Summary of Study ST003867
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 PR002423. The data can be accessed directly via it's Project DOI: 10.21228/M8FC13 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 | ST003867 |
| Study Title | Fatty-acid oxidation is a metabolic hallmark of human proliferative retinopathy |
| Study Type | comparison of vitreous humor from subjects with proliferative diabetic retinopathy to epiretinal membrane (control) |
| Study Summary | Healthy blood vessels supply neurons to preserve metabolic function. In blinding proliferative retinopathies (PRs), pathological neovascular tufts often emerge in lieu of needed physiological revascularization. Here we show that metabolic shifts in the neovascular niche define angiogenic fate. Fatty acid oxidation (FAO) metabolites accumulated in human and murine retinopathy samples. Neovascular tufts with a distinct single-cell transcriptional signature highly expressed FAO enzymes. The deletion of Sirt3, an FAO regulator, shifted the neovascular niche metabolism from FAO to glycolysis and suppressed tuft formation. This metabolic transition increased Vegf expression in astrocytes and reprogrammed pathological neovessels to a physiological phenotype, hastening vascular regeneration of the ischemic retina and improving vision. Hence, strategies to change the metabolic environment of vessels could promote a regenerative phenotype in vascular diseases. In this experiment, we used nontargeted metabolomics to measure metabolite profiles of vitreous humor from subjects with proliferative diabetic retinopathy. Vitreous samples were collected adjacent to leaky pathological neovascular tufts that characterize PR. Amongst the top 25 most significantly dysregulated metabolites, we observed an accumulation of acylcarnitines in human neovascular PR samples compared to control subjects with epiretinal membranes. Fatty acylcarnitines are by-products of fatty-acid beta-oxidation (FAO), the process of oxidizing fatty acids in mitochondria to produce acetyl-CoA (Fig. 1b). 5 of the 6 most enriched metabolic pathways in human PR pertained to FA metabolism, including long and short-chain saturated FAO pathways. |
| Institute | Broad Institute of MIT and Harvard |
| Department | Metabolomics Platform |
| Last Name | Clish |
| First Name | Clary |
| Address | 300 Binney Street, Cambridge, MA, 02142, USA |
| clary@broadinstitute.org | |
| Phone | 617-714-7654 |
| Submit Date | 2025-04-06 |
| Num Groups | 2 |
| Total Subjects | 15 |
| Num Males | 9 |
| Num Females | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| 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: | PR002423 |
| Project DOI: | doi: 10.21228/M8FC13 |
| Project Title: | Fatty-acid oxidation is a metabolic hallmark of human proliferative retinopathy |
| Project Summary: | In this experiment, we used nontargeted metabolomics to measure metabolite profiles of vitreous humor from subjects with proliferative diabetic retinopathy. Vitreous samples were collected adjacent to leaky pathological neovascular tufts that characterize PR. Amongst the top 25 most significantly dysregulated metabolites, we observed an accumulation of acylcarnitines in human neovascular PR samples compared to control subjects with epiretinal membranes. |
| Institute: | Broad Institute of MIT and Harvard |
| Department: | Metabolomics Platform |
| Last Name: | Clish |
| First Name: | Clary |
| Address: | 300 BineyStreet, Cambridge, MA, 02142, USA |
| Email: | clary@broadinstitute.org |
| Phone: | 617-714-7654 |
| Publications: | submitted |
| Contributors: | Gael Cagnone, Sheetal Pundir, Charlotte Betus, Tapan Agnihotri, Anli Ren, Jin SungKim, Noémie-Rose Harvey, Emilie Heckel, Mei Xi Chen, Anu Situ, Perrine Gaub, Nicholas Kim, Ashim Das, Severine Leclerc, Florian Wünnemann, Louis Berillon, Gregor Andelfinger, Sergio Crespo-Garcia, Alexandre Dubrac, Flavio A. Rezende, Clary B. Clish, Bruno Maranda, José Carlos Rivera, Lois E. H. Smith, Przemyslaw Sapieha, JeanSébastien Joyal |
Subject:
| Subject ID: | SU004001 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 35-84 |
| 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 | Dianosis | Disease Status |
|---|---|---|---|---|
| SA424709 | QC01 | pooled vitreous QC | NA | NA |
| SA424710 | QC02 | pooled vitreous QC | NA | NA |
| SA424711 | QC03 | pooled vitreous QC | NA | NA |
| SA424694 | 136 | Vitreous humor | Epiretinal membrane (ERM) | Control |
| SA424695 | 15 | Vitreous humor | Epiretinal membrane (ERM) | Control |
| SA424696 | 14 | Vitreous humor | Epiretinal membrane (ERM) | Control |
| SA424697 | 108 | Vitreous humor | Epiretinal membrane (ERM) | Control |
| SA424698 | 16 | Vitreous humor | Epiretinal membrane (ERM) | Control |
| SA424699 | 153 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with macular edema and pre-retinal hemorrhage |
| SA424700 | 126 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with neovascular glaucoma |
| SA424701 | 142 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with tractional retinal detachments |
| SA424702 | 86 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage |
| SA424703 | 87 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage |
| SA424704 | 77 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage |
| SA424705 | 76 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage |
| SA424706 | 144 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage and cataract |
| SA424707 | 85 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage and tractional retinal detachments |
| SA424708 | 124 | Vitreous humor | Proliferative diabetic retinopathy (PDR) | Active with vitreous hemorrhage and tractional retinal detachments |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO003994 |
| Collection Summary: | The study conforms to the tenets of the Declaration of Helsinki, and approval of the human clinical protocol and informed consent were obtained from the Maisonneuve-Rosemont Hospital Ethics Committee (CER: 10059). All patients previously diagnosed with proliferative diabetic retinopathy or epiretinal membrane were followed clinically, and surgery was performed by a single vitreoretinal surgeon when indicated by 'standard-of-care' guidelines. Informed consent was obtained. Undiluted vitreous samples were aspirated in the region adjacent to neovascular tufts or epiretinal membrane (control) and were frozen on dry ice immediately after biopsy and stored at –80°C. All patients received their first anti-VEGF injection after vitreous sampling; they did not have prior anti-VEGF or photocoagulation treatment. Medication details are provided in the metadata table, except for four deceased diabetic patients whose records were no longer available (NA). Sex and gender factors were not analyzed due to insufficient statistical power when disaggregated. |
| Collection Protocol ID: | CER: 10059 |
| Sample Type: | Vitreous humor |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004010 |
| Treatment Summary: | No treatment was used in the study |
Sample Preparation:
| Sampleprep ID: | SP004007 |
| Sampleprep Summary: | Samples were thawed on ice, vortexes, and aliquoted to prepare extracts for three different LC-MS methods: HILIC-pos: 10 µL of vitreous sample was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each vitreous sample was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. |
Chromatography:
| Chromatography ID: | CH004820 |
| Chromatography Summary: | HILIC-pos: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the positive ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2.1mm,3um,100Å) |
| Column Temperature: | 30 |
| Flow Gradient: | 0-0.5 min, isocratic 95% B; 0.5-10.5 min, gradient to 40% B; 10.5-15 min, isocratic 40% B; 15-17 min, gradient to 95% B |
| Flow Rate: | 250 uL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004821 |
| Chromatography Summary: | HILIC-neg: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the negative ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna NH2 (150 x 2 mm,5um,100Å) |
| Column Temperature: | 30 |
| Flow Gradient: | 0-10 min, gradient from 90% B to 0% B; 10-12 min, isocratic 0% B; 12-14 min, gradient from 0% B to 90% B |
| Flow Rate: | 400 uL/min |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% methanol/25% acetonitrile; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006355 |
| Analysis Type: | MS |
| Chromatography ID: | CH004820 |
| Num Factors: | 8 |
| Num Metabolites: | 188 |
| Rt Units: | Minutes |
| Units: | peak areas |
| Analysis ID: | AN006356 |
| Analysis Type: | MS |
| Chromatography ID: | CH004821 |
| Num Factors: | 8 |
| Num Metabolites: | 63 |
| Rt Units: | Minutes |
| Units: | peak area |
