The BU-RU TBRU program is composed of four research projects that are described in full below. Their goals are to:
- Discover biomarkers to stratify risk of individuals with latent and persistent TB infection and promote their use in targeting preventive therapy.
- Use the rabbit model to establish models of latent and persistent TB that are comparable to humans in rates of Mtb replication and mutation, image findings, and sites of reactivation; and validate the use of the model to study new drugs, regimens and immunotherapies, that can be translated into the clinic.
- Discover biomarkers of Mtb persistence and treatment relapse to allow individualized short course treatment regimens and as surrogate endpoints in clinical trials.
- Unravel the role of bacterial factors such as high minimum inhibitory concentrations (MIC) (within the drug susceptible range) in persistence and investigate the genetic mechanisms for loss of persistence phenotypes that can provide a new focus for development of drugs, regimens and schedules uniquely active against persisting organisms.
Biomarker Discovery | We will use cutting-edge technology that includes Illumina’s Next-Generation whole genome sequencing platform and SOMAScan Technology for transcriptome- and proteomic-based biomarker discovery through the analysis of splice variants, novel transcripts, gene fusions, and multiple human proteins. We propose a novel hypothesis that the phenotype of memory T cells can predict whether viable Mtb are still surviving in the host. We will apply multiparametric flow cytometry coupled with the computational method of Cytokine Fingerprinting to identify patterns in the effector and memory T cell subsets that will address this hypothesis. Further, we will use tetramers to isolate antigen-specific T cells for cell surface phenotyping and RNA-Seq for gene expression. This will for the first time combine the power of cytomics with genomics in host biomarker discovery in TB.
In our search for biomarkers, we will quantify and compare the levels of interferon (IFN)-gamma (γ), interleukin (IL)-17, IL-4, and IL-10 in samples from patients with different statuses of TB infection. We will also use FDG PET/CT scan (positron emission tomography-computed tomography using 18F-fluoro-2-deoxy-glucose) as a surrogate of inflammatory activity to identify patterns of imaging findings that correlate with specific outcomes (particularly relapse versus non-relapse and progression to infection versus control of the latent focus).
Animal Model | There is a critical need to develop an animal model that reflects the human spectrum of latency. Mice and macaques have both shown limitations in filling this role. We use the New Zealand White Rabbit and an infectious Mtb strain CDC1551 as the model for LTBI in humans. Rabbits infected with this strain develop a primary infection that is rapidly contained, with Mtb soon becoming undetectable, as in human latency. To this animal model we will apply innovative approaches and techniques that include primary infection with complex bar-coded Mtb pool that will allow the study of replication dynamics and anatomical spread of latent Mtb; novel loss of persistence (LOP) mutants such as our ΔwhiB6 mutant, which will enable us to dissect the bacterial factors required for survival during LTBI; and innovative PET-CT imaging techniques that will allow us to study progression from infection to latency to disease. We will also use this model to test vaccine candidates and new treatment interventions. Ultimately, we hope to uncover the key to eradicating the paucibacillary state in treated TB patients and shortening TB therapy, identify the bacterial genes required for persistence, develop a dynamic model of drug-induced paucibacillary disease, and identify bacterial predictors of clinical relapse.