#METABOLOMICS WORKBENCH usauamber_20231109_102504 DATATRACK_ID:4451 STUDY_ID:ST002979 ANALYSIS_ID:AN004896 VERSION 1 CREATED_ON 11-21-2023 #PROJECT PR:PROJECT_TITLE Integrated multi-omics reveals mTOR-LPL-driven dysregulated lipid metabolism PR:PROJECT_TITLE induces neuronal hyperexcitability in human microglia of tuberous sclerosis PR:PROJECT_TITLE complex PR:PROJECT_SUMMARY Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disorder PR:PROJECT_SUMMARY caused by mutations in either TSC1 or TSC2. There's evidence suggests a PR:PROJECT_SUMMARY connection between microglia activation and epilepsy as well as cognitive PR:PROJECT_SUMMARY impairment in TSC patients. However, how the causal variants of TSC1/2 genes PR:PROJECT_SUMMARY identified in TSC patients affect human microglia and how they contribute to the PR:PROJECT_SUMMARY neurological manifestations. This project is focus on this problem using human PR:PROJECT_SUMMARY microglia generated from induced pluripotent stem cells (iPSCs) derived from a PR:PROJECT_SUMMARY TSC patient. PR:INSTITUTE St Jude Children's Research Hospital PR:LAST_NAME Xie PR:FIRST_NAME Boer PR:ADDRESS 262 Danny Thomas Place, Memphis, TN, 38105, USA PR:EMAIL xbr429@gmail.com PR:PHONE (901) 595-7499 PR:DOI http://dx.doi.org/10.21228/M8XT6T #STUDY ST:STUDY_TITLE Untargeted lipidomics profiling of TSC microglia ST:STUDY_SUMMARY In this study, human microglia from induced pluripotent stem cells (iPSCs) ST:STUDY_SUMMARY derived from a TSC patient cohort were generated . With a comprehensively ST:STUDY_SUMMARY molecular and cellular characterization on TSC microglia, including ST:STUDY_SUMMARY transcriptomics, proteomics/phosphopreteomics, and lipidomics, patient-carrying ST:STUDY_SUMMARY TSC2 mutations lead to aberrant lipid metabolism were found, in particular, ST:STUDY_SUMMARY upregulated glycerophosphocholines and fatty acyls in TSC microglia, resulting ST:STUDY_SUMMARY in increased phagocytosis and inflammation. Strikingly, the dysregulated lipid ST:STUDY_SUMMARY metabolism in TSC microglia is driven by hyper-activation of mTOR-LPL pathway. ST:STUDY_SUMMARY Furthermore, cellular and electrophysiological assessments of neuron/microglia ST:STUDY_SUMMARY co-cultures revealed that TSC microglia directly affect neuronal development and ST:STUDY_SUMMARY excitability as well as neuronal network activity, which could be largely ST:STUDY_SUMMARY ameliorated by mTOR/LPL inhibition ST:INSTITUTE St Jude Children's Research Hospital ST:LAST_NAME Xie ST:FIRST_NAME Boer ST:ADDRESS 262 Danny Thomas Place, Memphis, TN, 38105, USA ST:EMAIL xbr429@gmail.com ST:PHONE (901) 595-7499 ST:SUBMIT_DATE 2023-11-09 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - TSC10-1 Genotype:TSC mutation RAW_FILE_NAME=13.raw SUBJECT_SAMPLE_FACTORS - TSC10-2 Genotype:TSC mutation RAW_FILE_NAME=14.raw SUBJECT_SAMPLE_FACTORS - TSC10-3 Genotype:TSC mutation RAW_FILE_NAME=15.raw SUBJECT_SAMPLE_FACTORS - TSC10-Homo-1 Genotype:TSC mutation RAW_FILE_NAME=16.raw SUBJECT_SAMPLE_FACTORS - TSC10-Homo-2 Genotype:TSC mutation RAW_FILE_NAME=17.raw SUBJECT_SAMPLE_FACTORS - TSC10-Homo-3 Genotype:TSC mutation RAW_FILE_NAME=18.raw SUBJECT_SAMPLE_FACTORS - TSC7-1 Genotype:TSC mutation RAW_FILE_NAME=10.raw SUBJECT_SAMPLE_FACTORS - TSC7-2 Genotype:TSC mutation RAW_FILE_NAME=11.raw SUBJECT_SAMPLE_FACTORS - TSC7-3 Genotype:TSC mutation RAW_FILE_NAME=12.raw SUBJECT_SAMPLE_FACTORS - TSC7-4 Genotype:TSC mutation RAW_FILE_NAME=26.raw SUBJECT_SAMPLE_FACTORS - 12C1-1 Genotype:wildtype RAW_FILE_NAME=19.raw SUBJECT_SAMPLE_FACTORS - 12C1-2 Genotype:wildtype RAW_FILE_NAME=20.raw SUBJECT_SAMPLE_FACTORS - 12C1-3 Genotype:wildtype RAW_FILE_NAME=21.raw SUBJECT_SAMPLE_FACTORS - 12C1-4 Genotype:wildtype RAW_FILE_NAME=22.raw SUBJECT_SAMPLE_FACTORS - 426-1 Genotype:wildtype RAW_FILE_NAME=04.raw SUBJECT_SAMPLE_FACTORS - 426-2 Genotype:wildtype RAW_FILE_NAME=05.raw SUBJECT_SAMPLE_FACTORS - 426-3 Genotype:wildtype RAW_FILE_NAME=06.raw SUBJECT_SAMPLE_FACTORS - 426-4 Genotype:wildtype RAW_FILE_NAME=24.raw SUBJECT_SAMPLE_FACTORS - C1-2-1 Genotype:wildtype RAW_FILE_NAME=01.raw SUBJECT_SAMPLE_FACTORS - C1-2-2 Genotype:wildtype RAW_FILE_NAME=02.raw SUBJECT_SAMPLE_FACTORS - C1-2-3 Genotype:wildtype RAW_FILE_NAME=03.raw SUBJECT_SAMPLE_FACTORS - C1-2-4 Genotype:wildtype RAW_FILE_NAME=23.raw SUBJECT_SAMPLE_FACTORS - PGP1-1 Genotype:wildtype RAW_FILE_NAME=07.raw SUBJECT_SAMPLE_FACTORS - PGP1-2 Genotype:wildtype RAW_FILE_NAME=08.raw SUBJECT_SAMPLE_FACTORS - PGP1-3 Genotype:wildtype RAW_FILE_NAME=09.raw SUBJECT_SAMPLE_FACTORS - PGP1-4 Genotype:wildtype RAW_FILE_NAME=25.raw #COLLECTION CO:COLLECTION_SUMMARY Cell line and sample collection were done at Emory University CO:SAMPLE_TYPE Neurons #TREATMENT TR:TREATMENT_SUMMARY No treatment applied. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Lipids were extracted from cell by cold isopropanol (10:1 v/v, solvent to SP:SAMPLEPREP_SUMMARY sample). Extracted lipids were dried under nitrogen gas, resuspended in 65% SP:SAMPLEPREP_SUMMARY acetonitrile, 30% isopropanol and 5% water. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_COMMENTS https://www.sigmaaldrich.com/US/en/product/supelco/54271u CH:INSTRUMENT_NAME Waters NanoAcquity CH:COLUMN_NAME Supelco Ascentis Express C18 (15 cm X 300 µm, 2.7µm) CH:COLUMN_TEMPERATURE RT CH:FLOW_GRADIENT 10-75%B in 34min CH:FLOW_RATE - CH:SOLVENT_A 60% water/40% acetonitrile; 10 mM ammonium formate; 0.1% formic acid CH:SOLVENT_B 90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid CH:CHROMATOGRAPHY_TYPE Reversed phase #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS MS1:120k resolution, 100-1200 m/z, 3e6 AGC, 50 ms maximal ion time MS2:top 20, MS:MS_COMMENTS 30k resolution, 2e5 AGC, 45 ms maximal ion time, stepped HCD NCE at 30, 75, 150 MS:MS_COMMENTS In-house JUMPm software and Shiny were used for data processing, feature MS:MS_COMMENTS assignment and statistic analysis MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST002979_AN004896_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Minutes #END