Summary of Study ST003438
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 PR002121. The data can be accessed directly via it's Project DOI: 10.21228/M8FV6T 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 | ST003438 |
| Study Title | Unbiased genetic screening and metabolomics identifies glial adenosine metabolism as a therapeutic target in Parkinson’s disease |
| Study Summary | Parkinson’s disease (PD) is the second most common neurodegenerative disorder and lacks disease-modifying therapies. We developed a Drosophila model for identifying novel glial- based therapeutic targets for PD. Human α-synuclein is expressed in neurons and individual genes are independently knocked down in glia. We performed a large forward genetic screen, knocking down the entire Drosophila kinome in glia in α-synuclein expressing flies. Among the top hits were five genes (Ak1, Ak6, Adk1, Adk2, and awd) involved in adenosine metabolism. Knockdown of each gene improved locomotor dysfunction, rescued neurodegeneration, and increased brain adenosine levels. We determined that the mechanism of neuroprotection involves adenosine itself, as opposed to a downstream metabolite. We dove deeper into the mechanism for one gene, Ak1, finding rescue of dopaminergic neuron loss, α-synuclein aggregation, and bioenergetic dysfunction after glial Ak1 knockdown. We performed metabolomics in Drosophila and in human PD patients, allowing us to comprehensively characterize changes in purine metabolism and identify potential biomarkers of dysfunctional adenosine metabolism in people. These experiments support glial adenosine as a novel therapeutic target in PD. |
| Institute | Broad Institute of MIT and Harvard |
| Last Name | Avila-Pacheco |
| First Name | Julian |
| Address | 415 Main Street |
| jravilap@broadinstitute.org | |
| Phone | (617) 714-1729 |
| Submit Date | 2024-08-27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002121 |
| Project DOI: | doi: 10.21228/M8FV6T |
| Project Title: | Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s disease |
| Project Type: | Metabolomic profiling of Parkinson's Disease Drosophila model |
| Project Summary: | Parkinson’s disease (PD) is the second most common neurodegenerative disorder and lacks disease-modifying therapies. We developed a Drosophila model for identifying novel glial- based therapeutic targets for PD. Human α-synuclein is expressed in neurons and individual genes are independently knocked down in glia. We performed a forward genetic screen, knocking down the entire Drosophila kinome in glia in α-synuclein expressing flies. Among the top hits were five genes (Ak1, Ak6, Adk1, Adk2, and awd) involved in adenosine metabolism. Knockdown of each gene improved locomotor dysfunction, rescued neurodegeneration, and increased brain adenosine levels. We determined that the mechanism of neuroprotection involves adenosine itself, as opposed to a downstream metabolite. We dove deeper into the mechanism for one gene, Ak1, finding rescue of dopaminergic neuron loss, α-synuclein aggregation, and bioenergetic dysfunction after glial Ak1 knockdown. We performed metabolomics in Drosophila and in human PD patients, allowing us to comprehensively characterize changes in purine metabolism and identify potential biomarkers of dysfunctional adenosine metabolism in people. These experiments support glial adenosine as a novel therapeutic target in PD. |
| Institute: | Broad Institute of MIT and Harvard |
| Last Name: | Avila-Pacheco |
| First Name: | Julian |
| Address: | 415 Main Street |
| Email: | jravilap@broadinstitute.org |
| Phone: | (617) 714-1729 |
| Contributors: | Sodders M, Kumari N, Okorie E, Shen M, Lakhani M, Marathi A, Sarkar S, Scherzer CR, Clish C, Feany MB, Olsen AL, Bullock K, Pierce K, Dennis C, Jeanfavre D, Avila-Pacheco, J |
Subject:
| Subject ID: | SU003565 |
| Subject Type: | Insect |
| Subject Species: | Drosophila melanogaster |
| Taxonomy ID: | 7227 |
Factors:
Subject type: Insect; Subject species: Drosophila melanogaster (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample_ID |
|---|---|---|---|
| SA378327 | 3S | Fly heads | Control |
| SA378328 | 2S | Fly heads | Control |
| SA378329 | 1S | Fly heads | Control |
| SA378330 | 6SA | Fly heads | Control + AKI-KD |
| SA378331 | 5SA | Fly heads | Control + AKI-KD |
| SA378332 | 4SA | Fly heads | Control + AKI-KD |
| SA378333 | 9Q | Fly heads | Synuclein |
| SA378334 | 8Q | Fly heads | Synuclein |
| SA378335 | 7Q | Fly heads | Synuclein |
| SA378336 | 10QA | Fly heads | Synuclein + AKI-KD |
| SA378337 | 12QA | Fly heads | Synuclein + AKI-KD |
| SA378338 | 11QA | Fly heads | Synuclein + AKI-KD |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003558 |
| Collection Summary: | Metabolomics on fly heads was performed using a platform that relies on a combination of four non-targeted liquid chromatography mass spectrometry (LC-MS) methods which measure both polar and non-polar metabolites23. n = 3 replicates per genotype of 25 fly heads each. |
| Sample Type: | Heads |
Treatment:
| Treatment ID: | TR003574 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP003572 |
| Sampleprep Summary: | Sample homogenates were generated by homogenizing the fly heads in 100 µL water using a TissueLyser II (QIAGEN) bead mill set to two 2 min intervals at 20. |
Combined analysis:
| Analysis ID | AN005649 | AN005650 | AN005651 | AN005652 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | Reversed phase | HILIC | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2 mm, 3 µm) | Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) | Phenomenex Luna NH2 (150 x 2.1mm, 3um) | Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Abundances | Abundances | Abundances | Abundances |
Chromatography:
| Chromatography ID: | CH004288 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2 mm, 3 µm) |
| Column Temperature: | 30C |
| Flow Gradient: | Isocratically with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes |
| Flow Rate: | 250 µL/min |
| Solvent A: | 100% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004289 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40C |
| Flow Gradient: | The column was eluted at a flow rate of 450 µL/min isocratically for 1 minute at 80% mobile phase A, followed by a linear gradient to 80% mobile-phase B over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B. |
| Flow Rate: | 450 µL/min |
| Solvent A: | 95% water/5% methanol; 10 mM ammonium acetate; 0.1% acetic acid |
| Solvent B: | 100% methanol; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004290 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna NH2 (150 x 2.1mm, 3um) |
| Column Temperature: | 30C |
| Flow Gradient: | The column was eluted with initial conditions of 10% mobile phase A and 90% mobile phase B followed by a 10 min linear gradient to 100% mobile phase A. |
| Flow Rate: | 400 µL/min |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004291 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um) |
| Column Temperature: | 45C |
| Flow Gradient: | The column was eluted isocratically at a flow rate of 450 µL/min with 20% mobile phase A for 3 minutes followed by a linear gradient to 100% mobile phase B over 12 minutes. |
| Flow Rate: | 450 µL/min |
| Solvent A: | 100% water; 0.01% formic acid |
| Solvent B: | 100% acetonitrile; 0.01% acetic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005373 |
| Analysis ID: | AN005649 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005374 |
| Analysis ID: | AN005650 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005375 |
| Analysis ID: | AN005651 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005376 |
| Analysis ID: | AN005652 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | NEGATIVE |
