Summary of Study ST001492
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 PR001010. The data can be accessed directly via it's Project DOI: 10.21228/M84T3J 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 | ST001492 |
| Study Title | Global metabolomics of IFNy cued neurogenic NSCs seeded on hydrogel |
| Study Summary | Neural stem cells (NSCs) provide a strategy to replace damaged neurons following traumatic central nervous system injuries. A major hurdle to translation of this therapy is that direct application of NSCs to CNS injury does not support sufficient neurogenesis due to lack of proper cues. To provide prolonged spatial cues to NSCs IFN-γ was immobilized to biomimetic hydrogel substrate to supply physical and biochemical signals to instruct the encapsulated NSCs to be neurogenic. However, the immobilization of factors, including IFN-γ, versus soluble delivery of the same factor, has been incompletely characterized especially with respect to activation of signaling and metabolism in cells over longer time points. In this study, protein and metabolite changes in NSCs induced by immobilized versus soluble IFN-γ at 7 days were evaluated. Soluble IFN-γ, refreshed daily over 7 days, elicited stronger responses in NSCs compared to immobilized IFN-γ indicating that immobilization may not sustain signaling or has altered ligand/receptor interaction and integrity. However, both IFN-γ delivery types supported increased βIII tubulin expression in parallel with canonical and non-canonical receptor-signaling compared to no IFN-γ. Global metabolomics and pathway analysis revealed that soluble and immobilized IFN-γ altered metabolic pathway activities including energy, lipid and amino acid synthesis, with soluble IFN-γ having the greatest metabolic impact overall. |
| Institute | University of Akron |
| Department | Chemistry |
| Laboratory | Shriver lab |
| Last Name | Baumann |
| First Name | Hannah |
| Address | 190 E. Buchtel Common |
| hjb17@zips.uakron.edu | |
| Phone | 4198864033 |
| Submit Date | 2020-09-11 |
| Num Groups | 3 |
| Publications | Metabolomic and Signaling Programs Induced by Immobilized versus Soluble IFN γ in Neural Stem Cells |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-10-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001010 |
| Project DOI: | doi: 10.21228/M84T3J |
| Project Title: | Global metabolomics of IFNy cued neurogenic NSCs seeded on hydrogel |
| Project Summary: | Neural stem cells (NSCs) provide a strategy to replace damaged neurons following traumatic central nervous system injuries. A major hurdle to translation of this therapy is that direct application of NSCs to CNS injury does not support sufficient neurogenesis due to lack of proper cues. To provide prolonged spatial cues to NSCs IFN-γ was immobilized to biomimetic hydrogel substrate to supply physical and biochemical signals to instruct the encapsulated NSCs to be neurogenic. However, the immobilization of factors, including IFN-γ, versus soluble delivery of the same factor, has been incompletely characterized especially with respect to activation of signaling and metabolism in cells over longer time points. In this study, protein and metabolite changes in NSCs induced by immobilized versus soluble IFN-γ at 7 days were evaluated. Soluble IFN-γ, refreshed daily over 7 days, elicited stronger responses in NSCs compared to immobilized IFN-γ indicating that immobilization may not sustain signaling or has altered ligand/receptor interaction and integrity. However, both IFN-γ delivery types supported increased βIII tubulin expression in parallel with canonical and non-canonical receptor-signaling compared to no IFN-γ. Global metabolomics and pathway analysis revealed that soluble and immobilized IFN-γ altered metabolic pathway activities including energy, lipid and amino acid synthesis, with soluble IFN-γ having the greatest metabolic impact overall. |
| Institute: | University of Akron |
| Department: | Chemistry |
| Laboratory: | Shriver lab |
| Last Name: | Baumann |
| First Name: | Hannah |
| Address: | 190 E. Buchtel Common, Akron, OH, 44325, USA |
| Email: | hjb17@zips.uakron.edu |
| Phone: | 4196100269 |
| Funding Source: | NIH |
| Publications: | Metabolomic and Signaling Programs Induced by Immobilized versus Soluble IFN γ in Neural Stem Cells |
Subject:
| Subject ID: | SU001566 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Genotype Strain: | Fischer 344 |
| Age Or Age Range: | 6 wk |
| Gender: | Female |
| Animal Animal Supplier: | Envigo |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment group |
|---|---|---|
| SA125860 | C3 | immobilized IFNy |
| SA125861 | C1 | immobilized IFNy |
| SA125862 | C4 | immobilized IFNy |
| SA125863 | C2 | immobilized IFNy |
| SA125864 | A3 | no IFN y |
| SA125865 | A4 | no IFN y |
| SA125866 | A1 | no IFN y |
| SA125867 | A2 | no IFN y |
| SA125868 | B3 | soluble IFNy |
| SA125869 | B1 | soluble IFNy |
| SA125870 | B2 | soluble IFNy |
| SA125871 | B4 | soluble IFNy |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO001561 |
| Collection Summary: | Neural stem cells were collected from the subventricular zone of the brain in a 6-8 wk old rat. Papain tissue dissociation was used to isolate cells and the neurosphere culture system used to expand them for up to 7 passages. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR001581 |
| Treatment Summary: | Neurospheres were dissociated and plated onto laminin functionalized soft chitosan hydrogel surfaces. Three groups were grown for 7 days on their substrate in basal media . One group had no IFNy, another group 300 ng/mL soluble IFNy and the final group 300 ng/mL hydrogel immobilized IFNy. |
Sample Preparation:
| Sampleprep ID: | SP001574 |
| Sampleprep Summary: | NSC seeded gels were snap frozen and stored at -80C until extraction. Two gels were combined per group and extracted using a modified Bligh and Dyer extraction technique. In brief, 100 uL of methanol was added to each sample then underwent a series of snap freezing, sonication and vortexing three times. 750 μl of 1:2 chloroform:methanol was added to each homogenized sample, vortexed, then an additional 250 μL of chloroform was added, finally 250 μL water was added, all solvents used were LC grade. Samples were stored in -20 overnight and centrifuged to separate the phase layers and solidify the protein precipitate interface. Aqueous and organic layers were separated, dried down using Centrivap (Labconco) and stored in the -80 C until use. Aqueous portions of the extract were resuspended in 200 μL of 35% acetonitrile. |
Combined analysis:
| Analysis ID | AN002474 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Eksigent microLC 200 |
| Column | Phenomenex Luna NH2(150 x 1.0mm,3um) |
| MS Type | ESI |
| MS instrument type | Triple TOF |
| MS instrument name | ABI Sciex 5600+ TripleTOF |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH001812 |
| Chromatography Summary: | The mobile phases for separation consisted of water (A) and acetonitrile (B), both supplemented with 5 mM ammonium acetate and adjusted to pH 7.3 using ammonium hydroxide. The gradient proceeded at a flow rate of 30 μL/min as follows: 98% B at 0 min, 95% B at 1 min, 80% B at 5 min, 46% B at 6 min, 14.7% B at 13 min, 0% B at 17 min, 100% B at 17.1 min, and 100% B at 23 min. |
| Chromatography Comments: | Phenomenex (Luna 3 μ NH2 100 Å, 150 mm × 1.0 mm) |
| Instrument Name: | Eksigent microLC 200 |
| Column Name: | Phenomenex Luna NH2(150 x 1.0mm,3um) |
| Solvent A: | 100% water |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002294 |
| Analysis ID: | AN002474 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | Independent data acquisition was used with rolling collision energy for selected parent ions.Retention times and mass to charge values were aligned between samples using MarkerView software. Putative metabolite identifications were made using metaboanalyst, masstrix and HMDB softwares/databases. |
| Ion Mode: | POSITIVE |
