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"PROJECT":{"PROJECT_TITLE":"Deep Metabolic Phenotyping of Newborn Cord Blood Reveals Maternal-Fetal Interactions and Disease Risk","PROJECT_SUMMARY":"Metabolites are small molecules circulating in the mother, placental, and fetal blood that can have a profound effect on a developing fetus (1, 2). Many metabolites from pregnant mothers cross the placenta to provide energy, structural components, essential nutrients, and signals to the developing fetus (3, 4). Issues with proper transmission of metabolites to the fetus, whether through gestational diabetes, placental insufficiency, or other sources can permanently damage the fetus (5-7). However, quantification of many metabolites entering and exiting the fetus are unknown; associations between microbial metabolites in umbilical cords and disease have not been thoroughly investigated; and there remains a lack of quantifiable metabolic effects of some of the most common medications administered during pregnancy and parturition. Here we identified and quantified many metabolites with a gradient between arterial and venous cord blood; we demonstrated that exogenous metabolites in umbilical cords associate with many health outcomes; and we show that medications can profoundly alter the metabolic milieu of the fetus. We greatly expanded the number of metabolites that demonstrate a gradient between arterial and venous blood, indicating absorption by the fetus, including several essential fatty acids. The microbial metabolites 3-indolepropionic acid, hydroxyhippuric acid and others are associated with many newborn diseases. Lastly, we show that exogenous medications like bupivacaine and betamethasone can have a profound impact on newborn metabolic profile. This study is the most comprehensive study of umbilical cord metabolic and disease associations to date. It reveals important aspects of fetal biology, like the reliance on specific essential fatty acid and taurine. It suggests several interventions in pregnant mothers that may help newborn health, including new fatty acids. This study serves as a valuable reference for investigators wishing to better understand the impact of medications on the developing fetus and neonate.","INSTITUTE":"Stanford University","DEPARTMENT":"Department of Genetics","LABORATORY":"Snyder Lab","LAST_NAME":"Lancaster","FIRST_NAME":"Samuel","ADDRESS":"240 Pasteur Dr, BMI bldg 4400, Stanford California, 94305","EMAIL":"slancast@stanford.edu","PHONE":"(612)-600-4033"},

"STUDY":{"STUDY_TITLE":"Deep Metabolic Phenotyping of Newborn Cord Blood Reveals Maternal-Fetal Interactions and Disease Risk","STUDY_SUMMARY":"Metabolites are small molecules circulating in the mother, placental, and fetal blood that can have a profound effect on a developing fetus (1, 2). Many metabolites from pregnant mothers cross the placenta to provide energy, structural components, essential nutrients, and signals to the developing fetus (3, 4). Issues with proper transmission of metabolites to the fetus, whether through gestational diabetes, placental insufficiency, or other sources can permanently damage the fetus (5-7). However, quantification of many metabolites entering and exiting the fetus are unknown; associations between microbial metabolites in umbilical cords and disease have not been thoroughly investigated; and there remains a lack of quantifiable metabolic effects of some of the most common medications administered during pregnancy and parturition. Here we identified and quantified many metabolites with a gradient between arterial and venous cord blood; we demonstrated that exogenous metabolites in umbilical cords associate with many health outcomes; and we show that medications can profoundly alter the metabolic milieu of the fetus. We greatly expanded the number of metabolites that demonstrate a gradient between arterial and venous blood, indicating absorption by the fetus, including several essential fatty acids. The microbial metabolites 3-indolepropionic acid, hydroxyhippuric acid and others are associated with many newborn diseases. Lastly, we show that exogenous medications like bupivacaine and betamethasone can have a profound impact on newborn metabolic profile. This study is the most comprehensive study of umbilical cord metabolic and disease associations to date. It reveals important aspects of fetal biology, like the reliance on specific essential fatty acid and taurine. It suggests several interventions in pregnant mothers that may help newborn health, including new fatty acids. This study serves as a valuable reference for investigators wishing to better understand the impact of medications on the developing fetus and neonate.","INSTITUTE":"Stanford University","DEPARTMENT":"Department of Genetics","LABORATORY":"Snyder Lab","LAST_NAME":"Lancaster","FIRST_NAME":"Samuel","ADDRESS":"240 Pasteur Dr, BMI bldg 4400, Stanford California, 94305","EMAIL":"slancast@stanford.edu","STUDY_TYPE":"Untargeted MS and Targeted MS","PHONE":"(612)-600-4033"},

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"Sample ID":"289",
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{
"Subject ID":"-",
"Sample ID":"290",
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"Sample ID":"CB246-V",
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"Additional sample data":{"RAW_FILE_NAME":"CB246-V.raw"}
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"Additional sample data":{"RAW_FILE_NAME":"CB265-V.raw"}
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"COLLECTION":{"COLLECTION_SUMMARY":"Plasma was collected from umbilical cords at the Lucile Packard Children’s Hospital Stanford with permission from the Institutional Review Board (IRB #46411). All umbilical cords were collected and sent for clinically-indicated testing to Pathology where blood gas analysis was performed following Stanford protocol. Leftover and discarded samples were obtained for research. Arterial and venous blood were extracted from umbilical cords by heparinized syringe and transferred to low binding tubes.","SAMPLE_TYPE":"Blood (plasma)"},

"TREATMENT":{"TREATMENT_SUMMARY":"Samples were centrifuged at 1300g for 10 minutes. Plasma was aliquoted in cryovials and frozen at -80°C."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites and lipids were extracted in 96-well high throughput fashion using a liquid-liquid biphasic separation with cold methyl tert-butyl ether (MTBE), methanol, and water. To begin, 1 mL MTBE was added to 40 μl of plasma and spiked with 40 μl of deuterated lipid internal standards (Sciex, cat# 5040156, lot# LPISTDKIT-103). The samples were agitated at 4°C for 30 minutes. After the addition of 250 μl cold water, samples were vortexed for 1 minute then centrifuged at 3,800 g for 5 minutes at 4°C. The upper organic phase contained the lipids while the lower aqueous phase contained metabolites with precipitated proteins at the bottom of the tube. For quality control, reference plasma samples (40 μl plasma), as well as controls lacking samples (blanks), were processed in parallel. 1) Metabolites: To further precipitate proteins, 500 μl 1:1:1 acetone: acetonitrile: methanol spiked with 16 labeled metabolite internal standards was added to 300 μl of the aqueous phase and 200 μl of the organic phase and incubated overnight at -20°C. After centrifugation at 3,800 g for 10 min at 4°C, the metabolic extracts were dried down under a stream of nitrogen gas and resuspended in 100 μl 50/50 methanol/water for LC-MS. 2) Complex lipids: 700 µl of the organic phase was dried down under a stream of nitrogen and resolubilized in 200 μl of methanol for storage at -20°C until analysis. The day of the analysis, samples were dried down, resuspended in 300 μl of 10 mM ammonium acetate in 90/10 methanol/toluene, and centrifuged at 3,800 g for 5 min at 4°C."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"None (Direct infusion)","INSTRUMENT_NAME":"Shimazdu LC-30AD","COLUMN_NAME":"None","SOLVENT_A":"9:1 Methanol Toluene with 10 mM ammonium acetate","SOLVENT_B":"N/A","FLOW_GRADIENT":"N/A","FLOW_RATE":"0.15 ml/min","COLUMN_TEMPERATURE":"20"},

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

"MS":{"INSTRUMENT_NAME":"ABI Sciex 5500 QTrap","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Lipidyzer data were reported by the Lipidomics Workflow Manager (LWM, v1.0.5.0) software which calculates concentrations for each detected lipid as average intensity of the analyte MRM relative to the average intensity of the most structurally similar internal standard (IS) MRM multiplied by its concentration. Lipids detected in less than 2/3 of the samples were discarded and missing values were imputed by drawing from a random distribution of low values class-wise in the corresponding sample. Data quality was verified by ensuring clustering of the quality control replicates analyzed on a PCA plot. We detected lipid species belonging to 13 classes (e.g. CE, CER, DAG, FFA, HCER, LCER, DCER, LPE, LPC, PC, PE, SM, TAG) and their abundance were reported as concentrations in nmol/g. The Q1 and Q3 mass provided in the metadata were used to target specific lipid classes. Lipids with the designated Q1 mass, also known as the parent ion, are selected from the first quadrupole. The lipids are then fragmented and sent to the third quadrupole. In the third quadrupole, the desired lipid class is selected based on its Q3 mass."},

"MS_METABOLITE_DATA":{
"Units":"Relative Abundance",

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