Summary of Study ST001859
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 PR001172. The data can be accessed directly via it's Project DOI: 10.21228/M86T2S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001859 |
| Study Title | dTor affects the fat body lipidome via Nep1r1, Ctdnep1 and Lipin |
| Study Summary | Quantitative MS analysis was performed on ten 4 day-old Drosophila larval fat bodies homogenized in 50µl D-PBS (Dulbecco’s Phosphate Buffered Saline without Mg2+ and Ca2+) by Lipotype using previously described methods (Grillet et al, 2016). |
| Institute | VIB-KU Leuven |
| Department | Dept. of Neurosciences, KU Leuven, 3000 Leuven, Belgium |
| Last Name | Jacquemyn |
| First Name | Julie |
| Address | ON 4, 6e verd Campus Gasthuisberg, Herestraat 49, bus 602, Leuven, NA, 3000, Belgium |
| julie.jacquemyn@kuleuven.be | |
| Phone | 0032479570951 |
| Submit Date | 2021-06-22 |
| Analysis Type Detail | MS(Dir. Inf.) |
| Release Date | 2021-07-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001172 |
| Project DOI: | doi: 10.21228/M86T2S |
| Project Title: | Torsin and NEP1R1-CTDNEP1 affect interphase NPC insertion by lipid-dependent and -independent mechanisms |
| Project Type: | MS analysis performed by Lipotype on Drosophila larval fat body tissue |
| Project Summary: | The interphase nuclear envelope is extensively remodeled during nuclear pore complex insertion. The process is relatively poorly understood, including why it requires the Torsin ATPases that also regulate NE-localized lipid metabolism. Here we show that fly dTorsin affects lipid metabolism through the NEP1R1-CTDNEP1 phosphatase/ Lipin phosphatidic acid phosphatase pathway. At a cellular level, fly and mouse Torsins removed NEP1R1-CTDNEP1 from the NE to, in turn, exclude Lipin from the nucleus. NEP1R1-CTDNEP1 downregulation also restored nuclear pore membrane fusion in post-mitotic dTorsinKO fat body cells. However, Lipin downregulation was ineffective and membrane fusion defects did not correlate with lipidomic abnormalities. Further testing confirmed that membrane fusion continued in cells with excess Lipin function. It also led to the surprising finding that excess PA metabolism inhibited recruitment of the inner ring complex Nup35 subunit, resulting in elongated channel-like structures in place of mature nuclear pores. We conclude that the NEP1R1-CTDNEP1 phosphatase affects interphase NPC biogenesis by lipid-dependent and lipid-independent mechanisms and this explains some of the pleiotropic effects of Torsins. |
| Institute: | VIB-KU Leuven |
| Department: | Dept. of Neurosciences, KU Leuven, 3000 Leuven, Belgium |
| Last Name: | Jacquemyn |
| First Name: | Julie |
| Address: | ON 4, 6e verd Campus Gasthuisberg, Herestraat 49, bus 602, 3000 Leuven, Belgium |
| Email: | julie.jacquemyn@kuleuven.be |
| Phone: | 032479570951 |
Subject:
| Subject ID: | SU001936 |
| Subject Type: | Invertebrate |
| Subject Species: | Drosophila melanogaster |
| Taxonomy ID: | 7227 |
| Age Or Age Range: | Developmentally-staged-larvae were collected (randomized) 4 days after placing male and female flies in fresh vials for a 12-hour period. |
| Gender: | Male and female |
Factors:
Subject type: Invertebrate; Subject species: Drosophila melanogaster (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA174315 | s3-3 | dTorKO Ctdnep1 |
| SA174316 | s3-1 | dTorKO Ctdnep1 |
| SA174317 | s3-2 | dTorKO Ctdnep1 |
| SA174318 | s4-3 | dTorKO Lipin |
| SA174319 | s4-1 | dTorKO Lipin |
| SA174320 | s4-2 | dTorKO Lipin |
| SA174321 | s1-2 | dTorKO Luciferase |
| SA174322 | s1-1 | dTorKO Luciferase |
| SA174323 | s1-3 | dTorKO Luciferase |
| SA174324 | s2-2 | dTorKO Nep1r1 |
| SA174325 | s2-3 | dTorKO Nep1r1 |
| SA174326 | s2-1 | dTorKO Nep1r1 |
| SA174327 | s9-2 | w- Ctdnep1 |
| SA174328 | s9-3 | w- Ctdnep1 |
| SA174329 | s9-1 | w- Ctdnep1 |
| SA174330 | s8-3 | w- Lipin |
| SA174331 | s8-2 | w- Lipin |
| SA174332 | s8-1 | w- Lipin |
| SA174333 | s5-2 | w- Luciferase |
| SA174334 | s5-1 | w- Luciferase |
| SA174335 | s5-3 | w- Luciferase |
| Showing results 1 to 21 of 21 |
Collection:
| Collection ID: | CO001929 |
| Collection Summary: | Fat body tissues of the indicated genotypes were collected and stored at -80°C until processed for MS analysis. Quantitative MS analysis was performed on ten 4 day-old Drosophila larval fat bodies homogenized in 50µl D-PBS (Dulbecco’s Phosphate Buffered Saline without Mg2+ and Ca2+) by Lipotype using previously described methods (Grillet et al, 2016). |
| Sample Type: | Insect tissue |
Treatment:
| Treatment ID: | TR001948 |
| Treatment Summary: | In this study we did not apply any additional treatment(s) to the samples. |
Sample Preparation:
| Sampleprep ID: | SP001942 |
| Sampleprep Summary: | Lipids from fat body tissues of indicated genotypes were extracted using chloroform and methanol (1). Samples were spiked with lipid class-specific internal standards prior to extraction. After drying and resuspending in MS acquisition mixture, lipid extracts were subjected to mass spectrometric analysis. Sample preparations were done by Lipotype. (1) Sampaio, J. L. et al. Membrane lipidome of an epithelial cell line. Proceedings of the National Academy of Sciences 108, 1903–1907 (2011). |
Combined analysis:
| Analysis ID | AN003013 | AN003014 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | None (Direct infusion) | None (Direct infusion) |
| Chromatography system | none | none |
| Column | none | none |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | pmol | pmol |
Chromatography:
| Chromatography ID: | CH002233 |
| Chromatography Summary: | NA |
| Instrument Name: | none |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS002802 |
| Analysis ID: | AN003013 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Spectra acquisition Mass spectra were acquired on a hybrid quadrupole/Orbitrap mass spectrometer equipped with an automated nano-flow electrospray ion source in both positive and negative ion mode. Data processing and normalization Lipid identification using LipotypeXplorer (2) was performed on unprocessed (*.raw format) mass spectra. For MS-only mode, lipid identification was based on the molecular masses of the intact molecules. MSMS mode included the collision induced fragmentation of lipid molecules and lipid identification was based on both the intact masses and the masses of the fragments. Prior to normalization and further statistical analysis lipid identifications were filtered according to mass accuracy, occupation threshold, noise and background. Lists of identified lipids and their intensities were stored in a database optimized for the particular structure inherent to lipidomic datasets. Intensity of lipid class-specific internal standards was used for lipid quantification. (2) Herzog, R. et al. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 12, R8 (2011). |
| Ion Mode: | POSITIVE |
| MS ID: | MS002803 |
| Analysis ID: | AN003014 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Spectra acquisition Mass spectra were acquired on a hybrid quadrupole/Orbitrap mass spectrometer equipped with an automated nano-flow electrospray ion source in both positive and negative ion mode. Data processing and normalization Lipid identification using LipotypeXplorer (2) was performed on unprocessed (*.raw format) mass spectra. For MS-only mode, lipid identification was based on the molecular masses of the intact molecules. MSMS mode included the collision induced fragmentation of lipid molecules and lipid identification was based on both the intact masses and the masses of the fragments. Prior to normalization and further statistical analysis lipid identifications were filtered according to mass accuracy, occupation threshold, noise and background. Lists of identified lipids and their intensities were stored in a database optimized for the particular structure inherent to lipidomic datasets. Intensity of lipid class-specific internal standards was used for lipid quantification. (2) Herzog, R. et al. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 12, R8 (2011). |
| Ion Mode: | NEGATIVE |
