Summary of Study ST001186

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 PR000798. The data can be accessed directly via it's Project DOI: 10.21228/M8J399 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.

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Study IDST001186
Study TitleUntargeted metabolomics on control and compound-treated STHdhQ111 cells and control STHdhQ7 cells
Study SummaryCells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 14 protective compounds for 24 hours. Wild type cells were also treated with serum-free DMEM with vehicle (Q7SST) as an additional control for 24 hours. We examined the compounds' metabolomic effects on the cells using untargeted mass spectrometry, which measured lipids and polar metabolites.
Institute
Massachusetts Institute of Technology
LaboratoryFraenkel Lab
Last NamePatel-Murray
First NameNatasha
Address77 Massachusetts Avenue, Building 16 Room 244
Emailnlpm@mit.edu
Phone6179490941
Submit Date2019-05-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-01-22
Release Version1
Natasha Patel-Murray Natasha Patel-Murray
https://dx.doi.org/10.21228/M8J399
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000798
Project DOI:doi: 10.21228/M8J399
Project Title:A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules
Project Summary:High-throughput screening and gene signature analyses frequently identify lead therapeutic compounds with unknown modes of action (MoAs), and the resulting uncertainties can lead to the failure of clinical trials. We developed an approach for uncovering MoAs through an interpretable machine learning model of transcriptomics, epigenomics, metabolomics, and proteomics. Examining compounds with beneficial effects in models of Huntington’s Disease, we found common MoAs for compounds with unrelated structures, connectivity scores, and binding targets. The approach also predicted highly divergent MoAs for two FDA-approved antihistamines. We experimentally validated these effects, demonstrating that one antihistamine activates autophagy, while the other targets bioenergetics. The use of multiple omics was essential, as some MoAs were virtually undetectable in specific assays. Our approach does not require reference compounds or large databases of experimental data in related systems and thus can be applied to the study of agents with uncharacterized MoAs and to rare or understudied diseases.
Institute:Massachusetts Institute of Technology
Laboratory:Fraenkel Lab
Last Name:Patel-Murray
First Name:Natasha
Address:77 Massachusetts Avenue
Email:nlpm@mit.edu
Phone:6179490941

Subject:

Subject ID:SU001253
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Time Treatment
SA082420DOP_21 4-Deoxypyridoxine
SA082421Clio_11 Clioquinol
SA082422Cypro_11 Cyproheptadine
SA082423Cyst_21 Cysteamine
SA082424DKI_11 Diacylglycerol kinase inhibitor II
SA082425Dime_31 Dimethyl fumarate
SA082426FTYP_31 Fingolimod phosphate
SA082427Halo_31 Haloperidol
SA082428Lox_21 Loxapine
SA082429Mec_31 Meclizine
SA082430Nico_21 Nicotinamide
SA082431Nort_21 Nortriptyline
SA082432Pizo_31 Pizotifen
SA082433Q111SST_11 Q111SST_Control
SA082434Q7SST_11 Q7SST_Control
SA082435Seli_11 Selisistat
SA082436NaB_21 Sodium Butyrate
SA082437TSA_31 Trichostatin A
SA082438DOP_32 4-Deoxypyridoxine
SA082439Clio_22 Clioquinol
SA082440Cypro_22 Cyproheptadine
SA082441Cyst_32 Cysteamine
SA082442DKI_22 Diacylglycerol kinase inhibitor II
SA082443Dime_12 Dimethyl fumarate
SA082444FTYP_12 Fingolimod phosphate
SA082445Halo_12 Haloperidol
SA082446Lox_32 Loxapine
SA082447Mec_12 Meclizine
SA082448Nico_32 Nicotinamide
SA082449Nort_32 Nortriptyline
SA082450Pizo_12 Pizotifen
SA082451Q111SST_22 Q111SST_Control
SA082452Q7SST_22 Q7SST_Control
SA082453Seli_22 Selisistat
SA082454NaB_32 Sodium Butyrate
SA082455TSA_12 Trichostatin A
SA082456DOP_13 4-Deoxypyridoxine
SA082457Clio_33 Clioquinol
SA082458Cypro_33 Cyproheptadine
SA082459Cyst_13 Cysteamine
SA082460DKI_33 Diacylglycerol kinase inhibitor II
SA082461Dime_23 Dimethyl fumarate
SA082462FTYP_23 Fingolimod phosphate
SA082463Halo_23 Haloperidol
SA082464Lox_13 Loxapine
SA082465Mec_23 Meclizine
SA082466Nico_13 Nicotinamide
SA082467Nort_13 Nortriptyline
SA082468Pizo_23 Pizotifen
SA082469Q111SST_33 Q111SST_Control
SA082470Q7SST_33 Q7SST_Control
SA082471Seli_33 Selisistat
SA082472NaB_13 Sodium Butyrate
SA082473TSA_23 Trichostatin A
Showing results 1 to 54 of 54

Collection:

Collection ID:CO001247
Collection Summary:STHdhQ111 cells were grown on 10cm dishes in triplicate at a seeding density of 1.06 million cells/well. Compound- or vehicle-treated cells were washed with cold 0.9% NaCl. To each 10cm dish of cells, 660uL LC/MS-grade methanol containing internal standards and 330uL LC/MS-grade water were added. Cells were scraped and transferred to Eppendorf tubes, where 450uL chloroform was added. Samples were vortexed at maximum speed (20,817 rcf) for 10 minutes at 4°C. Each layer was collected separately, avoiding the precipitate at the interface of the two layers, and dried by speedvac.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001268
Treatment Summary:STHdh cells were incubated in serum-free medium with a compound or vehicle control for 24 hours.

Sample Preparation:

Sampleprep ID:SP001261
Sampleprep Summary:For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis.

Combined analysis:

Analysis ID AN001975 AN001976 AN001977 AN001978
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Ascentis Express C18 (150 x 2.1mm,2.7um) Ascentis Express C18 (150 x 2.1mm,2.7um) EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Peak area Peak area Peak Area Peak Area

Chromatography:

Chromatography ID:CH001426
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Ascentis Express C18 (150 x 2.1mm,2.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001427
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
Chromatography Type:HILIC

MS:

MS ID:MS001829
Analysis ID:AN001975
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017).
Ion Mode:POSITIVE
  
MS ID:MS001830
Analysis ID:AN001976
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017).
Ion Mode:NEGATIVE
  
MS ID:MS001831
Analysis ID:AN001977
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded.
Ion Mode:POSITIVE
  
MS ID:MS001832
Analysis ID:AN001978
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded.
Ion Mode:NEGATIVE
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