Our program consists of 3 Projects supported by 8 Technology Cores:
- In the first project, we will broadly sample the components, interactions and states of the TB molecular network during in vitro culture under hypoxic and reaeration conditions. To do so, we will integrate chromatin immunoprecipitation followed by Solexa sequencing (ChIP-Seq), transcriptomics, and comparative genomics to map the topology and baseline state of the gene regulatory network; we will apply proteomics and glycomics to identify the components and states of the corresponding protein network; and we will apply lipidomics and metabolomics to catalog the relevant components and states of the metabolic network. This first project will provide baseline in vitro measurements for understanding the molecular network of TB.
- In the second project, we will measure the state of both the host and Mtb networks in a human macrophage culture model. To do so, we will profile the levels of proteins, glycoproteins, metabolites, and lipids, and identify the gene expression state and active regulatory interactions of both Mtb derived from infected host cells (THP-1 cells). We will also apply the same profiling to the infected host cells themselves, and uninfected host cells. This project will provide insight into the response of both the macrophage and Mtb networks, and dialog that occurs between these cells, as a result of infection.
- In the third project, we will bioinformatically integrate profiling data and develop predictive computational models of the Mtb regulatory and metabolic networks. This project proceeds in parallel and iteratively with all other projects. The models developed will allow us to derive hypotheses and make predictions about the TB networks that can be validated through the other projects. Validation will in turn be used to improve the models. Ultimately, we will use these models to make predictions of Mtb state during infection in vivo.
To implement these projects we will establish 8 Technology Cores. We will establish five cores around the following high-throughput systems profiling approaches: (1) Transcriptomics, (2) ChIP-Seq, (3) Metabolomics, (4) Proteomics, (5) Glycomics, and (6) Lipidomics. We will establish two sample production and distribution cores: (1) an in vitro Culturing and Sample Distribution Core, and (2) a Host Cell Culturing and Sample Distribution Core. We will also establish a Bioinformatics Core.
The relationship between projects and cores is schematized in grey arrows. The investigators responsible for the projects and cores are described here.