Summary of Study ST002403
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 | ST002403 |
| Study Title | Deep multi-omic profiling reveals extensive mitochondrial remodeling driven by glycemia in early diabetic kidney disease (Mitochondria) |
| 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 transporter 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 | Baker Heart and Diabetes Institute |
| Laboratory | Metabolomics |
| Last Name | Huynh |
| First Name | Kevin |
| Address | 75 Commercial Road, Melbourne, 3004 |
| kevin.huynh@baker.edu.au | |
| Phone | 0385321537 |
| Submit Date | 2022-11-20 |
| Num Groups | 3 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-12-01 |
| 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: | SU002492 |
| 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 | group | type |
|---|---|---|---|
| SA240108 | #739_mito | black | mito |
| SA240109 | #704_mito | black | mito |
| SA240110 | #730_mito | black | mito |
| SA240111 | #740_mito | black | mito |
| SA240112 | #753_mito | black | mito |
| SA240113 | #755_mito | black | mito |
| SA240114 | #754_mito | black | mito |
| SA240115 | #722_mito | black | mito |
| SA240116 | #734_mito | black | mito |
| SA240117 | #716_mito | black | mito |
| SA240118 | #710_mito | black | mito |
| SA240119 | #717_mito | black | mito |
| SA240120 | #712_mito | blue | mito |
| SA240121 | #748_mito | blue | mito |
| SA240122 | #714_mito | blue | mito |
| SA240123 | #749_mito | blue | mito |
| SA240124 | #737_mito | blue | mito |
| SA240125 | #744_mito | blue | mito |
| SA240126 | #725_mito | blue | mito |
| SA240127 | #720_mito | blue | mito |
| SA240128 | #752_mito | blue | mito |
| SA240129 | #713_mito | blue | mito |
| SA240130 | #724_mito | blue | mito |
| SA240131 | #711_mito | blue | mito |
| SA240132 | #701_mito | red | mito |
| SA240133 | #745_mito | red | mito |
| SA240134 | #733_mito | red | mito |
| SA240135 | #746_mito | red | mito |
| SA240136 | #719_mito | red | mito |
| SA240137 | #726_mito | red | mito |
| SA240138 | #723_mito | red | mito |
| SA240139 | #727_mito | red | mito |
| SA240140 | #728_mito | red | mito |
| SA240141 | #732_mito | red | mito |
| SA240142 | #731_mito | red | mito |
| SA240143 | #715_mito | red | mito |
| Showing results 1 to 36 of 36 |
Collection:
| Collection ID: | CO002485 |
| Collection Summary: | Mitochondria were isolated by differential centrifugation. Freshly harvested renal cortex (50 mg) was finely minced and gently homogenized with glass Teflon tissue grinders in 2 ml ice-cold isolation medium, pH 7.2 (70 mM sucrose, 210 mM mannitol, 5 mM HEPES, 1mM EGTA). The homogenate was centrifuged at 800 g for 5 min at 4C and the resulting supernatant was centrifuged at 8,000 g for 10 min at 4C. After washing with 0.5 ml ice-cold isolation buffer, the mitochondrial pellet was resuspended in 200 l ice-cold isolation medium. Total protein was determined by the bicinchoninic acid method according to the manufacturer’s instructions (BCA Protein Assay Kit, Pierce-Thermo Fisher Scientific, Melbourne, Australia). |
| Sample Type: | Mitochondria |
Treatment:
| Treatment ID: | TR002504 |
| 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 (79). 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. |
Sample Preparation:
| Sampleprep ID: | SP002498 |
| Sampleprep Summary: | Lipidomic analysis. Lipids were extracted from mitochondrial isolates using a single-phase chloroform/methanol extraction as described previously (87). Briefly, 20 volumes of chloroform:methanol (2:1) were added to the sample along with a series of internal standards. Samples were vortexed and centrifuged on a rotary mixer for 10 min. Following 30 min of sonication on a sonicator bath, samples were rested for 20 min before being centrifuged at 13,000 g for 10 min. Supernatants were transferred into a 96 well plate, dried down, and reconstituted in 50 µL H2O saturated butanol, before being sonicated for 10 min. Following the addition of 50 µL of methanol with 10 mM ammonium formate, samples were centrifuged at 4000 rpm on a plate centrifuge and transferred into glass vials with inserts for mass spectrometry analysis. |
Combined analysis:
| Analysis ID | AN003917 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ |
| Ion Mode | POSITIVE |
| Units | pmol per mg |
Chromatography:
| Chromatography ID: | CH002899 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 60 |
| Flow Gradient: | Non-linear |
| Flow Rate: | 0.4ml/minute |
| Solvent A: | 50% water/30% acetonitrile/20% isopropanol; 10mM ammonium formate |
| Solvent B: | 1% water/9% acetonitrile/90% isopropanol; 10mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003656 |
| Analysis ID: | AN003917 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Lipid extraction. Muscle homogenates/mitochondrial isolates were extracted using a modified single-phase chloroform/methanol extraction as described previously [Weir et al. 2016]. In brief, 20 volumes of chloroform:methanol (2:1) was added to the sample along with a series of internal standards. Samples were vortexed and spun on a rotoary mixer for 10 minutes. After sonication on a sonicator bath for 30 minutes, samples were rested for a further 20 minutes prior to centrifugation at 13,000 x g for 10 minutes. Supernatants were transferred into a 96 well plated, dried down and reconstituted in 50L water saturated butanol and sonicated for 10 minutes. After the addition of 50l of methanol with 10mM ammonium formate, the samples were spun down again at 4000RPM on a plate centrifuge (Heraeus multifuge 1S-R, ThermoFisher) and transferred into glass vials with inserts for mass spectrometry analysis. Targeted lipidomics analysis. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed according to previously published methods, with slight modification for tissue samples [Huynh et al. 2019]. Sample extracts were analysed using either (i) a 4000 QTRAP mass spectrometer (Sciex) for cardiolipins as described preciously [Tan et al. 2020] or (ii) an Agilent 6490 QQQ mass spectrometer all other lipid species. Lipids run on the Agilent 6490 were measured using scheduled multiple reaction monitoring with the following conditions: Isolation widths for Q1 and Q3 were set to “unit” resolution (0.7 amu), gas temperature, 150°C, nebulizer 20psi, sheath gas temperature 200°C, gas flow rate 17L/min, capillary voltage 3500V and sheath gas flow 10L/min. The list of MRMs used and chromatographic conditions were extensively described previously [Huynh et al. 2019] |
| Ion Mode: | POSITIVE |
