Summary of Study ST003533
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 PR002174. The data can be accessed directly via it's Project DOI: 10.21228/M8MC1N 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 | ST003533 |
| Study Title | Nutrient intervention protects against retinal dysfunction caused by disrupted peroxisomal fatty acid oxidation |
| Study Summary | Dyslipidemia is a significant contributor to many eye diseases, but the lipid processing pathways are not fully understood. Peroxisomes oxidize very long-chain fatty acids and generate docosahexaenoic acid. Mutations in peroxisomal genes can result in severe neural retinal dysfunction. However, therapeutic approaches for peroxisomal diseases remain scarce. In this study, we found impaired retinal function and altered retinal metabolism in mice lacking the first enzyme of peroxisomal fatty acid oxidation (ACOX1). Supplementation of the depleted metabolite pyruvate or the depleted omega-3 fatty acid docosahexaenoic acid mitigated the progression of retinal dysfunction in Acox1 KO mice. Nutrient intervention may therefore offer a promising therapeutic approach for peroxisomal diseases. |
| Institute | Boston Children's Hospital |
| Last Name | Fu |
| First Name | Zhongjie |
| Address | 1 Blackfan Circle, Boston, MA 02114 |
| Zhongjie.Fu@childrens.harvard.edu | |
| Phone | 6179192534 |
| Submit Date | 2024-09-25 |
| Num Groups | 2 |
| Total Subjects | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-05-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002174 |
| Project DOI: | doi: 10.21228/M8MC1N |
| Project Title: | Nutrient intervention protects against retinal dysfunction caused by disrupted peroxisomal fatty acid oxidation |
| Project Summary: | We performed metabolomics of Acox1 KO vs. Acox1 WT retinas to determine the impact of peroxisomal fatty acid deficiency on retinal metabolism during development. |
| Institute: | Boston Children's Hospital |
| Last Name: | Fu |
| First Name: | Zhongjie |
| Address: | 1 Blackfan Circle, Boston, MA 02114 |
| Email: | Zhongjie.Fu@childrens.harvard.edu |
| Phone: | 617-919-2534 |
Subject:
| Subject ID: | SU003662 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA387384 | KO-1 | Retina | KO-1 |
| SA387385 | KO-2 | Retina | KO-2 |
| SA387386 | KO-3 | Retina | KO-3 |
| SA387387 | WT-1 | Retina | WT-1 |
| SA387388 | WT-2 | Retina | WT-2 |
| SA387389 | WT-3 | Retina | WT-3 |
| SA387375 | Blank_0 | - | - |
| SA387376 | Blank_1 | - | - |
| SA387377 | Blank_2 | - | - |
| SA387378 | Blank_3 | - | - |
| SA387379 | Blank_4 | - | - |
| SA387380 | Blank_5 | - | - |
| SA387381 | ISTD_0 | - | - |
| SA387382 | ISTD_1 | - | - |
| SA387383 | ISTD_2 | - | - |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO003655 |
| Collection Summary: | Acox1 KO vs. Acox1 WT retinas were collected at postnatal day P30, and 3 samples were generated per group with 8 retinas pooled per sample. Samples were prepared for untargeted MS-based metabolomics. |
| Sample Type: | Retina |
Treatment:
| Treatment ID: | TR003671 |
| Treatment Summary: | Mice for metabolomics experiments were not subjected to any treatment. Acox1 KO mice were compared to Acox1 WT mice. |
Sample Preparation:
| Sampleprep ID: | SP003669 |
| Sampleprep Summary: | Pooled mouse retinas were weighed out and extracted with cold methanol at a concentration of 10mg tissue per 1ml of methanol buffer. Samples were homogenized with silicon beads and then spun down. Supernatant was taken off the top and dried down in a speed vacuum, then reconstituted in water before a 2ul LC-MS injection for untargeted polar global metabolomics. |
| Sampleprep Protocol ID: | SP002600 |
Chromatography:
| Chromatography ID: | CH004407 |
| Chromatography Summary: | Solvent A was at pH 9.0 2uL of sample were injected onto pHILIC column with a gradient of 80% ACN dropping to 20% acetonitrile over a 30 minute period, followed by a return and hold to 80% acetonitrile. |
| Instrument Name: | Thermo Ultimate 3000 |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm, 5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min) |
| Flow Rate: | 0.1mL/min |
| Solvent A: | 100% water; 10 mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN005804 |
| Laboratory Name: | Metabolomics Core Resource Laboratory |
| Analysis Type: | MS |
| Software Version: | 4.1 |
| Chromatography ID: | CH004407 |
| Num Factors: | 7 |
| Num Metabolites: | 471 |
| Rt Units: | Minutes |
| Units: | intensity |
