Summary of Study ST004396
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 PR002783. The data can be accessed directly via it's Project DOI: 10.21228/M8XK1H 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 | ST004396 |
| Study Title | More intracellular polar metabolomics on Lymphoblastoid cell lines (LCL) between individuals with Fragile X Syndrome (FXS) and from typically developing (TD) male controls. (Repeat on cell from more patients) |
| Study Summary | Metabolic changes are related to Fragile X mental retardation protein (FMRP) level. Additional patient-derived lymphoblast cell lines (LCLs) intracellular polar metabolites were measured to confirm this. FXS3 and TD6 showed persistent reductions in a number of metabolites including serine. |
| Institute | UMass Chan Medical School |
| Last Name | UMass Chan |
| First Name | Spinelli Lab |
| Address | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| spinellilab@gmail.com | |
| Phone | (508) 856-8989 ext. 68148 |
| Submit Date | 2025-11-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002783 |
| Project DOI: | doi: 10.21228/M8XK1H |
| Project Title: | Metabolic Reprogramming during Human Neuron Differentiation Indicates Glutaminase as a Key Determinant in Fragile X Syndrome |
| Project Summary: | Metabolic homeostasis gone awry is a contributor to, if not an underlying cause of, several neurologic disorders. Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by a trinucleotide repeat expansion in FMR1 and consequent loss of the encoded protein FMRP, which results in downstream molecular, neurologic, and mitochondrial deficits that are linked to cognitive impairment. In human postmortem brain, many metabolites and solute carrier proteins are coordinately dysregulated, which also occurs during differentiation of human iPSCs into excitatory neurons. Metabolic tracing in FXS neurons demonstrates a dearth of glutamine deamidation to glutamate, which reduces anaplerosis into the TCA cycle, potentially hindering bioenergetic and biosynthetic functions of mitochondria. Mechanistically, aberrant expression of glutaminase isoforms in FXS is responsible for reduced glutaminolysis, thereby altering glutamate levels which may contribute to FXS. |
| Institute: | UMass Chan Medical School |
| Last Name: | UMass Chan |
| First Name: | Richter Lab |
| Address: | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| Email: | spinellilab@gmail.com |
| Phone: | (508) 856-8989 ext. 68148 |
Subject:
| Subject ID: | SU004555 |
| 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 | Sample source | Genotype |
|---|---|---|---|
| SA521193 | FXS1 | Male Homo sapien Lymphoblastoid cell lines | FXS |
| SA521194 | FXS3 | Male Homo sapien Lymphoblastoid cell lines | FXS |
| SA521195 | TD4 | Male Homo sapien Lymphoblastoid cell lines | TD |
| SA521196 | TD6 | Male Homo sapien Lymphoblastoid cell lines | TD |
| Showing results 1 to 4 of 4 |
Collection:
| Collection ID: | CO004548 |
| Collection Summary: | Lymphoblastoid cell lines (LCLs) were obtained from the Coriell Institute, including three from individuals with Fragile X Syndrome (GM07365 (FXS1), GM03200 (FXS3) and GM06897 (FXS2)) and two from typically developing male controls (GM24086 (WT6) and GM06890 (WT4)). |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR004564 |
| Treatment Summary: | The cells were cultured in RPMI 1640 medium (Sigma-Aldrich) supplemented with 15% fetal bovine serum (FBS) and 2.5% L-glutamine, maintained at 37°C with 5% CO₂ in T25 flasks. |
Sample Preparation:
| Sampleprep ID: | SP004561 |
| Sampleprep Summary: | For extraction on cell pellets from in-vitro cultures, samples were incubated on dry ice with cold 80% methanol. The extracts were spun down and the supernatant was vacuum dried before resuspending in LC/MS grade water. |
Chromatography:
| Chromatography ID: | CH005572 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 20 min, 80% - 20% B; 0.5 min, 20% - 80% B; 7.5min, 80% B |
| Flow Rate: | 0.15ml/min |
| Solvent A: | 100% water; 0.1% ammonium hydroxide; 20mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN007347 |
| Analysis Type: | MS |
| Chromatography ID: | CH005572 |
| Num Factors: | 2 |
| Num Metabolites: | 82 |
| Units: | Peak area |
| Analysis ID: | AN007348 |
| Analysis Type: | MS |
| Chromatography ID: | CH005572 |
| Num Factors: | 2 |
| Num Metabolites: | 104 |
| Units: | Peak area |
