Understanding Tuberculous Meningitis Using Omics Studies

This protocol addresses the knowledge gaps in Tuberculous Meningitis (TBM) by integrating clinical data and specimen bio-archives with state-of-the-art omics technology and computational biology in global collaborators. Performing omics studies on Vietnamese TB patients will allow Vietnamese individuals specifically to benefit from any advances identified in disease prevention or treatment.


Adjunctive corticosteroids in TBM treatment seem beneficial in some patients but ineffective or even harmful in others, maybe as a result of the highly variable inflammation and immunopathology in TBM.

Clinical trials have only proven the benefit of adjunctive corticosteroids on survival rate in HIV-negative patients, with no apparent reduction in long-term neurological disability and uncertain effect in HIV-infected patients. Therefore, there is a clear need to optimise host-directed therapy in TBM.

Omics are new technologies used to explore large amounts of data representing an entire set of genes or molecules, such as proteins, lipids, or metabolites, in a cell or patient. We propose to use omics studies (i.e., genomics, transcriptomics, metabolomics and proteomics) to investigate pathogenesis and treatment responses in TBM patients.


  • To define transcriptomic and metabolism in TBM & their genetic regulation using state-of-the-art LC-MS platforms and a combination of genome-wide SNP-typing of DNA from the same patient group and whole genome sequencing of a subset.
  • To identify biomarkers predicting the effect of corticosteroids and discover potential new targets for host-directed therapy by integrating clinical and neuro-radiological data with CSF transcriptomics, metabolomics, and host genotype.

Study design

This study integrates data and specimens from large studies in Vietnam and Indonesia with state-of-the-art omics technology and systems biology in the Netherlands and USA, including:

  • Genome-wide SNP-array;
  • Whole genome sequencing;
  • RNA sequencing and transcriptomics;
  • Metabolomics;
  • Proteomics;
  • Antibodies.


Shah JA, Warr AJ, Graustein AD, Saha A, Dunstan SJ, Thuong NTT, Thwaites GE, Caws M, Thai PVK, Bang ND, Chau TTH, Khor CC, Li Z, Hibberd M, Chang X, Nguyen FK, Hernandez CA, Jones MA, Sassetti CM, Fitzgerald KA, Musvosvi M, Gela A, Hanekom WA, Hatherill M, Scriba TJ, Hawn TR
J Immunol
February 25, 2022
DOI: 10.4049/jimmunol.2100671


Professor Michael Inouye

Professor Michael Inouye

Professor Reinout van Crevel

Professor Reinout van Crevel

Skip to content