Summary of Study ST004099

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 PR002575. The data can be accessed directly via it's Project DOI: 10.21228/M8SV6X 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 IDST004099
Study TitleA genome-scale metabolic model for deciphering the host metabolic perturbations during Mycobacterium tuberculosis infection
Study TypeMetabolomics
Study SummaryConventional tuberculosis (TB) research predominantly relies on forward-designed experiments, such as studying host responses to Mycobacterium tuberculosis (Mtb) gene knockouts. While informative, these approaches offer only a partial view of host-pathogen interactions and often overlook the broader alterations in the host microenvironment during infection. To address this limitation, we adopted a backtracing strategy to retrospectively identify host metabolic modulators and link them to specific Mtb virulence factors. Using RNA-seq data from Mtb-infected mouse lung tissue, we integrated transcriptomic profiles into a genome-scale metabolic model to predict host metabolic genes essential for Mtb survival. This analysis identified 18 host proteins as putative modulators. We then constructed a host-pathogen protein interaction network, which connected these host factors to 9 Mtb proteins. Experimental validation using Mtb knockdown strains confirmed that three genes Rv1970, Rv0243, and Rv2234 play key roles in manipulating host responses rather than supporting intrinsic bacterial viability. Further, we employed targeted proteomics and untargeted metabolomics analyses on THP-1 macrophages infected with these KD strains to dissect the host-pathogen interaction mechanisms in greater detail. These findings in troduce a novel framework for decoding host-pathogen interactions and lay the groundwork for future host-directed therapy (HDT) strategies targeting Mtb-induced host vulnerabilities.
Institute
Translational health science and technology institute
DepartmentNCD
LaboratoryBiomarker lab
Last NameKumar
First NameYashwant
AddressNCR Biotech Science Cluster,, Faridabad, Haryana, 121001, India
Emaily.kumar@thsti.res.in
Phone+911292876496
Submit Date2025-08-04
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-08-25
Release Version1
Yashwant Kumar Yashwant Kumar
https://dx.doi.org/10.21228/M8SV6X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002575
Project DOI:doi: 10.21228/M8SV6X
Project Title:A genome-scale metabolic model for deciphering the host metabolic perturbations during Mycobacterium tuberculosis infection
Project Type:Metabolomics
Project Summary:Conventional tuberculosis (TB) research predominantly relies on forward-designed experiments, such as studying host responses to Mycobacterium tuberculosis (Mtb) gene knockouts. While informative, these approaches offer only a partial view of host-pathogen interactions and often overlook the broader alterations in the host microenvironment during infection. To address this limitation, we adopted a backtracing strategy to retrospectively identify host metabolic modulators and link them to specific Mtb virulence factors. Using RNA-seq data from Mtb-infected mouse lung tissue, we integrated transcriptomic profiles into a genome-scale metabolic model to predict host metabolic genes essential for Mtb survival. This analysis identified 18 host proteins as putative modulators. We then constructed a host-pathogen protein interaction network, which connected these host factors to 9 Mtb proteins. Experimental validation using Mtb knockdown strains confirmed that three genes Rv1970, Rv0243, and Rv2234 play key roles in manipulating host responses rather than supporting intrinsic bacterial viability. Further, we employed targeted proteomics and untargeted metabolomics analyses on THP-1 macrophages infected with these KD strains to dissect the host-pathogen interaction mechanisms in greater detail. These findings in troduce a novel framework for decoding host-pathogen interactions and lay the groundwork for future host-directed therapy (HDT) strategies targeting Mtb-induced host vulnerabilities.
Institute:Translational health science and technology institute
Department:NCD
Laboratory:Biomarker lab
Last Name:Kumar
First Name:Yashwant
Address:NCR Biotech Science Cluster,, Faridabad, Haryana, 121001, India
Email:y.kumar@thsti.res.in
Phone:01292876496
Funding Source:THSTI

Subject:

Subject ID:SU004246
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Sample source
SA47452837Rv0243+Atc1 Acute monocytic leukemia cell line
SA47453431Rv0243-Atc1 Acute monocytic leukemia cell line
SA47452938Rv0243+Atc2 Acute monocytic leukemia cell line
SA47453532Rv0243-Atc2 Acute monocytic leukemia cell line
SA47453039Rv0243+Atc3 Acute monocytic leukemia cell line
SA47453633Rv0243-Atc3 Acute monocytic leukemia cell line
SA47453140Rv0243+Atc4 Acute monocytic leukemia cell line
SA47453734Rv0243-Atc4 Acute monocytic leukemia cell line
SA47453241Rv0243+Atc5 Acute monocytic leukemia cell line
SA47453835Rv0243-Atc5 Acute monocytic leukemia cell line
SA47453342Rv0243+Atc6 Acute monocytic leukemia cell line
SA47453936Rv0243-Atc6 Acute monocytic leukemia cell line
SA47454013Rv0410+Atc1 Acute monocytic leukemia cell line
SA4745467Rv0410-Atc1 Acute monocytic leukemia cell line
SA47454114Rv0410+Atc2 Acute monocytic leukemia cell line
SA4745478Rv0410-Atc2 Acute monocytic leukemia cell line
SA47454215Rv0410+Atc3 Acute monocytic leukemia cell line
SA4745489Rv0410-Atc3 Acute monocytic leukemia cell line
SA47454316Rv0410+Atc4 Acute monocytic leukemia cell line
SA47454910Rv0410-Atc4 Acute monocytic leukemia cell line
SA47454417Rv0410+Atc5 Acute monocytic leukemia cell line
SA47455011Rv0410-Atc5 Acute monocytic leukemia cell line
SA47454518Rv0410+Atc6 Acute monocytic leukemia cell line
SA47455112Rv0410-Atc6 Acute monocytic leukemia cell line
SA47455261Rv1970+Atc1 Acute monocytic leukemia cell line
SA47455855Rv1970-Atc1 Acute monocytic leukemia cell line
SA47455362Rv1970+Atc2 Acute monocytic leukemia cell line
SA47455956Rv1970-Atc2 Acute monocytic leukemia cell line
SA47455463Rv1970+Atc3 Acute monocytic leukemia cell line
SA47456057Rv1970-Atc3 Acute monocytic leukemia cell line
SA47455564Rv1970+Atc4 Acute monocytic leukemia cell line
SA47456158Rv1970-Atc4 Acute monocytic leukemia cell line
SA47455665Rv1970+Atc5 Acute monocytic leukemia cell line
SA47456259Rv1970-Atc5 Acute monocytic leukemia cell line
SA47455766Rv1970+Atc6 Acute monocytic leukemia cell line
SA47456360Rv1970-Atc6 Acute monocytic leukemia cell line
SA47456425Rv2234+Atc1 Acute monocytic leukemia cell line
SA47457019Rv2234-Atc1 Acute monocytic leukemia cell line
SA47456526Rv2234+Atc2 Acute monocytic leukemia cell line
SA47457120Rv2234-Atc2 Acute monocytic leukemia cell line
SA47456627Rv2234+Atc3 Acute monocytic leukemia cell line
SA47457221Rv2234-Atc3 Acute monocytic leukemia cell line
SA47456728Rv2234+Atc4 Acute monocytic leukemia cell line
SA47457322Rv2234-Atc4 Acute monocytic leukemia cell line
SA47456829Rv2234+Atc5 Acute monocytic leukemia cell line
SA47457423Rv2234-Atc5 Acute monocytic leukemia cell line
SA47456930Rv2234+Atc6 Acute monocytic leukemia cell line
SA47457524Rv2234-Atc6 Acute monocytic leukemia cell line
SA47457649Rv3774+Atc1 Acute monocytic leukemia cell line
SA47458243Rv3774-Atc1 Acute monocytic leukemia cell line
SA47457750Rv3774+Atc2 Acute monocytic leukemia cell line
SA47458344Rv3774-Atc2 Acute monocytic leukemia cell line
SA47457851Rv3774+Atc3 Acute monocytic leukemia cell line
SA47458445Rv3774-Atc3 Acute monocytic leukemia cell line
SA47457952Rv3774+Atc4 Acute monocytic leukemia cell line
SA47458546Rv3774-Atc4 Acute monocytic leukemia cell line
SA47458053Rv3774+Atc5 Acute monocytic leukemia cell line
SA47458647Rv3774-Atc5 Acute monocytic leukemia cell line
SA47458154Rv3774+Atc6 Acute monocytic leukemia cell line
SA47458748Rv3774-Atc6 Acute monocytic leukemia cell line
SA4745881Uninfected1 Acute monocytic leukemia cell line
SA4745892Uninfected2 Acute monocytic leukemia cell line
SA4745903Uninfected3 Acute monocytic leukemia cell line
SA4745914Uninfected4 Acute monocytic leukemia cell line
SA4745925Uninfected5 Acute monocytic leukemia cell line
SA4745936Uninfected6 Acute monocytic leukemia cell line
Showing results 1 to 66 of 66

Collection:

Collection ID:CO004239
Collection Summary:THP-1 cells (2x10^6) were seeded in 6-well plates and treated with 50 ng/mL PMA for 36 hours to induce differentiation. After PMA treatment, the medium was replaced with fresh RPMI, and the cells were allowed to mature for an additional 24 hours. Mtb infection was performed at a MOI of 5 and un-infected cells were maintained in parallel culture as control. After 4 hours of infection, extracellular bacteria were removed by three washes with pre-warmed PBS. A complete RPMI medium supplemented with 400 ng/mL ATc was added to the wells to induce the knockdown effect. The infected cells were incubated for 48 hours before being washed again with pre-warmed PBS.
Sample Type:Human acute monocytic leukemia cell line

Treatment:

Treatment ID:TR004255
Treatment Summary:THP-1 cells (2x10^6) were seeded in 6-well plates and treated with 50 ng/mL PMA for 36 hours to induce differentiation. After PMA treatment, the medium was replaced with fresh RPMI, and the cells were allowed to mature for an additional 24 hours. Mtb infection was performed at a MOI of 5 and un-infected cells were maintained in parallel culture as control. After 4 hours of infection, extracellular bacteria were removed by three washes with pre-warmed PBS. A complete RPMI medium supplemented with 400 ng/mL ATc was added to the wells to induce the knockdown effect. The infected cells were incubated for 48 hours before being washed again with pre-warmed PBS.

Sample Preparation:

Sampleprep ID:SP004252
Sampleprep Summary:To quench metabolism and extract metabolites, 1 mL of chilled methanol (HPLC grade; Sigma) was added to the cells. The cells were harvested on ice using a scraper, and the resulting extracts were transferred to pre-cooled microcentrifuge tubes (MCTs) maintained at 4°C. The extracts were vortexed for 15 minutes and centrifuged at 12000 rpm for 10 minutes at 4°C. After centrifugation, the supernatants were transferred to fresh pre-cooled MCTs (4°C), dried under vacuum, and reconstituted. The reconstituted samples were stored at -80°C until further analysis by liquid chromatography-mass spectrometry (LC-MS).

Chromatography:

Chromatography ID:CH005163
Chromatography Summary:Extracted metabolites were separated on UPLC ultimate 3,000. Data were acquired on the reverse phase and HILIC column with positive and negative ionization modes. The reverse phase column was HSS T3, and the HILIC column was XBridge BEH Amide (Waters Corporation).
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm)
Column Temperature:40°C
Flow Gradient:1% B to 95% B in 10 minutes
Flow Rate:300 µL/min
Solvent A:100% Water; 0.1% Formic acid
Solvent B:100% Methanol; 0.1% Formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH005164
Chromatography Summary:Extracted metabolites were separated on UPLC ultimate 3,000. Data were acquired on the reverse phase and HILIC column with positive and negative ionization modes. The reverse phase column was HSS T3, and the HILIC column was XBridge BEH Amide (Waters Corporation).
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters XBridge BEH Amide (100 x 2.1 mm, 2.5 µm)
Column Temperature:40°C
Flow Gradient:85% B and proceeds to 10% B over 14 minutes
Flow Rate:200 µL/min
Solvent A:100% Water; 20 mM ammonium acetate (pH-9.0)
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006795
Analysis Type:MS
Chromatography ID:CH005163
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004099_AN006795_Results.txt
Units:relative intensity
  
Analysis ID:AN006796
Analysis Type:MS
Chromatography ID:CH005163
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004099_AN006796_Results.txt
Units:relative intensity
  
Analysis ID:AN006797
Analysis Type:MS
Chromatography ID:CH005164
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004099_AN006797_Results.txt
Units:relative intensity
  
Analysis ID:AN006798
Analysis Type:MS
Chromatography ID:CH005164
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST004099_AN006798_Results.txt
Units:relative intensity
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