Summary of Study ST002377
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 PR001529. The data can be accessed directly via it's Project DOI: 10.21228/M8298N 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 | ST002377 |
| Study Title | Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups (Pnpla7-knockout) |
| Study Summary | Choline supplies methyl groups for regeneration of methionine and the methyl donor S-adenosylmethionine in the liver. Here we demonstrate that the catabolism of membrane phosphatidylcholine (PC) into water-soluble glycerophosphocholine (GPC) by the phospholipase/lysophospholipase PNPLA8-PNPLA7 axis enables endogenous choline stored in hepatic PC to be utilized in methyl metabolism. PNPLA7-deficient mice show marked decreases in hepatic GPC, choline, and several metabolites related to the methionine cycle, accompanied by various signs of methionine insufficiency including growth retardation, hypoglycemia, hypolipidemia, increased energy consumption, reduced adiposity, increased FGF21, and an altered histone/DNA methylation landscape. Moreover, PNPLA8-deficient mice recapitulate most of these phenotypes. In contrast to wild-type mice fed a methionine/choline-deficient diet, both knockout strains display a decreased hepatic triglyceride likely via reductions of lipogenesis and GPC-derived glycerol flux. Collectively, our findings highlight the biological importance of phospholipid catabolism driven by PNPLA8/PNPLA7 in methyl group flux and triglyceride synthesis in the liver. |
| Institute | Tokyo Metropolitan Institute of Medical Science |
| Last Name | Hirabayashi |
| First Name | Tetsuya |
| Address | 2-6-1 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan |
| hirabayashi-tt@igakuken.or.jp | |
| Phone | +81-3-5316-3100 |
| Submit Date | 2022-11-30 |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-12-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001529 |
| Project DOI: | doi: 10.21228/M8298N |
| Project Title: | Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups |
| Project Summary: | Choline supplies methyl groups for regeneration of methionine and the methyl donor S-adenosylmethionine in the liver. Here we demonstrate that the catabolism of membrane phosphatidylcholine (PC) into water-soluble glycerophosphocholine (GPC) by the phospholipase/lysophospholipase PNPLA8-PNPLA7 axis enables endogenous choline stored in hepatic PC to be utilized in methyl metabolism. PNPLA7-deficient mice show marked decreases in hepatic GPC, choline, and several metabolites related to the methionine cycle, accompanied by various signs of methionine insufficiency including growth retardation, hypoglycemia, hypolipidemia, increased energy consumption, reduced adiposity, increased FGF21, and an altered histone/DNA methylation landscape. Moreover, PNPLA8-deficient mice recapitulate most of these phenotypes. In contrast to wild-type mice fed a methionine/choline-deficient diet, both knockout strains display a decreased hepatic triglyceride likely via reductions of lipogenesis and GPC-derived glycerol flux. Collectively, our findings highlight the biological importance of phospholipid catabolism driven by PNPLA8/PNPLA7 in methyl group flux and triglyceride synthesis in the liver. |
| Institute: | Tokyo Metropolitan Institute of Medical Science |
| Last Name: | Hirabayashi |
| First Name: | Tetsuya |
| Address: | 2-6-1 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan |
| Email: | hirabayashi-tt@igakuken.or.jp |
| Phone: | +81-3-5316-3100 |
Subject:
| Subject ID: | SU002466 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6N |
| Age Or Age Range: | 6-weeks old |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA237387 | KO3 | Pnpla7-knockout |
| SA237388 | KO4 | Pnpla7-knockout |
| SA237389 | KO6 | Pnpla7-knockout |
| SA237390 | KO2 | Pnpla7-knockout |
| SA237391 | KO5 | Pnpla7-knockout |
| SA237392 | KO1 | Pnpla7-knockout |
| SA237393 | WT3 | Wild-type |
| SA237394 | WT2 | Wild-type |
| SA237395 | WT4 | Wild-type |
| SA237396 | WT5 | Wild-type |
| SA237397 | WT6 | Wild-type |
| SA237398 | WT1 | Wild-type |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO002459 |
| Collection Summary: | Mice were deeply anesthetized and perfused intracardially with saline containing 1 mM MOPS (pH 7.4). Liver was rapidly removed, frozen on liquid nitrogen and stored at –80°C until further processing. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002478 |
| Treatment Summary: | No treatment in this study. |
Sample Preparation:
| Sampleprep ID: | SP002472 |
| Sampleprep Summary: | Tissues with internal standards were homogenized with ice-cold methanol and extracted by the Bligh–Dyer method using chloroform and methanol to separate and recover the water-soluble fractions. The supernatant was filtered through a 5-kDa cut-off filter (Ultrafree-MC-PLHCC, Human Metabolome Technologies) at 9,100 × g for 2 h at 4 °C, dried in a centrifugal evaporator at 1,500 rpm at 1,000 Pa, and resuspended in 50 μl of ultrapure water before metabolome analysis. |
Combined analysis:
| Analysis ID | AN003873 | AN003874 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | CE |
| Chromatography system | Agilent 7100 CE | Agilent 7100 CE |
| Column | Fused silica capillary i.d. 50 μm × 80 cm | Fused silica capillary i.d. 50 μm × 80 cm |
| MS Type | ESI | ESI |
| MS instrument type | TOF | Triple quadrupole |
| MS instrument name | Agilent 6224 TOF | Agilent 6490 QQQ |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | nmol | nmol |
Chromatography:
| Chromatography ID: | CH002870 |
| Instrument Name: | Agilent 7100 CE |
| Column Name: | Fused silica capillary i.d. 50 μm × 80 cm |
| Chromatography Type: | CE |
MS:
| MS ID: | MS003614 |
| Analysis ID: | AN003873 |
| Instrument Name: | Agilent 6224 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using automatic integration software MasterHands (ver.2.16.0.15 Keio University). Putative metabolites were assigned based on the m/z value and migration time using Human Metabolomic Technologies’ standard library and known–unknown peak library. Peak areas were normalized to internal standards and sample amounts. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003615 |
| Analysis ID: | AN003874 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using automatic integration software (MassHunter Quantitative Analysis B.06.00, Agilent Technologies). Putative metabolites were assigned based on the m/z value and migration time using Human Metabolomic Technologies’ standard library and known–unknown peak library. Peak areas were normalized to internal standards and sample amounts. |
| Ion Mode: | NEGATIVE |
