{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003608","ANALYSIS_ID":"AN005929","PROJECT_ID":"PR002231","VERSION":"1","CREATED_ON":"December 2, 2024, 2:48 pm"},

"PROJECT":{"PROJECT_TITLE":"Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses","PROJECT_SUMMARY":"Macrophages specialize in phagocytosis, a cellular process that eliminates extracellular matter, including microbes, through internalization and degradation. Despite the critical role of phagocytosis during bacterial infection, the fate of phagocytosed microbial cargo and its impact on host cell is poorly understood. Here, we reveal that ingested bacteria constitute an alternative nutrient source that skews immunometabolic host responses. Tracing stable isotope-labelled bacteria, we found that phagolysosomal degradation of bacteria provides carbon atoms and amino acids that are recycled into various metabolic pathways, including glutathione and itaconate biosynthesis, and satisfy macrophage bioenergetic needs. Metabolic recycling of microbially-derived nutrients is regulated by the nutrient sensing mTORC1 and intricately tied to microbial viability. Dead bacteria, as opposed to live ones, are enriched in cyclic- adenosine monophosphate (AMP), sustain the cellular AMP pool and subsequently activate AMP protein kinase (AMPK) to inhibit mTORC1. Consequently, killed bacteria strongly fuel metabolic recycling and support macrophage survival, but elicit decreased reactive oxygen species (ROS) production and a reduced IL-1β secretion compared to viable bacteria. These results reveal a novel insight into the fate of engulfed microbes and highlights a microbial viability-associated metabolite that triggers host metabolic and immune responses. Our findings hold promise for shaping immunometabolic intervention in various immune-related pathologies.","INSTITUTE":"University of Colorado Anschutz Medical Campus","LABORATORY":"Lab of Angelo D''Alessandro in collaboration with lab of Johan Garaude (INSERM, Fr)","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"STUDY":{"STUDY_TITLE":"Global metabolomics to compare metabolic profiles of live vs heat-killed thymidine-auxotrophe E. Coli","STUDY_SUMMARY":"Global metabolomics of live and heat-killed thymidine-auxotrophe Escherichia Coli K12 cultured or not in RPMI medium for 1h.","INSTITUTE":"University of Colorado Anschutz Medical Campus","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Escherichia coli","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"AA83eC-1_r5-",
"Factors":{"factor":"live","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-1_r5-"}
},
{
"Subject ID":"-",
"Sample ID":"AA83eC-2_r8-",
"Factors":{"factor":"live","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-2_r8-"}
},
{
"Subject ID":"-",
"Sample ID":"AA83eC-3_r1-",
"Factors":{"factor":"live","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-3_r1-"}
},
{
"Subject ID":"-",
"Sample ID":"AA83eC-4_r11-",
"Factors":{"factor":"dead","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-4_r11-"}
},
{
"Subject ID":"-",
"Sample ID":"AA83eC-5_r12-",
"Factors":{"factor":"dead","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-5_r12-"}
},
{
"Subject ID":"-",
"Sample ID":"AA83eC-6_r6-",
"Factors":{"factor":"dead","Sample source":"cells"},
"Additional sample data":{"RAW_FILE_NAME(raw file name)":"AA83eC-6_r6-"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"1E9 Bacteria were washed with cold PBS, frozen as dry cell pellet, and stored at -80˚C until processing.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Preparation of viable and killed bacteria: ThyA- E. coli were grown overnight with shaking in LB supplemented with thymidine (500 ug/ml) and trimethoprim (50 ug/ml), diluted 1/40, and grown until log-phase [optical density at 600 nm (OD600) of 0.8-1.2]. Bacteria were washed with PBS and subjected to heat-killing by re-suspension in PBS and subsequently incubation at 60˚C for 60-90 min. Efficient killing was confirmed by overnight plating on LB-agar plates."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites from frozen pellets were extracted at 1e9 cells per mL using ice cold 5:3:2 methanol:acetonitrile:water (v/v/v) with vigorous vortexing at 4 degrees C followed by centrifugation as described for 10 min at 18,000 g. Supernatants were maintained at 4°C until analysis that same day.","PROCESSING_STORAGE_CONDITIONS":"4℃","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Negative C18","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)","SOLVENT_A":"95% water/5% acetonitrile; 1 mM ammonium acetate","SOLVENT_B":"95% acetonitrile/5% water; 1 mM ammonium acetate","FLOW_GRADIENT":"0-0.5 min 0% B, 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B","FLOW_RATE":"450 uL/min","COLUMN_TEMPERATURE":"45","SAMPLE_INJECTION":"10 uL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap Exploris 120","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"We use a Thermo Orbitrap Exploris 120. Resolution 120,000, scan range 65-975 m/z, maximum injection time 100 ms, microscans 1, automatic gain control (AGC) detection duration 20 msec, source voltage 2.0 kV, capillary temperature 320 C, vaporizer temp 200 C, and sheath gas 50, auxiliary gas 10, and sweep gas 1 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database."},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"Aspartate","AA83eC-1_r5-":"1409291.62","AA83eC-2_r8-":"1422479.12","AA83eC-3_r1-":"1482790.62","AA83eC-4_r11-":"50124.42","AA83eC-5_r12-":"66228.27","AA83eC-6_r6-":"2594779.75"},{"Metabolite":"Glutamate","AA83eC-1_r5-":"9370041","AA83eC-2_r8-":"9965182","AA83eC-3_r1-":"9830204","AA83eC-4_r11-":"478054.53","AA83eC-5_r12-":"531809.81","AA83eC-6_r6-":"2062914.12"},{"Metabolite":"Glutamine","AA83eC-1_r5-":"79350.1","AA83eC-2_r8-":"107543.12","AA83eC-3_r1-":"106924.78","AA83eC-4_r11-":"0","AA83eC-5_r12-":"2614.04","AA83eC-6_r6-":"8220.31"},{"Metabolite":"Proline","AA83eC-1_r5-":"26164.38","AA83eC-2_r8-":"40644.21","AA83eC-3_r1-":"32125.55","AA83eC-4_r11-":"4670.14","AA83eC-5_r12-":"1577.74","AA83eC-6_r6-":"80248.98"},{"Metabolite":"ATP","AA83eC-1_r5-":"104299.53","AA83eC-2_r8-":"109805.81","AA83eC-3_r1-":"80054.21","AA83eC-4_r11-":"0","AA83eC-5_r12-":"0","AA83eC-6_r6-":"0"},{"Metabolite":"ADP","AA83eC-1_r5-":"1134279.38","AA83eC-2_r8-":"1111581.62","AA83eC-3_r1-":"1643609.88","AA83eC-4_r11-":"6785.48","AA83eC-5_r12-":"5481.42","AA83eC-6_r6-":"5092.03"},{"Metabolite":"AMP","AA83eC-1_r5-":"2283457.25","AA83eC-2_r8-":"2387506","AA83eC-3_r1-":"3142198.75","AA83eC-4_r11-":"21313.98","AA83eC-5_r12-":"21126.64","AA83eC-6_r6-":"19943.98"},{"Metabolite":"dAMP","AA83eC-1_r5-":"421190.59","AA83eC-2_r8-":"483367.38","AA83eC-3_r1-":"547162.56","AA83eC-4_r11-":"0","AA83eC-5_r12-":"0","AA83eC-6_r6-":"0"},{"Metabolite":"GDP","AA83eC-1_r5-":"274251.03","AA83eC-2_r8-":"250313.62","AA83eC-3_r1-":"301401.34","AA83eC-4_r11-":"1041.13","AA83eC-5_r12-":"4184.64","AA83eC-6_r6-":"2459.57"},{"Metabolite":"GMP","AA83eC-1_r5-":"1361403.12","AA83eC-2_r8-":"1513631.12","AA83eC-3_r1-":"2018037.88","AA83eC-4_r11-":"20090.47","AA83eC-5_r12-":"17887.51","AA83eC-6_r6-":"21270.26"},{"Metabolite":"CTP","AA83eC-1_r5-":"69679.74","AA83eC-2_r8-":"71014.25","AA83eC-3_r1-":"69346.3","AA83eC-4_r11-":"0","AA83eC-5_r12-":"0","AA83eC-6_r6-":"0"},{"Metabolite":"CDP","AA83eC-1_r5-":"684191","AA83eC-2_r8-":"667164.19","AA83eC-3_r1-":"882066.25","AA83eC-4_r11-":"211860.83","AA83eC-5_r12-":"195865.2","AA83eC-6_r6-":"144027.77"},{"Metabolite":"CMP","AA83eC-1_r5-":"1550957","AA83eC-2_r8-":"1818933.38","AA83eC-3_r1-":"2263162.75","AA83eC-4_r11-":"44465.5","AA83eC-5_r12-":"42487.43","AA83eC-6_r6-":"29847.42"},{"Metabolite":"dCMP","AA83eC-1_r5-":"453357","AA83eC-2_r8-":"462122.5","AA83eC-3_r1-":"478290.38","AA83eC-4_r11-":"0","AA83eC-5_r12-":"1591.11","AA83eC-6_r6-":"1036.78"},{"Metabolite":"UTP","AA83eC-1_r5-":"55270.92","AA83eC-2_r8-":"56518.43","AA83eC-3_r1-":"55600.52","AA83eC-4_r11-":"0","AA83eC-5_r12-":"0","AA83eC-6_r6-":"0"},{"Metabolite":"UDP","AA83eC-1_r5-":"823822.31","AA83eC-2_r8-":"778392.75","AA83eC-3_r1-":"984218","AA83eC-4_r11-":"15999.67","AA83eC-5_r12-":"9629.69","AA83eC-6_r6-":"0"},{"Metabolite":"UMP","AA83eC-1_r5-":"4518794.5","AA83eC-2_r8-":"4773795","AA83eC-3_r1-":"5532267.5","AA83eC-4_r11-":"60336.47","AA83eC-5_r12-":"53739.35","AA83eC-6_r6-":"38298.76"},{"Metabolite":"Uracil","AA83eC-1_r5-":"1973220.62","AA83eC-2_r8-":"1870286","AA83eC-3_r1-":"1138379.62","AA83eC-4_r11-":"54792.41","AA83eC-5_r12-":"60860.81","AA83eC-6_r6-":"56914.73"},{"Metabolite":"IMP","AA83eC-1_r5-":"27241.12","AA83eC-2_r8-":"34557.49","AA83eC-3_r1-":"15924.6","AA83eC-4_r11-":"0","AA83eC-5_r12-":"0","AA83eC-6_r6-":"0"},{"Metabolite":"Urate","AA83eC-1_r5-":"99581.56","AA83eC-2_r8-":"150954.48","AA83eC-3_r1-":"70794.38","AA83eC-4_r11-":"0","AA83eC-5_r12-":"2124.43","AA83eC-6_r6-":"33465.32"},{"Metabolite":"3'',5''-Cyclic 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