{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001258","ANALYSIS_ID":"AN002088","VERSION":"1","CREATED_ON":"September 30, 2019, 8:33 pm"},

"PROJECT":{"PROJECT_TITLE":"Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets","PROJECT_SUMMARY":"The filarial nematode Brugia malayi represents a leading cause of disability in the developing world, causing lymphatic filariasis in nearly 40 million people. Currently available drugs are not well-suited to mass drug administration efforts, so new treatments are urgently required. One potential vulnerability is the endosymbiotic bacteria Wolbachia—present in many filariae—which is vital to the worm. Genome scale metabolic networks have been used to study prokaryotes and protists and have proven valuable in identifying therapeutic targets, but only recently have been applied to eukaryotic organisms. Here, we present iDC625, the first compartmentalized metabolic model of a parasitic worm. We used this model to show how metabolic pathway usage allows the worm to adapt to different environments, and predict a set of 99 reactions essential to the survival of B. malayi. We validated three of those reactions with drug tests and demonstrated novel antifilarial properties for all three compounds.","INSTITUTE":"NYU Langone Health","LAST_NAME":"Jones","FIRST_NAME":"Drew","ADDRESS":"430 E29th Street, WT635A","EMAIL":"drew.jones@nyulangone.org","PHONE":"6465012054"},

"STUDY":{"STUDY_TITLE":"Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets","STUDY_SUMMARY":"The filarial nematode Brugia malayi represents a leading cause of disability in the developing world, causing lymphatic filariasis in nearly 40 million people. Currently available drugs are not well-suited to mass drug administration efforts, so new treatments are urgently required. One potential vulnerability is the endosymbiotic bacteria Wolbachia—present in many filariae—which is vital to the worm. Genome scale metabolic networks have been used to study prokaryotes and protists and have proven valuable in identifying therapeutic targets, but only recently have been applied to eukaryotic organisms. Here, we present iDC625, the first compartmentalized metabolic model of a parasitic worm. We used this model to show how metabolic pathway usage allows the worm to adapt to different environments, and predict a set of 99 reactions essential to the survival of B. malayi. We validated three of those reactions with drug tests and demonstrated novel antifilarial properties for all three compounds.","INSTITUTE":"Hospital for Sick Children, University of Toronto, NYU Langone Health","LAST_NAME":"Jones","FIRST_NAME":"Drew","ADDRESS":"430 E29th Street, WT635A","EMAIL":"drew.jones@nyulangone.org","PHONE":"6465012054"},

"SUBJECT":{"SUBJECT_TYPE":"Invertebrate","SUBJECT_SPECIES":"Brugia malayi","TAXONOMY_ID":"6279"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"S00869",
"Sample ID":"1 20AF",
"Factors":{"Group":"AF"}
},
{
"Subject ID":"S00870",
"Sample ID":"2 20AF",
"Factors":{"Group":"AF"}
},
{
"Subject ID":"S00871",
"Sample ID":"3 20AF",
"Factors":{"Group":"AF"}
},
{
"Subject ID":"S00872",
"Sample ID":"4 40AM",
"Factors":{"Group":"AM"}
},
{
"Subject ID":"S00873",
"Sample ID":"5 40AM",
"Factors":{"Group":"AM"}
},
{
"Subject ID":"S00874",
"Sample ID":"6 40AM",
"Factors":{"Group":"AM"}
},
{
"Subject ID":"S00875",
"Sample ID":"7 2e6 Mf",
"Factors":{"Group":"Mf"}
},
{
"Subject ID":"S00876",
"Sample ID":"8 2e6 Mf",
"Factors":{"Group":"Mf"}
},
{
"Subject ID":"S00877",
"Sample ID":"9 2e6 Mf",
"Factors":{"Group":"Mf"}
},
{
"Subject ID":"S00878",
"Sample ID":"10 200 L3",
"Factors":{"Group":"L3"}
},
{
"Subject ID":"S00879",
"Sample ID":"11 200 L3",
"Factors":{"Group":"L3"}
},
{
"Subject ID":"S00880",
"Sample ID":"12 200 L3",
"Factors":{"Group":"L3"}
},
{
"Subject ID":"SQ93_B_1",
"Sample ID":"Blank_1",
"Factors":{"Group":"Blank"}
},
{
"Subject ID":"SQ93_B_2",
"Sample ID":"Blank_2",
"Factors":{"Group":"Blank"}
},
{
"Subject ID":"SQ93_B_3",
"Sample ID":"Blank_3",
"Factors":{"Group":"Blank"}
},
{
"Subject ID":"SQ93_B_4",
"Sample ID":"Blank_4",
"Factors":{"Group":"Blank"}
},
{
"Subject ID":"SQ93_B_5",
"Sample ID":"Blank_5",
"Factors":{"Group":"Blank"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"All parasites were obtained from FR3 (Filariasis Research Reagent Resource Center; BEI Resources, Manassas, VA, USA) where they were isolated and separated by sex from infected gerbils (Meriones unguiculatus) or mosquitoes (Aedes aegypti). Worms were flash-frozen and shipped to the New York Blood Center for processing. Stages used for metabolomics analysis included L3 larvae from mosquitoes, adult male and female worms at 120dpi, and microfilaria. The number of worms per sample were 20 adult female worms, 40 adult males, 2X106 microfilariae, and 200 L3 larvae per biological replicate. Samples were washed in 1x PBS and run in triplicate. Adult male and female worms were picked individually from PBS and each biological was weighed. The microfilaria and L3 samples were spun down, the PBS pipetted off, and weighed directly into a metabolomics 2mL screw cap vial with total amounts ranging from 1.3 mg (adult males) to 15.8 mg (microfilaria). Metabolites were extracted and the data analyzed as described in the Supplementary Information.","SAMPLE_TYPE":"Worms"},

"TREATMENT":{"TREATMENT_SUMMARY":"All parasites were obtained from FR3 (Filariasis Research Reagent Resource Center; BEI Resources, Manassas, VA, USA) where they were isolated and separated by sex from infected gerbils (Meriones unguiculatus) or mosquitoes (Aedes aegypti). Worms were flash-frozen and shipped to the New York Blood Center for processing. Stages used for metabolomics analysis included L3 larvae from mosquitoes, adult male and female worms at 120dpi, and microfilaria. The number of worms per sample were 20 adult female worms, 40 adult males, 2X106 microfilariae, and 200 L3 larvae per biological replicate. Samples were washed in 1x PBS and run in triplicate. Adult male and female worms were picked individually from PBS and each biological was weighed. The microfilaria and L3 samples were spun down, the PBS pipetted off, and weighed directly into a metabolomics 2mL screw cap vial with total amounts ranging from 1.3 mg (adult males) to 15.8 mg (microfilaria). Metabolites were extracted and the data analyzed as described in the Supplementary Information."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolite extraction – The mass of the weighed worm samples was used to scale the metabolite extraction to a ratio of 16.5 mg / 1 mL extraction solvent. Freezing 80% acetonitrile was added directly to each vial containing the samples, along with zirconium disruption beads (0.5 mm, RPI) and homogenized for 3 min at 4°C in a BeadBlasterTM with a 30 sec on, 30 sec off pattern. The resulting lysate was centrifuged at 21,000 x g for 3 min, and 90% of the supernatant volume was transferred to a 1.5 mL microfuge tube for speed vacuum concentration, no heating. The dry extracts were resolublized in a volume of LCMS grade water 1/10th of that used for the homogenization step, sonicated in a water bath for 3 min, and transferred to a glass insert for analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"Waters Acquity BEH Phenyl (150 x 2.1mm, 1.7um)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Positive/Negative Polarity Switching"}

}