Summary of Study ST002382

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 PR001532. The data can be accessed directly via it's Project DOI: 10.21228/M8P11T This work is supported by NIH grant, U2C- DK119886.

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Study IDST002382
Study TitleDeep multi-omic profiling reveals extensive mitochondrial remodeling driven by glycemia in early diabetic kidney disease
Study SummaryChanges in mitochondrial energy metabolism are thought to be central to the development of diabetic kidney disease (DKD); however, whether this response is explicitly driven by systemic glucose concentrations remains unknown. Here, we show that titrating blood glucose concentrations in vivo directly impacts mitochondrial morphology and bioenergetics and remodels the mitochondrial proteome in the kidney in early DKD. Mitoproteomic analysis revealed profound metabolic disturbances induced by severe hyperglycemia, including upregulation of enzymes involved in the TCA cycle and fatty acid metabolism, enhanced ketogenesis as well as extensive dysregulation of the mitochondrial SLC25 carrier family. The metabolite and lipid landscape were perturbed by severe hyperglycemia; untargeted metabolomics and lipidomics confirmed the enrichment of TCA cycle metabolites, an increase in triglyceride concentrations, and extensive and specific cardiolipin remodeling. Lowering blood glucose to moderate hyperglycemia stabilized all three omic landscapes, partially prevented changes in mitochondrial morphology and bioenergetics, and improved kidney injury. This study provides insights into altered substrate utilization and energy generation in the kidney early in diabetes, during moderate and severe hyperglycemia and has implications for therapeutic strategies aiming at the reinvigoration of mitochondrial function and signaling in diabetes.
Institute
University of Melbourne
Last NameCaruana
First NameNikeisha
Address30 Flemington Rd, Parkville VIC 3052
Emailnikeisha.caruana@unimelb.edu.au
Phone0383442219
Submit Date2022-11-09
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-12-27
Release Version1
Nikeisha Caruana Nikeisha Caruana
https://dx.doi.org/10.21228/M8P11T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001532
Project DOI:doi: 10.21228/M8P11T
Project Title:Deep multi-omic profiling reveals extensive mitochondrial remodeling driven by glycemia in early diabetic kidney disease
Project Summary:Changes in mitochondrial energy metabolism are thought to be central to the development of diabetic kidney disease (DKD); however, whether this response is explicitly driven by systemic glucose concentrations remains unknown. Here, we show that titrating blood glucose concentrations in vivo directly impacts mitochondrial morphology and bioenergetics and remodels the mitochondrial proteome in the kidney in early DKD. Mitoproteomic analysis revealed profound metabolic disturbances induced by severe hyperglycemia, including upregulation of enzymes involved in the TCA cycle and fatty acid metabolism, enhanced ketogenesis as well as extensive dysregulation of the mitochondrial SLC25 carrier family. The metabolite and lipid landscape were perturbed by severe hyperglycemia; untargeted metabolomics and lipidomics confirmed the enrichment of TCA cycle metabolites, an increase in triglyceride concentrations, and extensive and specific cardiolipin remodeling. Lowering blood glucose to moderate hyperglycemia stabilized all three omic landscapes, partially prevented changes in mitochondrial morphology and bioenergetics, and improved kidney injury. This study provides insights into altered substrate utilization and energy generation in the kidney early in diabetes, during moderate and severe hyperglycemia and has implications for therapeutic strategies aiming at the reinvigoration of mitochondrial function and signaling in diabetes.
Institute:University of Melbourne
Last Name:Caruana
First Name:Nikeisha
Address:30 Flemington Rd, Parkville VIC, Melbourne, Victoria, 3052, Australia
Email:nikeisha.caruana@unimelb.edu.au
Phone:8344 2219

Subject:

Subject ID:SU002471
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA237835UNK-0046_6blank
SA237836UNK-0035_5blank
SA237837UNK-0024_4blank
SA237838UNK-0053_7blank
SA237839UNK-0054_8blank
SA237840UNK-0054_2blank
SA237841UNK-0053_9blank
SA237842UNK-0013_3blank
SA237783CG_740CTRL
SA237784CG_739CTRL
SA237785CG_734CTRL
SA237786CG_753CTRL
SA237787CGrerun_754CTRL
SA237788CG_755CTRL
SA237789CGrerun_755CTRL
SA237790CG_754CTRL
SA237791CG_722CTRL
SA237792CG_730CTRL
SA237793CG_710CTRL
SA237794CG_704CTRL
SA237795CG_717CTRL
SA237796CG_716CTRL
SA237797CG_749MHG
SA237798CG_748MHG
SA237799CG_725MHG
SA237800CG_714MHG
SA237801CGrerun_752MHG
SA237802CG_752MHG
SA237803CG_711MHG
SA237804CG_712MHG
SA237805CG_713MHG
SA237806CG_720MHG
SA237807CG_744MHG
SA237808CG_737MHG
SA237809CG_724MHG
SA237810UNK-0047_rerunQC
SA237811UNK-0041QC
SA237812UNK-0052_rerunQC
SA237813UNK-0052QC
SA237814UNK-0003QC
SA237815UNK-0047QC
SA237816UNK-0030QC
SA237817UNK-0019QC
SA237818UNK-0014QC
SA237819UNK-0008QC
SA237820UNK-0025QC
SA237821UNK-0036QC
SA237822CG_746SHG
SA237823CG_728SHG
SA237824CG_731SHG
SA237825CG_732SHG
SA237826CG_733SHG
SA237827CG_727SHG
SA237828CG_726SHG
SA237829CG_715SHG
SA237830CG_719SHG
SA237831CG_723SHG
SA237832CG_745SHG
SA237833CGrerun_746SHG
SA237834CG_701SHG
Showing results 1 to 60 of 60

Collection:

Collection ID:CO002464
Collection Summary:Metabolite extraction was carried out as previously described (96). Briefly, ~20-30 mg of kidney cortex was homogenized under cryogenic conditions in cryomill tubes containing beads for homogenization (Precellys bead-mill with a Cryolys attachment, Bertin Technologies, France) and 600 mL of 3:1 methanol:water (v/v) containing 0.5 nmol 13C6-sorbitol and 5 nmol 13C5,15N-valine as internal standards. Homogenates (480 mL) were subsequently vortexed in fresh Eppendorf tubes containing 120 ml chloroform. The resultant extracts were centrifuged to pellet cell debris and precipitated protein. The supernatant was used for subsequent analysis. In addition, an aliquot from each sample was pooled and re-aliquoted to generate pooled biological quality controls (PBQC). Samples and PBQCs were evaporated dry by speed vacuum centrifugation and then derivatized online using the Shimadzu AOC6000 autosampler robot with methoxyamine hydrochloride (30 mg/mL in pyridine) and N, O - bis (trimethylsilyl) trifluoroacetamide [BSTFA] + 1% chlorotrimethylsilane [TMCS] (both Thermo Fisher Scientific, Waltham, USA). Samples were left for 1 h before 1 µL was injected onto the GC column using a hot needle technique. Split (1:10) injections were performed for each sample.
Sample Type:Kidney

Treatment:

Treatment ID:TR002483
Treatment Summary:Male Sprague Dawley rats were housed in groups of three rats per cage in a temperature-controlled environment, with a 12 h light/dark cycle and ad libitum access to food and water. Experimental diabetes was induced in six week old male Sprague Dawley rats (200-250 g, n = 35) by i.v. injection of streptozotocin (55 mg/kg, sodium citrate buffer pH 4.5) following an overnight fast, as previously described (80). One group of rats received citrate buffer vehicle (0.42% in sterile saline, pH 4.5) as a non-diabetic control with normal blood glucose (NG) (n = 16). One week following STZ treatment, diabetic rats were further assigned to two groups: standard insulin therapy (n = 17 rats), resulting in severe hyperglycemia (SHG) and intensive insulin therapy (n = 19 rats), resulting in moderate hyperglycemia (MHG) using a single daily insulin injection (long-lasting Humulin NPH; Eli Lilly, Indianapolis, USA) to titrate blood glucose levels to >28 mM (1-2 units, s.c. per day) and ∼20 mM (6-7 units, s.c. per day) as required, respectively. Blood glucose and body weight were monitored weekly. Blood glucose was measured using a handheld glucometer (Accutrend; Boehringer Manheim Biochemica, Manheim, Germany) during the study time course. After the completion of the study, plasma glucose was measured using a colorimetric glucose assay kit from Cayman Chemical Company (Ann Arbor, MI, USA), performed according to the manufacturer’s instructions. Hemoglobin A1c (HbA1c) was determined by a Cobas Integra 400 autoanalyzer (Roche Diagnostics Corporation, USA). Plasma C-peptide was determined using a commercially available ELISA kit (Alpco, Salem, NH, USA) according to the manufacturer’s instructions. In the final week of the study, rats were placed individually into metabolic cages (Iffa Credo, L’Arbresele, France) for 24 hours to collect urine.

Sample Preparation:

Sampleprep ID:SP002477
Sampleprep Summary:The GC-MS system consisted of an AOC6000 autosampler, a 2030 Shimadzu gas chromatograph and a TQ8040 quadrupole mass spectrometer (Shimadzu, Japan), which was tuned according to the manufacturer’s recommendations using tris-(perfluorobutyl)-amine (CF43). GC-MS was performed on a 30 m Agilent DB-5 column with 1 µm film thickness and 0.25 mm internal diameter. The injection temperature (Inlet) and the MS transfer line were both set at 280°C and the ion source adjusted to 200°C. Helium was used as the carrier gas at a flow rate of 1 mL/min and argon gas was used as the collision cell gas to generate the multiple reaction monitoring (MRM) product ion. The analysis was performed under the following temperature program; start at injection 100°C, a hold for 4 minutes followed by a 10°C min-1 oven temperature ramp to 320°C followed by a final hold off of 11 minutes. Approximately 520 quantifying MRM targets were collected using Shimadzu Smart Database along with qualifier for each target, which covers about 350 endogenous metabolites and multiple 13C labelled internal standards. Both chromatograms and MRMs were evaluated using the Shimadzu GCMS browser and LabSolutions Insight software.

Combined analysis:

Analysis ID AN003881
Analysis type MS
Chromatography type GC
Chromatography system Shimadzu 2030
Column Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Shimazu TQ8040
Ion Mode UNSPECIFIED
Units Peak area

Chromatography:

Chromatography ID:CH002875
Instrument Name:Shimadzu 2030
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS003621
Analysis ID:AN003881
Instrument Name:Shimazu TQ8040
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:The GC-MS system consisted of an AOC6000 autosampler, a 2030 Shimadzu gas chromatograph and a TQ8040 quadrupole mass spectrometer (Shimadzu, Japan), which was tuned according to the manufacturer’s recommendations using tris-(perfluorobutyl)-amine (CF43). GC-MS was performed on a 30 m Agilent DB-5 column with 1 µm film thickness and 0.25 mm internal diameter. The injection temperature (Inlet) and the MS transfer line were both set at 280°C and the ion source adjusted to 200°C. Helium was used as the carrier gas at a flow rate of 1 mL/min and argon gas was used as the collision cell gas to generate the multiple reaction monitoring (MRM) product ion. The analysis was performed under the following temperature program; start at injection 100°C, a hold for 4 minutes followed by a 10°C min-1 oven temperature ramp to 320°C followed by a final hold off of 11 minutes. Approximately 520 quantifying MRM targets were collected using Shimadzu Smart Database along with qualifier for each target, which covers about 350 endogenous metabolites and multiple 13C labelled internal standards. Both chromatograms and MRMs were evaluated using the Shimadzu GCMS browser and LabSolutions Insight software.
Ion Mode:UNSPECIFIED
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