{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001186","ANALYSIS_ID":"AN001975","VERSION":"1","CREATED_ON":"June 2, 2019, 11:31 am"},

"PROJECT":{"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"},

"STUDY":{"STUDY_TITLE":"Untargeted metabolomics on control and compound-treated STHdhQ111 cells and control STHdhQ7 cells","STUDY_SUMMARY":"Cells 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","LABORATORY":"Fraenkel Lab","LAST_NAME":"Patel-Murray","FIRST_NAME":"Natasha","ADDRESS":"77 Massachusetts Avenue, Building 16 Room 244","EMAIL":"nlpm@mit.edu","PHONE":"6179490941"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Q7SST_1",
"Factors":{"Time":"1","Treatment":"Q7SST_Control"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Q7SST_2",
"Factors":{"Time":"2","Treatment":"Q7SST_Control"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Q7SST_3",
"Factors":{"Time":"3","Treatment":"Q7SST_Control"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Q111SST_1",
"Factors":{"Time":"1","Treatment":"Q111SST_Control"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Q111SST_2",
"Factors":{"Time":"2","Treatment":"Q111SST_Control"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Q111SST_3",
"Factors":{"Time":"3","Treatment":"Q111SST_Control"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Clio_1",
"Factors":{"Time":"1","Treatment":"Clioquinol"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Clio_2",
"Factors":{"Time":"2","Treatment":"Clioquinol"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Clio_3",
"Factors":{"Time":"3","Treatment":"Clioquinol"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Cypro_1",
"Factors":{"Time":"1","Treatment":"Cyproheptadine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Cypro_2",
"Factors":{"Time":"2","Treatment":"Cyproheptadine"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Cypro_3",
"Factors":{"Time":"3","Treatment":"Cyproheptadine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Cyst_1",
"Factors":{"Time":"3","Treatment":"Cysteamine"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Cyst_2",
"Factors":{"Time":"1","Treatment":"Cysteamine"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Cyst_3",
"Factors":{"Time":"2","Treatment":"Cysteamine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Dime_1",
"Factors":{"Time":"2","Treatment":"Dimethyl fumarate"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Dime_2",
"Factors":{"Time":"3","Treatment":"Dimethyl fumarate"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Dime_3",
"Factors":{"Time":"1","Treatment":"Dimethyl fumarate"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"DKI_1",
"Factors":{"Time":"1","Treatment":"Diacylglycerol kinase inhibitor II"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"DKI_2",
"Factors":{"Time":"2","Treatment":"Diacylglycerol kinase inhibitor II"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"DKI_3",
"Factors":{"Time":"3","Treatment":"Diacylglycerol kinase inhibitor II"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"DOP_1",
"Factors":{"Time":"3","Treatment":"4-Deoxypyridoxine"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"DOP_2",
"Factors":{"Time":"1","Treatment":"4-Deoxypyridoxine"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"DOP_3",
"Factors":{"Time":"2","Treatment":"4-Deoxypyridoxine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"FTYP_1",
"Factors":{"Time":"2","Treatment":"Fingolimod phosphate"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"FTYP_2",
"Factors":{"Time":"3","Treatment":"Fingolimod phosphate"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"FTYP_3",
"Factors":{"Time":"1","Treatment":"Fingolimod phosphate"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Halo_1",
"Factors":{"Time":"2","Treatment":"Haloperidol"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Halo_2",
"Factors":{"Time":"3","Treatment":"Haloperidol"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Halo_3",
"Factors":{"Time":"1","Treatment":"Haloperidol"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Lox_1",
"Factors":{"Time":"3","Treatment":"Loxapine"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Lox_2",
"Factors":{"Time":"1","Treatment":"Loxapine"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Lox_3",
"Factors":{"Time":"2","Treatment":"Loxapine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Mec_1",
"Factors":{"Time":"2","Treatment":"Meclizine"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Mec_2",
"Factors":{"Time":"3","Treatment":"Meclizine"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Mec_3",
"Factors":{"Time":"1","Treatment":"Meclizine"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"NaB_1",
"Factors":{"Time":"3","Treatment":"Sodium Butyrate"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"NaB_2",
"Factors":{"Time":"1","Treatment":"Sodium Butyrate"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"NaB_3",
"Factors":{"Time":"2","Treatment":"Sodium Butyrate"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Nico_1",
"Factors":{"Time":"3","Treatment":"Nicotinamide"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Nico_2",
"Factors":{"Time":"1","Treatment":"Nicotinamide"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Nico_3",
"Factors":{"Time":"2","Treatment":"Nicotinamide"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Nort_1",
"Factors":{"Time":"3","Treatment":"Nortriptyline"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Nort_2",
"Factors":{"Time":"1","Treatment":"Nortriptyline"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Nort_3",
"Factors":{"Time":"2","Treatment":"Nortriptyline"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Pizo_1",
"Factors":{"Time":"2","Treatment":"Pizotifen"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Pizo_2",
"Factors":{"Time":"3","Treatment":"Pizotifen"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Pizo_3",
"Factors":{"Time":"1","Treatment":"Pizotifen"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"Seli_1",
"Factors":{"Time":"1","Treatment":"Selisistat"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"Seli_2",
"Factors":{"Time":"2","Treatment":"Selisistat"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"Seli_3",
"Factors":{"Time":"3","Treatment":"Selisistat"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"-",
"Sample ID":"TSA_1",
"Factors":{"Time":"2","Treatment":"Trichostatin A"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"-",
"Sample ID":"TSA_2",
"Factors":{"Time":"3","Treatment":"Trichostatin A"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"-",
"Sample ID":"TSA_3",
"Factors":{"Time":"1","Treatment":"Trichostatin A"},
"Additional sample data":{"Batch":"3"}
}
],
"COLLECTION":{"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_SUMMARY":"STHdh cells were incubated in serum-free medium with a compound or vehicle control for 24 hours."},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Ascentis Express C18 2.1 × 150 mm 2.7 µm column"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Whitehead Institute Metabolite Profiling Core Facility"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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).","MS_RESULTS_FILE":"ST001186_AN001975_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}