Summary of Study ST002214
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 PR001414. The data can be accessed directly via it's Project DOI: 10.21228/M8Z42Q 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 | ST002214 |
| Study Title | The effects of PKM2 modulation and hypoxia on the metabolic landscape of Alzheimer patient-derived induced neurons |
| Study Summary | We have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed. |
| Institute | University of Colorado Denver |
| Last Name | Haines |
| First Name | Julie |
| Address | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| julie.haines@cuanschutz.edu | |
| Phone | 3037243339 |
| Submit Date | 2022-06-24 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-07-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001414 |
| Project DOI: | doi: 10.21228/M8Z42Q |
| Project Title: | Metabolic changes in Alzheimer patient-derived induced neurons and the effects of PKM2 modulation and hypoxia on their metabolic landscape |
| Project Summary: | We have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Metabolomic landscape and glucose flux in control versus AD were assessed. Additionally, their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed. |
| Institute: | University of Colorado Denver |
| Laboratory: | Lab of Angelo D'Alessandro in collaboration with lab of Jerome Mertens (Univ of Innsbruck) |
| Last Name: | Haines |
| First Name: | Julie |
| Address: | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| Email: | julie.haines@cuanschutz.edu |
| Phone: | 3037243339 |
Subject:
| Subject ID: | SU002300 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 50-90 yrs |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition | Treatment |
|---|---|---|---|
| SA211868 | 8020-C | Alzheimer patient | DMSO |
| SA211869 | 3131-C | Alzheimer patient | DMSO |
| SA211870 | 3053-C | Alzheimer patient | DMSO |
| SA211871 | 2800-C | Alzheimer patient | DMSO |
| SA211872 | 2800-S | Alzheimer patient | Shikonin |
| SA211873 | 8020-S | Alzheimer patient | Shikonin |
| SA211874 | 3053-S | Alzheimer patient | Shikonin |
| SA211875 | 3131-S | Alzheimer patient | Shikonin |
| SA211876 | 8011-DFO | non-demented control | CoDo Treatment |
| SA211877 | 2785-DFO | non-demented control | CoDo Treatment |
| SA211878 | 2785-C | non-demented control | GFP-overexpression |
| SA211879 | 2608-C | non-demented control | GFP-overexpression |
| SA211880 | 8011-C | non-demented control | GFP-overexpression |
| SA211881 | 2608-OE | non-demented control | PKM2-overexpression |
| SA211882 | 2785-OE | non-demented control | PKM2-overexpression |
| SA211883 | 8011-OE | non-demented control | PKM2-overexpression |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO002293 |
| Collection Summary: | For Metabolome, iNs were flow cytometry-isolated 21 days of conversion. iNs were sorted based on the expression of the PSA-NCAM surface markers using PSA-NCAM-PE (Miltenyi) and re-plated on Geltrex-coated wells. The following day, iNs were treated with 2.5 mM DGlucose-C13 for 6 hours and harvested using Tryple. Supernatant and cell pellets were shock frozen in liquid nitrogen. |
| Sample Type: | Biopsy |
Treatment:
| Treatment ID: | TR002312 |
| Treatment Summary: | After two weeks of conversion, cells were treated for 10 days with shikonin (10 µM, ChemCruz) before FACS sorting. Control iNs were FACS-sorted and plated on Geltrex-coated wells before transduction with pLVXTP-EGFP-PKM2 or pLVXTP-EGFP. Around 60 % of all neurons were successfully transduced. Five days after transduction, iNs were harvested for MS-analysis. Alternatively, cells were treated with CoDo for 6 hours before harvest. |
Sample Preparation:
| Sampleprep ID: | SP002306 |
| Sampleprep Summary: | Metabolites from frozen cell pellets were extracted at 150,000 cells/mL in cold 5:3:2 MeOH:acetonitrile:water. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C). Supernatants were split into two equal tubes and gently dried using a vacuum concentrator. One set of residues were resuspended in 12 uL of 0.1% formic acid (for positive ion mode). The other set of residues were resuspended in 12 uL of 1 mM ammonium acetate (for negative ion mode). |
Combined analysis:
| Analysis ID | AN003622 | AN003623 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002677 |
| Chromatography Summary: | Negative C18 cells |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Sample Injection: | 10 uL |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002678 |
| Chromatography Summary: | Positive C18 cells |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Sample Injection: | 10 uL |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003373 |
| Analysis ID: | AN003622 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003374 |
| Analysis ID: | AN003623 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | POSITIVE |
