Summary of Study ST004129
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.
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.
| Study ID | ST004129 |
| Study Title | Metabolomic analysis of TCA cycle intermediates in Mycobacterium tuberculosis-infected BMDMs. |
| Study Summary | TCA cycle intermediates were analysed for Mycobacterium tuberculosis (Mtb) (Mtb)-infected BMDMs either treated with vehicle control (0.2% DMSO) or 20uM meclizine. In another set, the same metabolites were measured for Mtb-infected BMDMs grown in 10mM glucose or galactose as the sole sugar sources in DMEM medium. |
| Institute | Indian Institute of Science |
| Last Name | Singh |
| First Name | Amit |
| Address | CIDR, IISc, Bangalore, Karnataka, India |
| common.aslab@gmail.com | |
| Phone | +918022933273 |
| Submit Date | 2025-08-18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-22 |
| Release Version | 1 |
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: | SU004278 |
| 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 |
|---|---|---|---|
| SA476566 | DMSO_a1 | Bone marrow-derived macrophages | DMSO |
| SA476567 | DMSO_a2 | Bone marrow-derived macrophages | DMSO |
| SA476568 | DMSO_a3 | Bone marrow-derived macrophages | DMSO |
| SA476569 | Gal_a1 | Bone marrow-derived macrophages | Galactose 10mM |
| SA476570 | Gal_b1 | Bone marrow-derived macrophages | Galactose 10mM |
| SA476571 | Gal_c1 | Bone marrow-derived macrophages | Galactose 10mM |
| SA476572 | Glu_a1 | Bone marrow-derived macrophages | Glucose 10mM |
| SA476573 | Glu_b1 | Bone marrow-derived macrophages | Glucose 10mM |
| SA476574 | Glu_c1 | Bone marrow-derived macrophages | Glucose 10mM |
| SA476575 | Mec_a1 | Bone marrow-derived macrophages | Mec 20uM |
| SA476576 | Mec_a2 | Bone marrow-derived macrophages | Mec 20uM |
| SA476577 | Mec_a3 | Bone marrow-derived macrophages | Mec 20uM |
| SA476578 | Uk5_a1 | Bone marrow-derived macrophages | UK5099 10uM |
| SA476579 | Uk5_a2 | Bone marrow-derived macrophages | UK5099 10uM |
| SA476580 | Uk5_a3 | Bone marrow-derived macrophages | UK5099 10uM |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO004271 |
| 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. |
| Sample Type: | Macrophages |
Treatment:
| Treatment ID: | TR004287 |
| 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: | SP004284 |
| Sampleprep Summary: | Metabolites were extracted, resuspended in required solvents (50% methanol for TCA cycle intermediates) and separated on a Synergi 4-µm Fusion-RP 80 Å LC column (150 × 4.6 mm, Phenomenex) using a Shimadzu Nexera UHPLC system. TCA cycle intermediates were derivatized prior to separation. Solvent system employed for TCA intermediates—Solvent A was 0.1% formic acid in water, and Solvent B was 0.1% formic acid in methanol. Chromatographic flow parameters followed previously established settings. Metabolite detection was performed using an AB Sciex Qtrap 5500 mass spectrometer with data acquired via Analyst 1.6.2 software (Sciex). TCA intermediates were analyzed in positive ion mode. Quantification was carried out by calculating peak areas using MultiQuant software (version 3.0.1). |
| Processing Storage Conditions: | -20℃ |
Chromatography:
| Chromatography ID: | CH005199 |
| Chromatography Summary: | Liquid Chromatography |
| Instrument Name: | Shimadzu Nexera UHPLC system |
| Column Name: | Phenomenex Synergi Fusion-RP (100 x 4.6mm,4um) |
| Column Temperature: | 40 |
| Flow Gradient: | Gradient 1: T = 0 min, 50% B; T = 2 min, 75% B; T = 6 min, 100% B; T = 15 min, 100% B; T = 17 min, 50% B; T = 21 min, stop; Gradient 2: T = 0 min, 50% B; T = 2 min, 65% B; T = 12 min, 90% B; T = 12.01 min, 100% B; T = 15 min, 100% B; T = 20 min, 50% B; T = 26 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: | AN006843 |
| Analysis Type: | MS |
| Chromatography ID: | CH005199 |
| Num Factors: | 5 |
| Num Metabolites: | 9 |
| Units: | peak area |
