Summary of Study ST001130
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 PR000755. The data can be accessed directly via it's Project DOI: 10.21228/M8367J 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 | ST001130 |
| Study Title | Urea cycle and 1C/serine metabolism in the prevention of oxygen induced retinopathy |
| Study Summary | Untargeted metabolite profiling links the urea cycle and 1C/serine metabolism in the prevention of oxygen induced retinopathy by hepatic HIF stabilization. Premature infants require oxygen supplementation to survive that is simultaneously toxic to developing tissues. We have demonstrated that hypoxia inducible factor (HIF) stabilization during hyperoxia prevents oxygen induced retinopathy (OIR) and lung disease. Here, untargeted metabolite profiling coupled to XCMS systems biology analysis finds that serine/1C and urea cycles dominate pathway enrichment graphs. MS1 peak areas and MS2 library matches reveal 50% or more increased levels of plasma and retina serine, glycine, hypotaurine, methionine, and taurine. In addition, N-acetylglutamate increased 4-fold in serum, while orotate, citrulline, arginine, aspartate, glutamine were at least 50% increased after HIF stabilization. Targeted data analysis in vivo finds that retinal serine and glycine were derived from liver. HIF-1α2lox/2lox; albumin-cre KO had reduced levels of serine and retinal glycine. Inhibition of 1C metabolism blocked rescue by HIF stabilization. The metabolic phenotype of mice protected from OIR by HIF stabilization is dependent on hepatic serine/1C metabolism and urea cycle. |
| Institute | Cole Eye Institute |
| Department | Cleveland Clinic |
| Last Name | Singh |
| First Name | Charandeep |
| Address | 9500 Euclid Avenue |
| cxs065@gmail.com | |
| Phone | (216) 444-8232 |
| Submit Date | 2019-01-31 |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-06-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000755 |
| Project DOI: | doi: 10.21228/M8367J |
| Project Title: | Plasma metabolite profiling |
| Project Type: | MS untargeted data |
| Project Summary: | Untargeted LC- data-dependent MS2 in positive mode to find difference in OIR model mice and FG-4592 treated mice plasma. |
| Institute: | Cole Eye Institute |
| Department: | Cleveland Clinic |
| Laboratory: | Dr. Jonathan Sears lab |
| Last Name: | Singh |
| First Name: | Charandeep |
| Address: | 9500 Euclid Avenue, Cleveland, Select One, 44195, USA |
| Email: | cxs065@gmail.com |
| Phone: | (216) 444-8232 |
Subject:
| Subject ID: | SU001191 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA078083 | Pos_hyper3incluMS2 | Hyperoxia |
| SA078084 | Pos_hyper4incluMS2 | Hyperoxia |
| SA078085 | Pos_hyper6incluMS2 | Hyperoxia |
| SA078086 | Pos_hyper2incluMS2 | Hyperoxia |
| SA078087 | Pos_hyper5incluMS2 | Hyperoxia |
| SA078088 | Pos_hyper1incluMS2 | Hyperoxia |
| SA078089 | Pos_FG1incluMS2 | Hyperoxia+FG4592 |
| SA078090 | Pos_FG2incluMS2 | Hyperoxia+FG4593 |
| SA078091 | Pos_FG3incluMS2 | Hyperoxia+FG4594 |
| SA078092 | Pos_FG4incluMS2 | Hyperoxia+FG4595 |
| SA078093 | Pos_FG5incluMS2 | Hyperoxia+FG4596 |
| SA078094 | Pos_FG6incluMS2 | Hyperoxia+FG4597 |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO001185 |
| Collection Summary: | To extract the blood samples, mice were anesthetized with ketamine/xylazine mix and then blood was extracted from the heart of the animal with a 27.5 gauge needle fixed onto a 1cc heparinized syringe and added to 1.5 ml tubes containing 1.5 µl of Heparin 10,000 USP units/ml (Hospira, Lake forest, IL, USA) and stored on ice until further use. Plasma was obtained from blood samples by centrifuging samples at 1,100 x g at 4⁰C for 20 min. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001206 |
| Treatment Summary: | All experimental procedures involving live animals were conducted in accordance with the guidelines of the NIH Guide for the Care and Use of Laboratory Animals and approved by the Cleveland Clinic institutional animal care and use committee (IACUC, protocol #2016-1677). Wild type C57BL/6J mice were supplied by the Jackson Laboratory (Bar Harbor, ME). OIR model was based on the previously described procedure developed by LE Smith(Smith et al, 1994) and was described in detail elsewhere(Hoppe et al, 2014b; Sears et al, 2008; Singh et al, 2018). Metabolomics experiment was performed on p10 old OIR model mice Smith LE, Wesolowski E, McLellan A, Kostyk SK, D'Amato R, Sullivan R, D'Amore PA (1994) Oxygen-induced retinopathy in the mouse. Investigative ophthalmology & visual science 35: 101-111 Sears JE, Hoppe G, Ebrahem Q, Anand-Apte B (2008) Prolyl hydroxylase inhibition during hyperoxia prevents oxygen-induced retinopathy. Proceedings of the National Academy of Sciences 105: 19898-19903 Singh C, Sharma A, Hoppe G, Song W, Bolok Y, Sears JE (2018) 3-Hydroxypyruvate Destabilizes Hypoxia Inducible Factor and Induces Angiostasis. Investigative Ophthalmology & Visual Science 59: 3440-3448 |
Sample Preparation:
| Sampleprep ID: | SP001199 |
| Sampleprep Summary: | Metabolites from plasma were extracted by adding 20 µl of plasma to 500 µl of 50% cold acetonitrile. Samples were centrifuged at 15,000 x g for 10 min and 400 µl supernatant was carefully removed into fresh tubes without disturbing the cell pellet. Supernatants were injected directly into the LC-MS |
Combined analysis:
| Analysis ID | AN001855 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | Area under the curve Arbitrary units |
Chromatography:
| Chromatography ID: | CH001342 |
| Chromatography Summary: | Chromatographic separation was performed on SeQuant ZIC-HILIC column with dimensions 150 x 2.1 mm, 3.5 µm, 100 Å (Merck, Darmstadt, Germany) attached to a precolumn SeQuant ZIC-HILIC with dimensions 20 x 2.1 mm, 3.5 µm, 100 Å (Merck, Darmstadt, Germany). The LC method used for separation of metabolites using the ZIC-HILIC column was adapted from Singh et al. al.(Singh et al, 2017). Briefly, gradient of solvent A (0.1% formic acid in water) and solvent B (0.08% formic acid in ACN) ramped from 80% B to 35% B in 23 minutes, followed by a wash step with 5% B from 25-30 min and then re-equilibration with 80% B from 25-30 min. Column oven was set to 20⁰C and a constant flow of solvents was set to 150 µl min-1. Samples were kept on 4⁰C auto-sampler throughout the measurements and 10 μl (plasma) of sample was injected. Singh C, Glaab E, Linster CL (2017) Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. The Journal of biological chemistry 292: 1005-1028 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 20 |
| Flow Gradient: | ramped from 80% B to 35% B in 23 minutes, followed by a wash step with 5% B from 25-30 min and then re-equilibration with 80% B from 25-30 min. |
| Flow Rate: | 150 µl/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.08% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001715 |
| Analysis ID: | AN001855 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC-MS data from ddMS2 measurement were converted to mzML format using compound discoverer (version 2.1) (Thermo Scientific, Bellefonte, PA, USA) Data were analyzed using XCMS online tool(Forsberg et al, 2018). The metabolites were mapped onto the mouse database available on XCMS(Forsberg et al, 2018). Data was also analyzed with MSdial tool to confirm some of the metabolite annotations, using library provided with the MSdial software(Lai et al, 2017; Tsugawa et al, 2015). Forsberg EM, Huan T, Rinehart D, Benton HP, Warth B, Hilmers B, Siuzdak G (2018) Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. Nat Protoc 13: 633-651 Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O (2017) Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature methods 15: 53 Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M (2015) MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nature methods 12: 523-526 |
| Ion Mode: | POSITIVE |
