Gene Expression Signatures Identify Biologically and Clinically Distinct Tuberculosis Endotypes

Abstract

In vitro, animal model and anecdotal clinical evidence suggests that tuberculosis (TB) is not a monomorphic disease, and that host response to TB is protean with multiple distinct molecular pathways and pathologies (endotypes). We used unbiased clustering to identify separate TB endotypes with distinctive gene expression patterns and different clinical outcomes. A discovery cohort that included 443 TB patients and 527 asymptomatic controls identified two TB endotypes exhibiting distinct gene expression in proliferation, metabolism, and immune pathways. Specifically, TB patient endotype A was characterized by increased expression of genes related to inflammation and immunity and decreased metabolism and proliferation; in contrast, endotype B expressed increased pathways related to metabolism and proliferation. The endotype signatures were validated using an independent RNA-seq validation cohort consisting of two studies that included 118 TB patients and 208 controls. A second validation cohort confirmed differential pathway activity between TB endotypes and demonstrated that TB patients in endotype A had slower time to culture conversion, increased risk of death, and increased risk of poor clinical outcomes. These observations suggest that endotypes reflect different functional immunity; this postulate was further supported by the observation that TB patients with the hyperinflammatory endotype showed hyporesponsive cytokine and chemokine responses. Collectively, these findings provide further evidence that metabolic and immune profiling could inform and optimize targeted endotype-specific therapies for TB.