Summary of Study ST001258

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000844. The data can be accessed directly via it's Project DOI: 10.21228/M8KQ4X This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study ID	ST001258
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	The Hospital for Sick Children; NYU Langone Health
Department
Last Name	Jones
First Name	Drew
Address	430 E29th Street, WT635A
Email	drew.jones@nyulangone.org
Phone	6465012054
Submit Date	2019-09-23
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2019-10-11
Release Version	1

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Project:

Project ID:	PR000844
Project DOI:	doi: 10.21228/M8KQ4X
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

Subject:

Subject ID:	SU001326
Subject Type:	Invertebrate
Subject Species:	Brugia malayi
Taxonomy ID:	6279

Factors:

Subject type: Invertebrate; Subject species: Brugia malayi (Factor headings shown in green)

mb_sample_id	local_sample_id	Group
SA091398	1 20AF	AF
SA091399	3 20AF	AF
SA091400	2 20AF	AF
SA091401	6 40AM	AM
SA091402	5 40AM	AM
SA091403	4 40AM	AM
SA091404	Blank_2	Blank
SA091405	Blank_3	Blank
SA091406	Blank_1	Blank
SA091407	Blank_5	Blank
SA091408	Blank_4	Blank
SA091409	10 200 L3	L3
SA091410	11 200 L3	L3
SA091411	12 200 L3	L3
SA091412	9 2e6 Mf	Mf
SA091413	7 2e6 Mf	Mf
SA091414	8 2e6 Mf	Mf

Showing results 1 to 17 of 17

Showing results 1 to 17 of 17

Collection:

Collection ID:	CO001320
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 ID:	TR001341
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.

Treatment ID:

TR001341

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.

Sample Preparation:

Sampleprep ID:	SP001334
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.

Sampleprep ID:

SP001334

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.

Combined analysis:

Analysis ID	AN002087	AN002088
Analysis type	MS	MS
Chromatography type	HILIC	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000 RS	Thermo Dionex Ultimate 3000 RS
Column	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)	Waters Acquity BEH Phenyl (150 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	UNSPECIFIED	UNSPECIFIED
Units

Chromatography:

Chromatography ID:	CH001524
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Chromatography Type:	HILIC

Chromatography ID:	CH001525
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Waters Acquity BEH Phenyl (150 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001938
Analysis ID:	AN002087
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Positive/Negative Polarity Switching
Ion Mode:	UNSPECIFIED

MS ID:	MS001939
Analysis ID:	AN002088
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Positive/Negative Polarity Switching
Ion Mode:	UNSPECIFIED