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.

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	ST002382
Study Title	Deep multi-omic profiling reveals extensive mitochondrial remodeling driven by glycemia in early diabetic kidney disease
Study 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 3052
Email	nikeisha.caruana@unimelb.edu.au
Phone	0383442219
Submit Date	2022-11-09
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-12-27
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA237835	UNK-0046_6	blank
SA237836	UNK-0035_5	blank
SA237837	UNK-0024_4	blank
SA237838	UNK-0053_7	blank
SA237839	UNK-0054_8	blank
SA237840	UNK-0054_2	blank
SA237841	UNK-0053_9	blank
SA237842	UNK-0013_3	blank
SA237783	CG_740	CTRL
SA237784	CG_739	CTRL
SA237785	CG_734	CTRL
SA237786	CG_753	CTRL
SA237787	CGrerun_754	CTRL
SA237788	CG_755	CTRL
SA237789	CGrerun_755	CTRL
SA237790	CG_754	CTRL
SA237791	CG_722	CTRL
SA237792	CG_730	CTRL
SA237793	CG_710	CTRL
SA237794	CG_704	CTRL
SA237795	CG_717	CTRL
SA237796	CG_716	CTRL
SA237797	CG_749	MHG
SA237798	CG_748	MHG
SA237799	CG_725	MHG
SA237800	CG_714	MHG
SA237801	CGrerun_752	MHG
SA237802	CG_752	MHG
SA237803	CG_711	MHG
SA237804	CG_712	MHG
SA237805	CG_713	MHG
SA237806	CG_720	MHG
SA237807	CG_744	MHG
SA237808	CG_737	MHG
SA237809	CG_724	MHG
SA237810	UNK-0047_rerun	QC
SA237811	UNK-0041	QC
SA237812	UNK-0052_rerun	QC
SA237813	UNK-0052	QC
SA237814	UNK-0003	QC
SA237815	UNK-0047	QC
SA237816	UNK-0030	QC
SA237817	UNK-0019	QC
SA237818	UNK-0014	QC
SA237819	UNK-0008	QC
SA237820	UNK-0025	QC
SA237821	UNK-0036	QC
SA237822	CG_746	SHG
SA237823	CG_728	SHG
SA237824	CG_731	SHG
SA237825	CG_732	SHG
SA237826	CG_733	SHG
SA237827	CG_727	SHG
SA237828	CG_726	SHG
SA237829	CG_715	SHG
SA237830	CG_719	SHG
SA237831	CG_723	SHG
SA237832	CG_745	SHG
SA237833	CGrerun_746	SHG
SA237834	CG_701	SHG

Showing results 1 to 60 of 60

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.

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.

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