Summary of Study ST004286

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 PR002703. The data can be accessed directly via it's Project DOI: 10.21228/M88851 This work is supported by NIH grant, U2C- DK119886.

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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 IDST004286
Study TitleLimitations in PPAR⍺-dependent mitochondrial programming restrain the differentiation of human stem cell-derived β cells - Study 2
Study SummaryPluripotent stem cell (SC)-derived islets offer hope as a renewable source for β cell replacement for type 1 diabetes (T1D), yet functional and metabolic immaturity may limit their long-term therapeutic potential. Here, we show that limitations in mitochondrial transcriptional programming impede the formation of SC-derived β (SC-β) cells. Utilizing transcriptomic profiling, assessments of chromatin accessibility, mitochondrial phenotyping, and lipidomics analyses, we observed that SC-β cells exhibit reduced oxidative and mitochondrial fatty acid metabolism compared to primary human islets that are related to limitations in key mitochondrial transcriptional networks. Surprisingly, we find that reductions in glucose-stimulated mitochondrial respiration in SC-islets were not associated with alterations in mitochondrial mass, structure, or genome integrity. In contrast, SC-islets show limited expression of targets of PPAR⍺, which regulate mitochondrial programming, yet whose functions in β cell differentiation are unknown. Importantly, treatment with WY14643, a potent PPAR⍺ agonist, induced expression of mitochondrial targets, improved insulin secretion, and increased the formation of SC-β cells both in vitro and following transplantation. Thus, PPAR⍺-dependent mitochondrial programming promotes the differentiation of SC-β cells and may be a promising target to improve β cell replacement efforts for T1D.
Institute
University of Michigan
DepartmentDivision of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine
LaboratoryScott A. Soleimanpour
Last NameArnipalli
First NameManikanta
Address3815-301B Green Brier apt, Ann Arbor, Michigan, 48105, USA
Emailmanikana@umich.edu
Phone734-272-8779
Submit Date2025-10-10
Raw Data AvailableYes
Raw Data File Type(s)mzML, d
Analysis Type DetailLC-MS
Release Date2025-11-03
Release Version1
Manikanta Arnipalli Manikanta Arnipalli
https://dx.doi.org/10.21228/M88851
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002703
Project DOI:doi: 10.21228/M88851
Project Title:Limitations in PPAR⍺-dependent mitochondrial programming restrain the differentiation of human stem cell-derived β cells
Project Summary:Pluripotent stem cell (SC)-derived islets offer hope as a renewable source for β cell replacement for type 1 diabetes (T1D), yet functional and metabolic immaturity may limit their long-term therapeutic potential. Here, we show that limitations in mitochondrial transcriptional programming impede the formation of SC-derived β (SC-β) cells. Utilizing transcriptomic profiling, assessments of chromatin accessibility, mitochondrial phenotyping, and lipidomics analyses, we observed that SC-β cells exhibit reduced oxidative and mitochondrial fatty acid metabolism compared to primary human islets that are related to limitations in key mitochondrial transcriptional networks. Surprisingly, we find that reductions in glucose-stimulated mitochondrial respiration in SC-islets were not associated with alterations in mitochondrial mass, structure, or genome integrity. In contrast, SC-islets show limited expression of targets of PPAR⍺, which regulate mitochondrial programming, yet whose functions in β cell differentiation are unknown. Importantly, treatment with WY14643, a potent PPAR⍺ agonist, induced expression of mitochondrial targets, improved insulin secretion, and increased the formation of SC-β cells both in vitro and following transplantation. Thus, PPAR⍺-dependent mitochondrial programming promotes the differentiation of SC-β cells and may be a promising target to improve β cell replacement efforts for T1D.
Institute:University of Michigan
Department:Division of Metabolism, Endocrinology and Diabetes and Department of Internal Medicine
Laboratory:Scott A. Soleimanpour
Last Name:Arnipalli
First Name:Manikanta
Address:3815-301B Green Brier apt, Ann Arbor, michigan, 48105, USA
Email:manikana@umich.edu
Phone:734-272-8779

Subject:

Subject ID:SU004439
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample type Sample source
SA498475S6 10_08_22Human Pancreas
SA498476WY 10_31_24Human Pancreas
SA498477Vehicle 11_5_24Human Pancreas
SA498478Vehicle 10_31_24Human Pancreas
SA498479WY 11_5_24Human Pancreas
SA498480WY 10_3_24Human Pancreas
SA498481Vehicle 10_3_24Human Pancreas
SA49848210_28_22 HI_5Human Pancreas
SA49848310_28_22 HI_4Human Pancreas
SA49848410_15_22 HI_3Human Pancreas
SA49848510_07_22 HI_2Human Pancreas
SA49848610_05_22 HI_1Human Pancreas
SA498487S6 12_10_22Human Pancreas
SA498488S1 11_16_22Human Pancreas
SA498489S1 9_14_22Human Pancreas
SA498490S5 9_29_22Human Pancreas
SA498491S5 9_25_22Human Pancreas
SA498492S5 12_01_22Human Pancreas
SA498493S4 9_22_22Human Pancreas
SA498494S4 9_18_22Human Pancreas
SA498495S4 11_24_22Human Pancreas
SA498496S3 9_18_22Human Pancreas
SA498497S3 9_14_22Human Pancreas
SA498498S3 11_20_22Human Pancreas
SA498499S2 12_19_22Human Pancreas
SA498500S2 9_16_22Human Pancreas
SA498501S2 11_18_22Human Pancreas
SA498502S1 12_17_22Human Pancreas
SA498503S6 10_04_22Human Pancreas
Showing results 1 to 29 of 29

Collection:

Collection ID:CO004432
Collection Summary:Cells were cultured according to Hogrebe et al4. On the day of sample collection, samples were incubated in MCDB 131 with 10.5 g BSA, 5.2 mL GlutaMAX, 5.2 mL P/S, 5 mg heparin, 5.2 mL MEM nonessential amino acids (Corning, 20–025-CI), 84 μg ZnSO4 (MilliporeSigma, 10883), 523 μL Trace Elements A (Corning, 25–021-CI), and 523 μL Trace Elements B (Corning, 25–022-CI) and either 5.5 mM or 20 mM glucose for 3 hr.
Sample Type:Pancreas

Treatment:

Treatment ID:TR004448
Treatment Summary:Treatment not applied.

Sample Preparation:

Sampleprep ID:SP004445
Sampleprep Summary:Media were removed, and Acyl carnitines were extracted with 500 μL solvent (8:1:1 ratio of methanol/Chloroform/water) containing stable isotope-labeled internal standards. The resulting homogenate was sonicated on ice for 10 sec. Samples were centrifuged at 15,000 rpm for 10 mins and 4°C. Supernatant is removed. Dry down at 45°C. Samples were reconstituted in 50 μL of 5 mM Ammonium Acetate, filtered and 4 μL were injected for analysis.

Chromatography:

Chromatography ID:CH005415
Chromatography Summary:an Agilent 6410 triple quadrupole MS system equipped with an Agilent 1200 LC System and an ESI source was utilized. Metabolite separation was achieved using gradient elution on a reverse phase XBridge C18 Column (50 mm × 2.1 mm, 2.5 μm, Waters, Milford, MA, USA) with the corresponding guard column (5 mm x 2.1 mm, 1.7 μm) maintained at 40°C. LC vials were maintained at 4°C in a thermostatic autosampler, and the injection volume was set at 4 µL. The mobile phase consisted of solvent A, 5 mM Ammonium Acetate, and solvent B, Acetonitrile. The flow rate was 0.25 mL/min. The gradient elution program was as follows: 0–8.50 min, 2% B; 1.5–9 min, linear gradient from 2% to 50% B; 9–14 min, linear gradient from 50% to 95% B; hold at 95% B for 3 min. The flow rate was 300 μL/min. Acylcarnitine species were each detected by their characteristic LC retention time in the MRM mode following ESI and comparing relative areas with those of corresponding standards. Concentrations of carnitine, acetylcarnitine (C2), propionylcarnitine (C3), butyrylcarnitine (C4), isovalerylcarnitine (C5), hexanoylcarnitine (C6), octanoylcarnitine (C8), myristoylcarnitine (C14), palmitoylcarnitine (C16), and oleoylcarnitine (C18) were calculated by ratios of peak areas of known concentrations of stable isotopically-labeled analogs.
Instrument Name:Agilent 6490
Column Name:Waters XBridge C18 (50 x 2.1 mm, 3 μm)
Column Temperature:40°C
Flow Gradient:The gradient elution program was as follows: 0–8.50 min, 2% B; 1.5–9 min, linear gradient from 2% to 50% B; 9–14 min, linear gradient from 50% to 95% B; hold at 95% B for 3 min.
Flow Rate:300 μL/min
Solvent A:100% Water; 5 mM Ammonium Acetate
Solvent B:100% Acetonitrile
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN007126
Analysis Type:MS
Chromatography ID:CH005415
Num Factors:1
Num Metabolites:14
Units:peak area
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