Summary of Study ST004134

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 PR002596. The data can be accessed directly via it's Project DOI: 10.21228/M8355F This work is supported by NIH grant, U2C- DK119886.

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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 IDST004134
Study TitleMetabolomic analysis of glycolytic intermediates in Mycobacterium tuberculosis-infected BMDMs (Bone marrow-derived macrophages)
Study SummaryGlycolytic intermediates were analyzed for Mycobacterium tuberculosis (Mtb) (Mtb)-infected BMDMs (Bone marrow-derived macrophages) either treated with vehicle control (0.2% DMSO) or 20 μM meclizine. In another set, the same metabolites were measured for Mtb-infected BMDMs grown in 10 mM glucose or galactose as the sole sugar sources in DMEM medium.
Institute
Indian Institute of Science
Last NameSingh
First NameAmit
AddressCentre for Infectious Disease Research, Bangalore, Karnataka, 560012, India
Emailcommon.aslab@gmail.com
Phone+918022933273
Submit Date2025-08-18
Raw Data AvailableYes
Raw Data File Type(s)mzML, wiff
Analysis Type DetailLC-MS
Release Date2025-08-22
Release Version1
Amit Singh Amit Singh
https://dx.doi.org/10.21228/M8355F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002596
Project DOI:doi: 10.21228/M8355F
Project Title:Bioenergetic reprogramming of macrophages reduces drug tolerance in Mycobacterium tuberculosis
Project Type:Research
Project Summary:Effective clearance of Mycobacterium tuberculosis (Mtb) requires targeting drug-tolerant populations within host macrophages. Here, we show that macrophage metabolic states govern redox heterogeneity and drug response in intracellular Mtb. Using a redox-sensitive fluorescent reporter (Mrx1-roGFP2), flow cytometry, and transcriptomics, we found that macrophages with high oxidative phosphorylation (OXPHOS) and low glycolysis harbor reductive, drug-tolerant Mtb, whereas glycolytically active macrophages generate mitochondrial ROS via reverse electron transport, imposing oxidative stress on Mtb and enhancing drug efficacy. Computational and genetic analyses identified Nrf2 as a key regulator linking host metabolism to bacterial redox state and drug tolerance. Pharmacological reprogramming of macrophages with the FDA-approved drug meclizine (MEC) shifted metabolism toward glycolysis, suppressed redox heterogeneity, and reduced Mtb drug tolerance in macrophages and mice. MEC exhibited no adverse interactions with frontline anti-TB drugs. These findings demonstrate the therapeutic potential of host metabolic reprogramming to overcome Mtb drug tolerance.
Institute:Indian Institute of Science
Department:Microbiology and Cell Biology
Last Name:Singh
First Name:Amit
Address:Centre for Infectious Disease Research, Bangalore, Karnataka, 560012, India
Email:common.aslab@gmail.com
Phone:+918022933273

Subject:

Subject ID:SU004283
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:8-10 weeks
Weight Or Weight Range:20-25
Gender:Female
Cell Biosource Or Supplier:Isolated from the bone marrow.

Factors:

Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Treatment
SA476791DMSO_a1Bone marrow-derived macrophages DMSO
SA476792DMSO_a2Bone marrow-derived macrophages DMSO
SA476793DMSO_a3Bone marrow-derived macrophages DMSO
SA476794Gal_a1Bone marrow-derived macrophages Galactose 10mM
SA476795Gal_b1Bone marrow-derived macrophages Galactose 10mM
SA476796Gal_c1Bone marrow-derived macrophages Galactose 10mM
SA476797Glu_a1Bone marrow-derived macrophages Glucose 10mM
SA476798Glu_b1Bone marrow-derived macrophages Glucose 10mM
SA476799Glu_c1Bone marrow-derived macrophages Glucose 10mM
SA476800Mec_a1Bone marrow-derived macrophages Mec 20uM
SA476801Mec_a2Bone marrow-derived macrophages Mec 20uM
SA476802Uk5_a2Bone marrow-derived macrophages UK5099 10uM
SA476803Uk5_a3Bone marrow-derived macrophages UK5099 10uM
Showing results 1 to 13 of 13

Collection:

Collection ID:CO004276
Collection Summary:Bone marrow of female C57BL/6 mice were isolated from the long bones of the legs, femur and tibia. The entire marrow was incubated for 6 days in culture medium- DMEM+10%FBS+2 mM glutamine+10 mM HEPES+1 mM sodium pyruvate+30 ng/ml macrophage colony-stimulating factor (MCSF) to differentiate monocytes into macrophages. Post 6 days, the attached cells were kept, and the supernatant was washed off. These cells were infected with Mycobacterium tuberculosis at an moi of 2 for 3 hours and 24 hours post infection kept under different treatment conditions described in the next section. During the entirety of the experiment, the cells were incubated at 37 °C and 5% CO2. Post-treatment, the cells were scraped off in 80% ethanol, heated at 80°C for 90 seconds, vortexed and heated again for 90 seconds at 80°C. Post heating, they were immediately transferred to an ice bath for 5 minutes.Post that,the cells were centrifuged at 10000 rpm for 5 minutes with the temperature maintained at 4°C. The supernatant was collected, lyophilised and stored at -80°C until further analysis described in "Sample prep".Post-treatment, the cells were scraped off in 80% ethanol, heated at 80°C for 90 seconds, vortexed and heated again for 90 seconds at 80°C. Post heating, they were immediately transferred to an ice bath for 5 minutes.
Collection Protocol Filename:BMDM_isolation_protocol.pdf
Sample Type:Macrophages

Treatment:

Treatment ID:TR004292
Treatment Summary:BMDMs were infected with Mtb at a multiplicity of infection (moi) of 2, post which the cells were divided into different treatment groups. They were either treated for 24 hours with vehicle control (0.2% DMSO), 10 μM UK5099, 20 μM Meclizine hydrochloride, 10 mM glucose or 10 mM galactose. During the treatment, cells were incubated at 37°C and 5% CO2. Post treatment, cells were scraped off and prepared for analysis as described in the "Sample prep" section.

Sample Preparation:

Sampleprep ID:SP004289
Sampleprep Summary:Metabolites were extracted, resuspended in required solvents (water for sugar phosphates) and separated on a Synergi 4-µm Fusion-RP 80 Å LC column (150 × 4.6 mm, Phenomenex) using a Shimadzu Nexera UHPLC system. Solvent system employed for sugar phosphates—Solvent A was 5 mM ammonium acetate in water, and Solvent B was 100% acetonitrile. Metabolite detection was performed using an AB Sciex Qtrap 5500 mass spectrometer with data acquired via Analyst 1.6.2 software (Sciex). Sugar phosphates were measured in negative ion mode. Quantification was carried out by calculating peak areas using MultiQuant software (version 3.0.1).
Processing Storage Conditions:-20℃

Chromatography:

Chromatography ID:CH005210
Chromatography Summary:Liquid Chromatography
Instrument Name:Shimadzu Nexera UHPLC system
Column Name:Phenomenex Synergi Fusion-RP (100 x 4.6mm,4um)
Column Temperature:25
Flow Gradient:T = 0 min, 0% B; T = 3 min, 5% B; T = 10 min, 60% B; T = 11 min, 95% B; T = 14 min, 95% B; T = 15 min, 5% B; T = 16 min, 0% B; T = 21 min, stop
Flow Rate:0.4 ml/min
Solvent A:0.1% formic acid in water
Solvent B:0.1% formic acid in methanol
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006854
Analysis Type:MS
Chromatography ID:CH005210
Num Factors:5
Num Metabolites:11
Units:peak area
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