. Following long-term in vitro cultivation, exclusively neural cells derived from sPD patients developed reduced mitochondrial respiration and glucose consumption reflecting an sPD-specific state of hypometabolism. A multilayered omics analysis based on transcriptomics, proteomics, and metabolomics allowed us to identify the citric acid cycle as being the bottleneck in sPD metabolism. A 13C metabolic flux analysis further unraveled the a-ketoglutarate dehydrogenase complex as being central for a reduced flux through the citric acid cycle. This resulted in a substrate availability problem for the electron transport chain and thus reduced mitochondrial oxygen consumption and ATP production. Notably, these alterations in cellular metabolism were evoked by altered SHH signal transduction due to dysfunctional primary cilia. Upon inhibiting the enhanced SHH signal transduction in sPD, glucose uptake and the activity of the a-ketoglutarate dehydrogenase complex could be restored. Thus, inhibiting overactive SHH signaling may be a potential neuroprotective therapy during the early stages of sPD.
Institute:	Helmholtz Centre for Environmental Research
Department:	Institute of Developmental Genetics
Last Name:	Schmidt
First Name:	Sebastian
Address:	Ingolstädter Landstraße 1, 85764 Munich, Germany
Email:	sebastian.schmidt@helmholtz-muenchen.de
Phone:	+4989318743660
Contributors:	Karsten Hiller, Alexander Heinz

Subject:

Subject ID:	SU002478
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female
Cell Biosource Or Supplier:	ForIPS consortium
Cell Strain Details:	Midbrain neuronal precursor cells differentiated from patient derived induced pluripotent stem cells

Factors:

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

mb_sample_id	local_sample_id	disease_state	13C_label
SA238064	blank_3_Glc	blank	Glucose
SA238065	blank_2_Glc	blank	Glucose
SA238066	blank_1_Glc	blank	Glucose
SA238067	blank_3_Gln	blank	Glutamine
SA238068	blank_1_Gln	blank	Glutamine
SA238069	blank_2_Gln	blank	Glutamine
SA238070	iG3G-R1-039_2_Glc	ctrl	Glucose
SA238071	iG3G-R1-039_3_Glc	ctrl	Glucose
SA238072	iG3G-R1-039_1_Glc	ctrl	Glucose
SA238073	i1JF-R1-018_3_Glc	ctrl	Glucose
SA238074	i1JF-R1-018_1_Glc	ctrl	Glucose
SA238075	i1E4-R1-003_2_Glc	ctrl	Glucose
SA238076	i1E4-R1-003_1_Glc	ctrl	Glucose
SA238077	i1JF-R1-018_2_Glc	ctrl	Glucose
SA238078	iO3H-R1-005_2_Glc	ctrl	Glucose
SA238079	i1E4-R1-003_3_Glc	ctrl	Glucose
SA238080	i82A-R1-002_3_Glc	ctrl	Glucose
SA238081	iO3H-R1-005_3_Glc	ctrl	Glucose
SA238082	iO3H-R1-005_1_Glc	ctrl	Glucose
SA238083	i82A-R1-002_2_Glc	ctrl	Glucose
SA238084	i82A-R1-002_1_Glc	ctrl	Glucose
SA238085	i1E4-R1-003_1_Gln	ctrl	Glutamine
SA238086	iG3G-R1-039_3_Gln	ctrl	Glutamine
SA238087	i1JF-R1-018_2_Gln	ctrl	Glutamine
SA238088	i1E4-R1-003_2_Gln	ctrl	Glutamine
SA238089	i1JF-R1-018_3_Gln	ctrl	Glutamine
SA238090	iG3G-R1-039_2_Gln	ctrl	Glutamine
SA238091	iO3H-R1-005_3_Gln	ctrl	Glutamine
SA238092	i82A-R1-002_3_Gln	ctrl	Glutamine
SA238093	i1JF-R1-018_1_Gln	ctrl	Glutamine
SA238094	i82A-R1-002_2_Gln	ctrl	Glutamine
SA238095	i82A-R1-002_1_Gln	ctrl	Glutamine
SA238096	iO3H-R1-005_1_Gln	ctrl	Glutamine
SA238097	iO3H-R1-005_2_Gln	ctrl	Glutamine
SA238098	i1E4-R1-003_3_Gln	ctrl	Glutamine
SA238099	iG3G-R1-039_1_Gln	ctrl	Glutamine
SA238100	iJ2C-R1-015_3_Glc	sPD	Glucose
SA238101	iJ2C-R1-015_2_Glc	sPD	Glucose
SA238102	iJ2C-R1-015_1_Glc	sPD	Glucose
SA238103	iC99-R1-007_3_Glc	sPD	Glucose
SA238104	iM89-R1-005_1_Glc	sPD	Glucose
SA238105	iM89-R1-005_2_Glc	sPD	Glucose
SA238106	iC99-R1-007_1_Glc	sPD	Glucose
SA238107	i88H-R1-002_3_Glc	sPD	Glucose
SA238108	iM89-R1-005_3_Glc	sPD	Glucose
SA238109	iR66-R1-007_1_Glc	sPD	Glucose
SA238110	iC99-R1-007_2_Glc	sPD	Glucose
SA238111	iPX7-R1-001_2_Glc	sPD	Glucose
SA238112	iR66-R1-007_2_Glc	sPD	Glucose
SA238113	i88H-R1-002_1_Glc	sPD	Glucose
SA238114	i88H-R1-002_2_Glc	sPD	Glucose
SA238115	iPX7-R1-001_1_Glc	sPD	Glucose
SA238116	iPX7-R1-001_3_Glc	sPD	Glucose
SA238117	iR66-R1-007_3_Glc	sPD	Glucose
SA238118	iAY6-R1-003_3_Glc	sPD	Glucose
SA238119	iAY6-R1-003_1_Glc	sPD	Glucose
SA238120	iAY6-R1-003_2_Glc	sPD	Glucose
SA238121	iPX7-R1-001_2_Gln	sPD	Glutamine
SA238122	iPX7-R1-001_1_Gln	sPD	Glutamine
SA238123	iPX7-R1-001_3_Gln	sPD	Glutamine
SA238124	i88H-R1-002_3_Gln	sPD	Glutamine
SA238125	iAY6-R1-003_3_Gln	sPD	Glutamine
SA238126	i88H-R1-002_2_Gln	sPD	Glutamine
SA238127	i88H-R1-002_1_Gln	sPD	Glutamine
SA238128	iC99-R1-007_1_Gln	sPD	Glutamine
SA238129	iM89-R1-005_1_Gln	sPD	Glutamine
SA238130	iM89-R1-005_2_Gln	sPD	Glutamine
SA238131	iJ2C-R1-015_3_Gln	sPD	Glutamine
SA238132	iJ2C-R1-015_2_Gln	sPD	Glutamine
SA238133	iJ2C-R1-015_1_Gln	sPD	Glutamine
SA238134	iM89-R1-005_3_Gln	sPD	Glutamine
SA238135	iC99-R1-007_2_Gln	sPD	Glutamine
SA238136	iR66-R1-007_3_Gln	sPD	Glutamine
SA238137	iAY6-R1-003_1_Gln	sPD	Glutamine
SA238138	iR66-R1-007_2_Gln	sPD	Glutamine
SA238139	iR66-R1-007_1_Gln	sPD	Glutamine
SA238140	iC99-R1-007_3_Gln	sPD	Glutamine
SA238141	iAY6-R1-003_2_Gln	sPD	Glutamine

Showing results 1 to 78 of 78

Showing results 1 to 78 of 78

Collection:

Collection ID:	CO002471
Collection Summary:	Neuronal precursor cells differentiated from patient derived induced pluripotent stem cells were seeded on Geltrex coated 6-well plates containing neuronal precursor maintenance medium at a density of 1,000,000 cells/well with six replicates per cell line. hNPCs were cultured at 37 °C, 7 % CO2, 21 % O2 for at least 72 h.
Sample Type:	Neurons
Storage Conditions:	-80?

Treatment:

Treatment ID:	TR002490
Treatment Summary:	Growth medium was replaced by a labeling medium containing the respective stable-isotope tracer instead of its unlabeled variant. Cells were cultured with either 1.25 mM [U-13C]-glutamine or 21.25 mM [U-13C]-glucose for 24 h.

Sample Preparation:

Sampleprep ID:	SP002484
Sampleprep Summary:	Subsequently, cell culture supernatant was stored for profiling the extracellular metabolome. Three replicates per cell line and blanks were washed with 0.9% NaCl and quenched with ice-cold methanol and ice-cold ddH2O (containing 1 µg/ml D6-glutaric acid as internal standard). Cells were scraped and extracts were added into tubes containing ice-cold chloroform. Following vortexing at 1,400 rpm for 20 min at 4°C and centrifugation at 17,000 g for 5 min at 4°C, 300 µl of the polar phase were transferred into GC glass vials with microinsert and dried under vacuum at 4°C. Dried extracts were derivatized using equal amounts of methoxylamine (20 mg/ml in pyridine) and MTBSTFA.

Sampleprep ID:

SP002484

Sampleprep Summary:

Subsequently, cell culture supernatant was stored for profiling the extracellular metabolome. Three replicates per cell line and blanks were washed with 0.9% NaCl and quenched with ice-cold methanol and ice-cold ddH2O (containing 1 µg/ml D6-glutaric acid as internal standard). Cells were scraped and extracts were added into tubes containing ice-cold chloroform. Following vortexing at 1,400 rpm for 20 min at 4°C and centrifugation at 17,000 g for 5 min at 4°C, 300 µl of the polar phase were transferred into GC glass vials with microinsert and dried under vacuum at 4°C. Dried extracts were derivatized using equal amounts of methoxylamine (20 mg/ml in pyridine) and MTBSTFA.

Combined analysis:

Analysis ID	AN003893
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890B gas chromatograph
Column	30 m DB-35 ms and 5 m Duruguard capillary column
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5977
Ion Mode	POSITIVE
Units	Mass isotopomer distributions

Chromatography:

Chromatography ID:	CH002883
Instrument Name:	Agilent 7890B gas chromatograph
Column Name:	30 m DB-35 ms and 5 m Duruguard capillary column
Chromatography Type:	GC

MS:

MS ID:	MS003633
Analysis ID:	AN003893
Instrument Name:	Agilent 5977
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	One microliter sample was injected into an SSL injector at 270 °C in a split or splitless mode. GC-MS analysis was performed using an Agilent 7890B gas chromatograph equipped with a 30 m DB-35 ms and 5 m Duruguard capillary column. Metabolites were detected in selected ion mode by an Agilent 5977 MSD system. The MetaboliteDetector software was used to analyze chromatograms, calculate mass isotopomer distributions (MIDs) and perform relative comparison of metabolite levels.
Ion Mode:	POSITIVE