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.
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.
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Study ID | ST003751 |
Study Title | Comprehensive Lipidomic Analysis Identifies Critical Lipid and Metabolic Pathway Shifts in Alport Syndrome |
Study 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 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 |
Department | Centro de Metabolómica y Bioanálisis (CEMBIO) |
Last Name | González |
First Name | Carolina |
Address | km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501 |
carolina.gonzalezriano@ceu.es | |
Phone | 646251045 |
Submit Date | 2025-02-21 |
Raw Data Available | Yes |
Raw Data File Type(s) | d |
Analysis Type Detail | LC-MS |
Release Date | 2025-03-17 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|---|
SA408391 | CA_2_5_Plasma | Plasma | ADAS |
SA408392 | CA_2_0_Plasma | Plasma | ADAS |
SA408393 | CA_2_1_Plasma | Plasma | ADAS |
SA408394 | CA_2_2_Plasma | Plasma | ADAS |
SA408395 | CA_2_3_Plasma | Plasma | ADAS |
SA408396 | CA_2_4_Plasma | Plasma | ADAS |
SA408397 | CA_2_6_Plasma | Plasma | ADAS |
SA408398 | CA_2_7_Plasma | Plasma | ADAS |
SA408399 | CA_2_8_Plasma | Plasma | ADAS |
SA408400 | CA_2_9_Plasma | Plasma | ADAS |
SA408401 | CA_2_10_Plasma | Plasma | ADAS |
SA408402 | CA_2_11_Plasma | Plasma | ADAS |
SA408403 | CO_4_7_Plasma | Plasma | Control |
SA408404 | CO_4_13_Plasma | Plasma | Control |
SA408405 | CO_4_12_Plasma | Plasma | Control |
SA408406 | CO_4_11_Plasma | Plasma | Control |
SA408407 | CO_4_10_Plasma | Plasma | Control |
SA408408 | CO_4_8_Plasma | Plasma | Control |
SA408409 | CO_4_0_Plasma | Plasma | Control |
SA408410 | CO_4_6_Plasma | Plasma | Control |
SA408411 | CO_4_5_Plasma | Plasma | Control |
SA408412 | CO_4_4_Plasma | Plasma | Control |
SA408413 | CO_4_3_Plasma | Plasma | Control |
SA408414 | CO_4_2_Plasma | Plasma | Control |
SA408415 | CO_4_1_Plasma | Plasma | Control |
SA408416 | CO_4_15_Plasma | Plasma | Control |
SA408417 | CO_4_14_Plasma | Plasma | Control |
SA408418 | CO_4_9_Plasma | Plasma | Control |
SA408419 | CO_4_16_Plasma | Plasma | Control |
SA408420 | CO_4_18_Plasma | Plasma | Control |
SA408421 | CO_4_19_Plasma | Plasma | Control |
SA408422 | CO_4_17_Plasma | Plasma | Control |
SA408423 | CO_1_14_Plasma | Plasma | DKD |
SA408424 | CO_1_7_Plasma | Plasma | DKD |
SA408425 | CO_1_6_Plasma | Plasma | DKD |
SA408426 | CO_1_5_Plasma | Plasma | DKD |
SA408427 | CO_1_4_Plasma | Plasma | DKD |
SA408428 | CO_1_3_Plasma | Plasma | DKD |
SA408429 | CO_1_2_Plasma | Plasma | DKD |
SA408430 | CO_1_1_Plasma | Plasma | DKD |
SA408431 | CO_1_0_Plasma | Plasma | DKD |
SA408432 | CO_1_11_Plasma | Plasma | DKD |
SA408433 | CO_1_12_Plasma | Plasma | DKD |
SA408434 | CO_1_13_Plasma | Plasma | DKD |
SA408435 | CO_1_10_Plasma | Plasma | DKD |
SA408436 | CO_1_8_Plasma | Plasma | DKD |
SA408437 | CO_1_9_Plasma | Plasma | DKD |
SA408438 | QC_11_Plasma | Plasma | Quality Control |
SA408439 | QC_1_Plasma | Plasma | Quality Control |
SA408440 | QC_2_Plasma | Plasma | Quality Control |
SA408441 | QC_3_Plasma | Plasma | Quality Control |
SA408442 | QC_4_Plasma | Plasma | Quality Control |
SA408443 | QC_5_Plasma | Plasma | Quality Control |
SA408444 | QC_6_Plasma | Plasma | Quality Control |
SA408445 | QC_7_Plasma | Plasma | Quality Control |
SA408446 | QC_23_Plasma | Plasma | Quality Control |
SA408447 | QC_22_Plasma | Plasma | Quality Control |
SA408448 | QC_12_Plasma | Plasma | Quality Control |
SA408449 | QC_20_Plasma | Plasma | Quality Control |
SA408450 | QC_19_Plasma | Plasma | Quality Control |
SA408451 | QC_18_Plasma | Plasma | Quality Control |
SA408452 | QC_17_Plasma | Plasma | Quality Control |
SA408453 | QC_16_Plasma | Plasma | Quality Control |
SA408454 | QC_15_Plasma | Plasma | Quality Control |
SA408455 | QC_14_Plasma | Plasma | Quality Control |
SA408456 | QC_13_Plasma | Plasma | Quality Control |
SA408457 | QC_8_Plasma | Plasma | Quality Control |
SA408458 | QC_9_Plasma | Plasma | Quality Control |
SA408459 | QC_10_Plasma | Plasma | Quality Control |
SA408460 | QC_21_Plasma | Plasma | Quality Control |
SA408461 | CA_1_1_Plasma | Plasma | XLAS |
SA408462 | CA_1_0_Plasma | Plasma | XLAS |
SA408463 | CA_1_50_Plasma | Plasma | XLAS |
SA408464 | CA_1_13_Plasma | Plasma | XLAS |
SA408465 | CA_1_22_Plasma | Plasma | XLAS |
SA408466 | CA_1_21_Plasma | Plasma | XLAS |
SA408467 | CA_1_20_Plasma | Plasma | XLAS |
SA408468 | CA_1_19_Plasma | Plasma | XLAS |
SA408469 | CA_1_18_Plasma | Plasma | XLAS |
SA408470 | CA_1_17_Plasma | Plasma | XLAS |
SA408471 | CA_1_16_Plasma | Plasma | XLAS |
SA408472 | CA_1_15_Plasma | Plasma | XLAS |
SA408473 | CA_1_14_Plasma | Plasma | XLAS |
SA408474 | CA_1_12_Plasma | Plasma | XLAS |
SA408475 | CA_1_24_Plasma | Plasma | XLAS |
SA408476 | CA_1_11_Plasma | Plasma | XLAS |
SA408477 | CA_1_10_Plasma | Plasma | XLAS |
SA408478 | CA_1_9_Plasma | Plasma | XLAS |
SA408479 | CA_1_8_Plasma | Plasma | XLAS |
SA408480 | CA_1_7_Plasma | Plasma | XLAS |
SA408481 | CA_1_6_Plasma | Plasma | XLAS |
SA408482 | CA_1_5_Plasma | Plasma | XLAS |
SA408483 | CA_1_3_Plasma | Plasma | XLAS |
SA408484 | CA_1_2_Plasma | Plasma | XLAS |
SA408485 | CA_1_49_Plasma | Plasma | XLAS |
SA408486 | CA_1_23_Plasma | Plasma | XLAS |
SA408487 | CA_1_4_Plasma | Plasma | XLAS |
SA408488 | CA_1_25_Plasma | Plasma | XLAS |
SA408489 | CA_1_38_Plasma | Plasma | XLAS |
SA408490 | CA_1_47_Plasma | Plasma | XLAS |
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 |