Summary of Study ST003352
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 PR001855. The data can be accessed directly via it's Project DOI: 10.21228/M8XT6T 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 | ST003352 |
| Study Title | Untargeted lipidomics profiling of LPL-overexpression and LPL-knockdown microglia |
| Study Summary | In this study, human microglia from induced pluripotent stem cells (iPSCs) derived from a TSC patient cohort were generated. Upregulated glycerophosphocholines and fatty acyls were found in TSC microglia, resulting in increased phagocytosis and inflammation. Strikingly, the dysregulated lipid metabolism in TSC microglia is driven by hyper-activation of mTOR-lipoprotein lipase (LPL) pathway. Furthermore, cellular and electrophysiological assessments of neuron/microglia co-cultures revealed that TSC microglia directly affect neuronal development and excitability as well as neuronal network activity, which could be largely ameliorated by mTOR/LPL inhibition. Through integrated multi-omics analysis, levels of glycerophosphocholines were found increased in the microglia of humans with tuberous sclerosis complex. To determine whether glycerophosphocholines are regulated by the LPL gene, we performed experiments with LPL overexpression in microglia and LPL knockdown in microglia. |
| Institute | St Jude Children's Research Hospital |
| Last Name | Chu |
| First Name | Mengqi |
| Address | 262 Danny Tomas Place, Memphis, Tennessee, 38104, USA |
| Mengqi.Chu@stjude.org | |
| Phone | 901-603-2366 |
| Submit Date | 2024-07-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001855 |
| Project DOI: | doi: 10.21228/M8XT6T |
| Project Title: | Integrated multi-omics reveals mTOR-LPL-driven dysregulated lipid metabolism induces neuronal hyperexcitability in human microglia of tuberous sclerosis complex |
| Project Summary: | Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disorder caused by mutations in either TSC1 or TSC2. There's evidence suggests a connection between microglia activation and epilepsy as well as cognitive impairment in TSC patients. However, how the causal variants of TSC1/2 genes identified in TSC patients affect human microglia and how they contribute to the neurological manifestations. This project is focus on this problem using human microglia generated from induced pluripotent stem cells (iPSCs) derived from a TSC patient. |
| Institute: | St Jude Children's Research Hospital |
| Last Name: | Xie |
| First Name: | Boer |
| Address: | 262 Danny Thomas Place, Memphis, TN, 38105, USA |
| Email: | xbr429@gmail.com |
| Phone: | (901) 595-7499 |
Subject:
| Subject ID: | SU003473 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment | Sample source |
|---|---|---|---|---|
| SA365700 | TSC_2 | TSC mutation | Control for Knockdown | iPSC |
| SA365701 | TSC_5 | TSC mutation | Control for Knockdown | iPSC |
| SA365702 | TSC_4 | TSC mutation | Control for Knockdown | iPSC |
| SA365703 | TSC_3 | TSC mutation | Control for Knockdown | iPSC |
| SA365704 | TSC_1 | TSC mutation | Control for Knockdown | iPSC |
| SA365705 | KD_2 | TSC mutation | LPL knockdown | iPSC |
| SA365706 | KD_1 | TSC mutation | LPL knockdown | iPSC |
| SA365707 | KD_3 | TSC mutation | LPL knockdown | iPSC |
| SA365708 | KD_4 | TSC mutation | LPL knockdown | iPSC |
| SA365709 | KD_5 | TSC mutation | LPL knockdown | iPSC |
| SA365710 | 426_5 | WT | Control for Overexpression | iPSC |
| SA365711 | 426_2 | WT | Control for Overexpression | iPSC |
| SA365712 | 426_4 | WT | Control for Overexpression | iPSC |
| SA365713 | 426_3 | WT | Control for Overexpression | iPSC |
| SA365714 | 426_1 | WT | Control for Overexpression | iPSC |
| SA365715 | LPL_2 | WT | LPL Overexpress | iPSC |
| SA365716 | LPL_3 | WT | LPL Overexpress | iPSC |
| SA365717 | LPL_4 | WT | LPL Overexpress | iPSC |
| SA365718 | LPL_5 | WT | LPL Overexpress | iPSC |
| SA365719 | LPL_1 | WT | LPL Overexpress | iPSC |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO003466 |
| Collection Summary: | Cell line and sample collection were done at Emory University All iPSC lines have been fully characterized and cultured on Corning matrigel matrix (Corning, 354234) coated plates in human iPSC mTeSR™1 media (Stemcell, 85850). hiPSC-microglia were generated using microglia differentiation media and microglia mature media. 2 million microglia cells were collected for each sample |
| Sample Type: | Microglia |
Treatment:
| Treatment ID: | TR003482 |
| Treatment Summary: | LPL overexpression and knockdown were achieved through lentivirus infection. LPL overexpression in a control cell line and knockdown in a TSC cell line were validated by qPCR and bulk RNA-RNAseq. |
Sample Preparation:
| Sampleprep ID: | SP003480 |
| Sampleprep Summary: | Lipids were extracted from cell by cold isopropanol (10:1 v/v, solvent to sample). Extracted lipids were dried under nitrogen gas, resuspended in 65% acetonitrile, 30% isopropanol and 5% water. |
Combined analysis:
| Analysis ID | AN005493 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters NanoAcquity |
| Column | Ascentis Express C18 (150 x 0.3mm, 2.7um, 90A) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | Intensity |
Chromatography:
| Chromatography ID: | CH004176 |
| Chromatography Summary: | HPLC Capillary column, Ascentis Express C18 column, 2.7 µm, 90 Å, 15 cm × 300 µm (Supelco, cat# 54271-U) |
| Instrument Name: | Waters NanoAcquity |
| Column Name: | Ascentis Express C18 (150 x 0.3mm, 2.7um, 90A) |
| Column Temperature: | 25 |
| Flow Gradient: | 10-75%B in 34min |
| Flow Rate: | 2 uL/min |
| Solvent A: | 60% water/40% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005219 |
| Analysis ID: | AN005493 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS1:120k resolution, 100-1200 m/z, 3e6 AGC, 50 ms maximal ion time MS2:top 20, 30k resolution, 2e5 AGC, 45 ms maximal ion time, stepped HCD NCE at 30, 75, 150 In-house JUMPm software and Shiny were used for data processing, feature assignment and statistic analysis |
| Ion Mode: | POSITIVE |
