Hypoxia, tuberculosis, and T cell dysfunction

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Abstract. After Mycobacterium tuberculosis (Mtb) infection, 5-10% of people develop clinically evident tuberculosis (TB), most within two years. This leads to 10 million new cases of TB and 1.5 million deaths each year. Why immunity fails and permits recrudescence in people that initially control Mtb is unknown. Risk factors include diabetes, malnutrition, alcoholism, cancer, and smoking, all which cause metabolic stress. Our long-term goal is to understand the drivers of immune failure and identify protective mechanisms of immunity. A major knowledge gap is how various metabolic insults affect cellular immunity in the infected lung. Our over-arching hypothesis is that that during TB, metabolic stressors such as granuloma hypoxia contribute to T cell dysfunction, degrade immunity, and impair Mtb containment. We and others find that T cells from patients with pulmonary TB and chronically Mtb-infected mice are dysfunctional. Dysfunctional CD8 T cells (e.g., exhausted CD8 T cells) have been intensively studied because of their role in tumor immunity. In contrast, far less is known about CD4 T cell dysfunction. We will investigate both CD4 and CD8 T cells and focus on CD4 T cells as they are crucial for immunity to Mtb. We will use the murine TB model to investigate how metabolic stress affects T cell function and contributes to TB pathogenesis. An important component of our strategy is to compare T cells from susceptible mice that develop hypoxic granulomas with T cells from resistant mouse strains. The first aim is to “Determine the relationship between metabolic perturbation and T cell dysfunction.” A high-resolution map of T cell responses to Mtb in susceptible and resistant mice will be assembled after performing scRNASeq, TCRseq, conventional flow cytometry and MetFlow (to assess cell metabolism). We will determine whether dysfunctional T cells differ in their control of Mtb in vitro and in vivo. Secondly, we will “Determine how hypoxia affects T cell immunity against Mtb.” Using hypoxia fate reporter mice, we will study how hypoxia affects T cell function in vivo. These studies will be coupled with mechanistic studies using hypoxic culture conditions in vitro. We will establish how hypoxia, metabolic stress, and T cell function are related, and whether hypoxia is detrimental to protective T cell responses during TB. Finally, Aim 3 will “Assess how metabolic interventions alter T cell function and TB outcome.” We predict that drugs that correct underlying metabolic perturbations can improve T cell function and enhance control of Mtb infection. Using the hypoxic mouse models, proof-of-principle experiments will be done to determine how drugs that affect neovascularization, target metabolism, or protect mitochondria, affect Mtb containment in vivo. Our studies will determine how hypoxia and metabolic stress affect immunity to Mtb and provide insight into why CD4 immunity fails. As T cells are essential in containing Mtb infection, we hypothesize that interventions to limit T cell dysfunction or improve their function will augment Mtb containment. Metabolic reprogramming of T cells in the tumor microenvironment is on the horizon. Our hypothesis embraces the idea that metabolic therapeutics could prevent or reverse T cell dysfunction and improve TB outcome.