Gene expression and immune responses in tuberculosis: the effect of Mycobacterium tuberculosis-specific- and type I interferon stimulation

Abstract

Type I interferon (IFN) signatures described in active TB (ATB) show potential as biomarkers for treatment monitoring and identification of individuals at risk of disease progression. The drivers or inducers of this profile have however not been identified The research outlined in this thesis sought to examine potential drivers of the IFN signature and tested the hypothesis that IFN-α- and/or IFN-β-driven transcriptomic signatures and cytokine responses could distinguish clinical TB states. Peripheral blood mononuclear cells (PBMCs) from individuals with ATB, latent TB infection (LTBI as defined by the QuantiFERON test), tuberculin skin test-reactive (TST-positive, QuantiFERON-negative), and healthy controls (HC) were stimulated with IFN-α or IFN-β or Mycobacterium tuberculosis whole cell lysate (Mtb WCL). mRNA expression of 51 ISGs was assessed using RT-qPCR and cytokine production assessed from culture supernatants using Milliplex assays. The results showed that LTBI could be distinguished from ATB by IFN-α-driven expression of FCGR1A gene; IFN-β-driven expression of FCGR1A, FCGR1B, and SOCS3 genes; and Mtb WCL-driven expression of IFI44, IFI44L, IFIT1, and IFITIM3 genes. Similarly, IFN-α- and IFN-β-driven IL-10 protein expression could distinguish LTBI from ATB. FCGR1A, IFIT1 and IL-10 genes drive disease progression, while SOCS3, IFI44, IFI44L, and IFITM3 genes control infection. The data also showed that genes involved in macrophage polarization could distinguish ATB from either LTBI or HC. IFN-α induced expression of MSR1 that drives a detrimental M2 phenotype, whereas IFN-β and Mtb WCL induced SOCS3 and STAT1 respectively, that drive a protective M1 phenotype. IFN-α/β and Mtb WCL stimulation induced divergent immune responses. IFN-α/β stimulation upregulated ISG expression but low cytokine induction whereas Mtb WCL stimulation induced low ISG expression but upregulated cytokines. These results illustrate that ISG and cytokine responses show specificity to IFN-α, IFN-β or Mtb WCL and can distinguish LTBI from ATB. Differentially expressed genes and cytokines show protective or detrimental effects that can determine M. tuberculosis infection outcomes. This thesis research contributes to the knowledge of type I IFN responses in TB that could be used in identification of possible therapeutic targets, and of ISGs and cytokines that can be used in the diagnosis of active and latent TB.