Summary of Study ST003347
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 PR002082. The data can be accessed directly via it's Project DOI: 10.21228/M8H24R 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 | ST003347 |
| Study Title | ADSL deficiency drives mitochondrial dysfunction and ERK2 dysregulation in a linear genotype to phenotype correlation |
| Study Summary | Adenylosuccinate lyase (ADSL) deficiency (ADSLd) is a rare autosomal recessive defect of purine metabolism associated with a wide range of clinical manifestations. Despite ADSL implication in purine synthesis, no additional molecular alterations have been identified as a cause of ADSLd besides the accumulation of toxic substrates. Here we uncover a novel association between ADSLd and mitochondrial dysfunction, which is characterized by an increase in fragmentation and reduction in respiration and ATP production. The extent of this mitochondrial dysfunction is directly proportional to the pathological manifestations of ADSLd, which are predominantly observed in tissues that rely heavily on mitochondria. Our analysis also unveils a striking defect in mitochondrial dynamics and transport, which are associated with the suppression of ERK2 and AKT function. Remarkably, the mitochondrial phenotype can be rescued in part by overexpression of a constitutive form of ERK2 or through the administration of purine intermediates. This scenario provides an alternative explanation of ADSLd onset, reorienting research towards developing innovative therapeutic strategies based on the restoration of mitochondrial metabolism. |
| Institute | Catholic University of the Sacred Heart |
| Last Name | Bordi |
| First Name | Matteo |
| Address | Largo Francesco Vito 1, Rome, Italy, 00168, Italy |
| matteo.bordi@unicatt.it | |
| Phone | +390630155135/5258 |
| Submit Date | 2024-07-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002082 |
| Project DOI: | doi: 10.21228/M8H24R |
| Project Title: | ADSL deficiency drives mitochondrial dysfunction and ERK2 dysregulation in a linear genotype to phenotype correlation |
| Project Summary: | Adenylosuccinate lyase (ADSL) deficiency (ADSLd) is a rare autosomal recessive defect of purine metabolism associated with a wide range of clinical manifestations. Despite ADSL implication in purine synthesis, no additional molecular alterations have been identified as a cause of ADSLd besides the accumulation of toxic substrates. Here we uncover a novel association between ADSLd and mitochondrial dysfunction, which is characterized by an increase in fragmentation and reduction in respiration and ATP production. The extent of this mitochondrial dysfunction is directly proportional to the pathological manifestations of ADSLd, which are predominantly observed in tissues that rely heavily on mitochondria. Our analysis also unveils a striking defect in mitochondrial dynamics and transport, which are associated with the suppression of ERK2 and AKT function. Remarkably, the mitochondrial phenotype can be rescued in part by overexpression of a constitutive form of ERK2 or through the administration of purine intermediates. This scenario provides an alternative explanation of ADSLd onset, reorienting research towards developing innovative therapeutic strategies based on the restoration of mitochondrial metabolism. |
| Institute: | Catholic University of the Sacred Heart |
| Last Name: | Bordi |
| First Name: | Matteo |
| Address: | Largo Francesco Vito 1, Rome, Italy, 00168, Italy |
| Email: | matteo.bordi@unicatt.it |
| Phone: | +390630155135/5258 |
Subject:
| Subject ID: | SU003468 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Sex |
|---|---|---|---|---|
| SA365169 | BT02-040 | Skin | A3V/R337X | F |
| SA365170 | BT02-039 | Skin | A3V/R337X | F |
| SA365171 | BT02-038 | Skin | A3V/R337X | F |
| SA365172 | BT02-037 | Skin | A3V/R337X | F |
| SA365173 | BT02-036 | Skin | A3V/R337X | F |
| SA365174 | BT02-021 | Skin | M26L/R396H | F |
| SA365175 | BT02-025 | Skin | M26L/R396H | F |
| SA365176 | BT02-023 | Skin | M26L/R396H | F |
| SA365177 | BT02-022 | Skin | M26L/R396H | F |
| SA365178 | BT02-024 | Skin | M26L/R396H | F |
| SA365179 | BT02-029 | Skin | M26L/R396H | M |
| SA365180 | BT02-027 | Skin | M26L/R396H | M |
| SA365181 | BT02-030 | Skin | M26L/R396H | M |
| SA365182 | BT02-028 | Skin | M26L/R396H | M |
| SA365183 | BT02-026 | Skin | M26L/R396H | M |
| SA365184 | BT02-035 | Skin | R309H/c.1191+5G->C | F |
| SA365185 | BT02-031 | Skin | R309H/c.1191+5G->C | F |
| SA365186 | BT02-032 | Skin | R309H/c.1191+5G->C | F |
| SA365187 | BT02-033 | Skin | R309H/c.1191+5G->C | F |
| SA365188 | BT02-034 | Skin | R309H/c.1191+5G->C | F |
| SA365189 | BT02-010 | Skin | Wildtype | F |
| SA365190 | BT02-009 | Skin | Wildtype | F |
| SA365191 | BT02-006 | Skin | Wildtype | F |
| SA365192 | BT02-008 | Skin | Wildtype | F |
| SA365193 | BT02-007 | Skin | Wildtype | F |
| SA365194 | BT02-005 | Skin | Wildtype | M |
| SA365195 | BT02-004 | Skin | Wildtype | M |
| SA365196 | BT02-003 | Skin | Wildtype | M |
| SA365197 | BT02-012 | Skin | Wildtype | M |
| SA365198 | BT02-013 | Skin | Wildtype | M |
| SA365199 | BT02-002 | Skin | Wildtype | M |
| SA365200 | BT02-011 | Skin | Wildtype | M |
| SA365201 | BT02-015 | Skin | Wildtype | M |
| SA365202 | BT02-014 | Skin | Wildtype | M |
| SA365203 | BT02-001 | Skin | Wildtype | M |
| Showing results 1 to 35 of 35 |
Collection:
| Collection ID: | CO003461 |
| Collection Summary: | 2x105 cells were plated onto 60mm plates in DMEM media (5 replicates for each cell type). After two days, before extraction, cells were counted using CASY cell counter (Omni Life Sciences) using a separate counting plate. After that, cells were washed at room temperature with PBS twice and then kept in a cold bath with dry ice and methanol before adding the metabolite extraction solution. |
| Sample Type: | Skin |
Treatment:
| Treatment ID: | TR003477 |
| Treatment Summary: | Cells were cultured in DMEM media supplemented with 10% FBS |
Sample Preparation:
| Sampleprep ID: | SP003475 |
| Sampleprep Summary: | Metabolite extraction solution (50% methanol, 30% acetonitrile, 20% ultrapure water, 5 µM final concentration valine-d8) was added to each well after the washes in PBS following the proportion of 1ml of extraction solution per million cells. The extracts were scraped and mixed at 4°C for 15 min. After final centrifugation at max speed for 15 min at 4°C, the supernatants were transferred into LC-MS vials. |
Combined analysis:
| Analysis ID | AN005482 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Dionex Ultimate 3000 UHPLC |
| Column | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH004165 |
| Instrument Name: | Dionex Ultimate 3000 UHPLC |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B. |
| Flow Rate: | 0.200 mL/min |
| Solvent A: | 100% water; 20 mM ammonium carbonate; 0.05% ammonium hydroxide |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005208 |
| Analysis ID: | AN005482 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites were measured with a Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (HRMS) coupled to a Dionex Ultimate 3000 UHPLC. The mass spectrometer was operated in full-scan, polarity-switching mode, with the spray voltage set to +4.5 kV/-3.5 kV, the heated capillary held at 320 °C, and the auxiliary gas heater held at 280 °C. The sheath gas flow was set to 55 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 0 unit. HRMS data acquisition was performed in a range of m/z = 70–900, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 120 ms. Metabolite identities were confirmed using two parameters: (1) precursor ion m/z was matched within 5 ppm of theoretical mass predicted by the chemical formula; (2) the retention time of metabolites was within 5% of the retention time of a purified standard run with the same chromatographic method. Chromatogram review and peak area integration were performed using the Thermo Fisher software Tracefinder 5.0 and the peak area for each detected metabolite was normalized against the total ion count (TIC) of that sample to correct any variations introduced from sample handling through instrument analysis. The normalized areas were used as variables for further statistical data analysis. |
| Ion Mode: | UNSPECIFIED |
