Summary of Study ST003751

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 PR002335. The data can be accessed directly via it's Project DOI: 10.21228/M8T25X This work is supported by NIH grant, U2C- DK119886.

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Study IDST003751
Study TitleComprehensive Lipidomic Analysis Identifies Critical Lipid and Metabolic Pathway Shifts in Alport Syndrome
Study SummaryAlport syndrome (AS) is a hereditary kidney disease caused by COL4A3-5 gene mutations, leading to glomerular basement membrane abnormalities. While the genetic and structural aspects of AS are well established, the mechanisms linking collagen IV defects to podocyte injury remain incompletely understood. Emerging evidence suggests that lipotoxicity and lipid dysregulation may play a pivotal role in mediating podocyte damage in AS, akin to its established role in diabetic kidney disease (DKD). We sought to identify plasma and urine lipid alterations in autosomal dominant and X-linked AS compared with DKD and healthy controls. Using liquid chromatography coupled to mass spectrometry (LC-MS), we annotated 580 and 203 lipid species in plasma and urine, respectively. Volcano plot and ROC analyses (AUC ≥ 0.80) identified key lipids, including urinary HexCer 18:0(3O)/24:0(2OH) and CAR 12:0. These analyses highlighted the most relevant lipotoxic pathways, which may warrant deeper investigation for drug development in AS. Compared to controls, AS exhibited unbalanced sphingolipid catabolism, ceramide overload, and impaired fatty acid β-oxidation, alongside phospholipid and cholesterol imbalances suggestive of compromised ABCA1-mediated lipid efflux and mitochondrial dysfunction. Comparisons with DKD indicated a shared lipotoxic environment with ceramide elevation and disrupted fatty acid metabolism. However, disease-specific adaptations emerged, with severe ABCA1 dysfunction and marked phospholipid/cholesterol derangements in DKD, whereas AS showed pronounced sphingomyelin depletion. These findings demonstrate that AS involves distinct lipidomic disruptions and underscore shared lipotoxic mechanisms. This improved understanding of disease-specific lipid imbalances provides new potential therapeutic targets to mitigate podocyte injury and slow progression of AS.
Institute
Universidad CEU San Pablo
DepartmentCentro de Metabolómica y Bioanálisis (CEMBIO)
Last NameGonzález
First NameCarolina
Addresskm 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501
Emailcarolina.gonzalezriano@ceu.es
Phone646251045
Submit Date2025-02-21
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2025-03-17
Release Version1
Carolina González Carolina González
https://dx.doi.org/10.21228/M8T25X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002335
Project DOI:doi: 10.21228/M8T25X
Project Title:Comprehensive Lipidomic Analysis Identifies Critical Lipid and Metabolic Pathway Shifts in Alport Syndrome
Project Summary:Alport syndrome (AS) is a hereditary kidney disease caused by COL4A3-5 gene mutations, leading to glomerular basement membrane abnormalities. While the genetic and structural aspects of AS are well established, the mechanisms linking collagen IV defects to podocyte injury remain incompletely understood. Emerging evidence suggests that lipotoxicity and lipid dysregulation may play a pivotal role in mediating podocyte damage in AS, akin to its established role in diabetic kidney disease (DKD). We sought to identify plasma and urine lipid alterations in autosomal dominant (ADAS) and X-linked AS (XLAS) compared with DKD and healthy controls. Using liquid chromatography coupled to mass spectrometry (LC-MS), we annotated 580 and 203 lipid species in plasma and urine, respectively. Volcano plot and ROC analyses (AUC ≥ 0.80) identified key lipids, including urinary HexCer 18:0(3O)/24:0(2OH) and CAR 12:0. These analyses highlighted the most relevant lipotoxic pathways, which may warrant deeper investigation for drug development in AS. Compared to controls, AS exhibited unbalanced sphingolipid catabolism, ceramide overload, and impaired fatty acid β-oxidation, alongside phospholipid and cholesterol imbalances suggestive of compromised ABCA1-mediated lipid efflux and mitochondrial dysfunction. Comparisons with DKD indicated a shared lipotoxic environment with ceramide elevation and disrupted fatty acid metabolism. However, disease-specific adaptations emerged, with severe ABCA1 dysfunction and marked phospholipid/cholesterol derangements in DKD, whereas AS showed pronounced sphingomyelin depletion. These findings demonstrate that AS involves distinct lipidomic disruptions and underscore shared lipotoxic mechanisms. This improved understanding of disease-specific lipid imbalances provides new potential therapeutic targets to mitigate podocyte injury and slow progression of AS.
Institute:Universidad CEU San Pablo
Department:Centro de MEtabolómica y Bioanálisis (CEMBIO)
Last Name:Gonzalez-Riano
First Name:Carolina
Address:Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Boadilla del Monte, Madrid, 28668, Spain
Email:car.gonzalez@ceindo.ceu.es
Phone:00 34 91 3724753
Funding Source:This work was supported by grants from the following entities: The Ministry of Science and Innovation of Spain (MICINN) and the European Regional Development Fund FEDER, grant number PID2021-122490NB-I00 (CGR, BF, SM and CB). Instituto de Salud Carlos III and the European Union’s European Regional Development Fund grants PI19/01624 and PI24/01711. European Union-Next generation EU, Mechanism for Recovery and Resilence (MRR) RICORS (RD21/0005/0030; RD24/0004/0014) (GFJ, ASF). Spanish Society of Nephrology (AS, TBB).

Subject:

Subject ID:SU003884
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Sample source Condition
SA408391CA_2_5_PlasmaPlasma ADAS
SA408392CA_2_0_PlasmaPlasma ADAS
SA408393CA_2_1_PlasmaPlasma ADAS
SA408394CA_2_2_PlasmaPlasma ADAS
SA408395CA_2_3_PlasmaPlasma ADAS
SA408396CA_2_4_PlasmaPlasma ADAS
SA408397CA_2_6_PlasmaPlasma ADAS
SA408398CA_2_7_PlasmaPlasma ADAS
SA408399CA_2_8_PlasmaPlasma ADAS
SA408400CA_2_9_PlasmaPlasma ADAS
SA408401CA_2_10_PlasmaPlasma ADAS
SA408402CA_2_11_PlasmaPlasma ADAS
SA408403CO_4_7_PlasmaPlasma Control
SA408404CO_4_13_PlasmaPlasma Control
SA408405CO_4_12_PlasmaPlasma Control
SA408406CO_4_11_PlasmaPlasma Control
SA408407CO_4_10_PlasmaPlasma Control
SA408408CO_4_8_PlasmaPlasma Control
SA408409CO_4_0_PlasmaPlasma Control
SA408410CO_4_6_PlasmaPlasma Control
SA408411CO_4_5_PlasmaPlasma Control
SA408412CO_4_4_PlasmaPlasma Control
SA408413CO_4_3_PlasmaPlasma Control
SA408414CO_4_2_PlasmaPlasma Control
SA408415CO_4_1_PlasmaPlasma Control
SA408416CO_4_15_PlasmaPlasma Control
SA408417CO_4_14_PlasmaPlasma Control
SA408418CO_4_9_PlasmaPlasma Control
SA408419CO_4_16_PlasmaPlasma Control
SA408420CO_4_18_PlasmaPlasma Control
SA408421CO_4_19_PlasmaPlasma Control
SA408422CO_4_17_PlasmaPlasma Control
SA408423CO_1_14_PlasmaPlasma DKD
SA408424CO_1_7_PlasmaPlasma DKD
SA408425CO_1_6_PlasmaPlasma DKD
SA408426CO_1_5_PlasmaPlasma DKD
SA408427CO_1_4_PlasmaPlasma DKD
SA408428CO_1_3_PlasmaPlasma DKD
SA408429CO_1_2_PlasmaPlasma DKD
SA408430CO_1_1_PlasmaPlasma DKD
SA408431CO_1_0_PlasmaPlasma DKD
SA408432CO_1_11_PlasmaPlasma DKD
SA408433CO_1_12_PlasmaPlasma DKD
SA408434CO_1_13_PlasmaPlasma DKD
SA408435CO_1_10_PlasmaPlasma DKD
SA408436CO_1_8_PlasmaPlasma DKD
SA408437CO_1_9_PlasmaPlasma DKD
SA408438QC_11_PlasmaPlasma Quality Control
SA408439QC_1_PlasmaPlasma Quality Control
SA408440QC_2_PlasmaPlasma Quality Control
SA408441QC_3_PlasmaPlasma Quality Control
SA408442QC_4_PlasmaPlasma Quality Control
SA408443QC_5_PlasmaPlasma Quality Control
SA408444QC_6_PlasmaPlasma Quality Control
SA408445QC_7_PlasmaPlasma Quality Control
SA408446QC_23_PlasmaPlasma Quality Control
SA408447QC_22_PlasmaPlasma Quality Control
SA408448QC_12_PlasmaPlasma Quality Control
SA408449QC_20_PlasmaPlasma Quality Control
SA408450QC_19_PlasmaPlasma Quality Control
SA408451QC_18_PlasmaPlasma Quality Control
SA408452QC_17_PlasmaPlasma Quality Control
SA408453QC_16_PlasmaPlasma Quality Control
SA408454QC_15_PlasmaPlasma Quality Control
SA408455QC_14_PlasmaPlasma Quality Control
SA408456QC_13_PlasmaPlasma Quality Control
SA408457QC_8_PlasmaPlasma Quality Control
SA408458QC_9_PlasmaPlasma Quality Control
SA408459QC_10_PlasmaPlasma Quality Control
SA408460QC_21_PlasmaPlasma Quality Control
SA408461CA_1_1_PlasmaPlasma XLAS
SA408462CA_1_0_PlasmaPlasma XLAS
SA408463CA_1_50_PlasmaPlasma XLAS
SA408464CA_1_13_PlasmaPlasma XLAS
SA408465CA_1_22_PlasmaPlasma XLAS
SA408466CA_1_21_PlasmaPlasma XLAS
SA408467CA_1_20_PlasmaPlasma XLAS
SA408468CA_1_19_PlasmaPlasma XLAS
SA408469CA_1_18_PlasmaPlasma XLAS
SA408470CA_1_17_PlasmaPlasma XLAS
SA408471CA_1_16_PlasmaPlasma XLAS
SA408472CA_1_15_PlasmaPlasma XLAS
SA408473CA_1_14_PlasmaPlasma XLAS
SA408474CA_1_12_PlasmaPlasma XLAS
SA408475CA_1_24_PlasmaPlasma XLAS
SA408476CA_1_11_PlasmaPlasma XLAS
SA408477CA_1_10_PlasmaPlasma XLAS
SA408478CA_1_9_PlasmaPlasma XLAS
SA408479CA_1_8_PlasmaPlasma XLAS
SA408480CA_1_7_PlasmaPlasma XLAS
SA408481CA_1_6_PlasmaPlasma XLAS
SA408482CA_1_5_PlasmaPlasma XLAS
SA408483CA_1_3_PlasmaPlasma XLAS
SA408484CA_1_2_PlasmaPlasma XLAS
SA408485CA_1_49_PlasmaPlasma XLAS
SA408486CA_1_23_PlasmaPlasma XLAS
SA408487CA_1_4_PlasmaPlasma XLAS
SA408488CA_1_25_PlasmaPlasma XLAS
SA408489CA_1_38_PlasmaPlasma XLAS
SA408490CA_1_47_PlasmaPlasma XLAS
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 241

Collection:

Collection ID:CO003877
Collection Summary:We collected urine and plasma samples from 63 case subjects with a diagnosis of ADAS (n=51) or XLAS (n=12). The inclusion criteria were a genetic analysis with pathogenic or likely pathogenic variants in COL4A3-5 with the presence of hematuria. The same samples were collected from 15 patients with biopsy-proven diabetic kidney disease (DKD) and from 20 healthy volunteers, who served as control groups. Clinical and demographic data were collected from the medical records. The study was conducted in accordance with the principles outlined in the Declaration of Helsinki with approval from the ethics committee of Hospital Universitario 12 de Octubre. Written consent was obtained from patients at the time of sample collection.
Sample Type:Plasma and urine

Treatment:

Treatment ID:TR003893
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP003890
Sampleprep Summary:PLASMA SAMPLES: Plasma samples underwent deproteinization and lipid extraction using an all-in-one single extraction method employing a solvent mixture composed of MeOH/MTBE/CHCl3 (4:3:3, v/v/v) for the isolation of non-polar lipids(1). The lipid extraction method started with thawing the samples on ice followed by a 2 min vortex homogenization. Subsequently, 40 µL of the plasma sample was mixed with 800 µL of the solvent mixture – also containing the internal standards (IS): 1 ppm C17-sphinganine and 2 ppm d31-palmitic acid –. The resulting mixture was vortex-mixed for 20 min followed by sample centrifugation at 16,100 x g for 10 min at 15 °C. Then, 300 µL of the supernatant were transferred to LC Chromacol (Thermo Fisher Scientific, Madrid, Sain) vials with insert and centrifuged at 16,100 x g for 10 min at 15 °C prior to the analysis. Blank solutions were prepared containing 40 µL of H2O and 800 µL of the solvent mixture and same procedure was followed. For quality control (QC) samples, three independent pools were prepared by pipetting 10 µL of each sample – for QCTOTAL –, 10 µL of Alport samples (cases 1 and 2) – for QCCASES –, and 10 µL of control samples (DM patients and healthy individuals) – for QCCONTROL–. Then 40 µL of each of the pools were transferred to Eppendorf™ tubes and 800 µL of the solvent mixture were added. The same procedure as in sample preparation was followed. Both blank and QC samples were processed in parallel with the rest of plasma samples. URINE SAMPLES: Urine samples were prepared at the "Centro de Metabolómica y Bioanálisis, CEMBIO" (Madrid, Spain), following a monophasic extraction method (MeOH:EtOH (1:1, v/v)), tested and developed in our laboratory to obtain the urine lipidomics fingerprint. Briefly, the samples were thawed on ice and then vortex-mixed for 2 min. On ice, 100 µL of urine sample was mixed with 300 µL of a cold (-20 °C) mixture of MeOH:EtOH (1:1, v/v), and a mixture of nonendogenous internal standards (C17-Sphinganine at 1 ppm and d31-palmitic acid at 2 ppm). Samples were vortex-mixed for 30 minutes. After centrifugation for 10 min at 16.1 rpm at 15 °C, 100 µL of the supernatant was collected and transferred into an HPLC-MS vial with a glass insert. Finally, all the vials were centrifuged at 2000g at 15 °C for 10 min before injecting into the system.

Combined analysis:

Analysis ID AN006158 AN006159 AN006160 AN006161
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
MS Type ESI ESI ESI ESI
MS instrument type QTOF QTOF QTOF QTOF
MS instrument name Agilent 6545 QTOF Agilent 6545 QTOF Agilent 6546 QTOF Agilent 6546 QTOF
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH004678
Chromatography Summary:The Agilent 1290 Infinity II Multisampler system was employed with a multiwash option, and 1 µL of extracted samples was injected. The multisampler temperature was maintained at 15 °C to ensure the stability of compounds and prevent lipid precipitation. For chromatographic separation, an Agilent InfinityLab Poroshell 120 ECC18 (3.0 × 100 mm, 2.7 µm) (Agilent Technologies) column and a compatible guard column (Agilent InfinityLab Poroshell 120 ECC18, 3.0 × 5 mm, 2.7 µm) were employed and held at 50 °C. The chromatography gradient was initiated at 70% of B at 0–1 min, increased to 86% at 3.5–10 min, and reached 100% B at 11–17 min. The initial conditions were restored by minute 17, followed by a 2-minute re-equilibration, resulting in a total running time of 19 min. The mobile phases for positive and negative ionization modes comprised (A) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in a 9:1 water/methanol ratio and (B) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in a 2:3:5 acetonitrile/methanol/isopropanol ratio. The flow rate was maintained at 0.6 mL/min. The multisampler's multiwash strategy involved a methanol:isopropanol (50:50, v/v) mixture with a 15-second wash time and an aqueous:organic phases (30:70, v/v) mixture to achieve the initial conditions.
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:50 °C
Flow Gradient:Started at 70% of B at 0–1 min, 1-3.5min linear from 70% B to 86% B, 86% B at 3.5–10 min, 10-11min linear from 86% B to 100% B, and 100% B at 11–17 min
Flow Rate:0.6 mL/min
Solvent A:90% water/10% methanol; 10 mM ammonium acetate; 0.2 mM ammonium fluoride
Solvent B:20% acetonitrile/30% methanol/50% isopropanol; 10 mM ammonium acetate; 0.2 mM ammonium fluoride
Chromatography Type:Reversed phase

MS:

MS ID:MS005863
Analysis ID:AN006158
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 40 to 1700 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds was infused throughout the whole analysis: purine (C5H4N4) at m/z 121.0509 and HP-0921 (C18H18O6N3P3F24) at m/z 922.0098. These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction.
Ion Mode:POSITIVE
  
MS ID:MS005864
Analysis ID:AN006159
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 40 to 1700 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds was infused throughout the whole analysis: purine (C5H4N4) at m/z 119.0363 and HP-0921 (C18H18O6N3P3F24) at m/z 980.0163 (HP-0921 + acetate). These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction.
Ion Mode:NEGATIVE
  
MS ID:MS005865
Analysis ID:AN006160
Instrument Name:Agilent 6546 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 40 to 1700 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds was infused throughout the whole analysis: purine (C5H4N4) at m/z 121.0509 and HP-0921 (C18H18O6N3P3F24) at m/z 922.0098. These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction.
Ion Mode:POSITIVE
  
MS ID:MS005866
Analysis ID:AN006161
Instrument Name:Agilent 6546 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 40 to 1700 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds was infused throughout the whole analysis: purine (C5H4N4) at m/z 119.0363 and HP-0921 (C18H18O6N3P3F24) at m/z 980.0163 (HP-0921 + acetate). These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction.
Ion Mode:NEGATIVE
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