Research Article: In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis

Date Published: March 17, 2016

Publisher: Public Library of Science

Author(s): Lucy C. K. Bell, Gabriele Pollara, Mellissa Pascoe, Gillian S. Tomlinson, Rannakoe J. Lehloenya, Jennifer Roe, Richard Meldau, Robert F. Miller, Alan Ramsay, Benjamin M. Chain, Keertan Dheda, Mahdad Noursadeghi, Sarah M Fortune.


Increased risk of tuberculosis (TB) associated with HIV-1 infection is primarily attributed to deficient T helper (Th)1 immune responses, but most people with active TB have robust Th1 responses, indicating that these are not sufficient to protect against disease. Recent findings suggest that favourable outcomes following Mycobacterium tuberculosis infection arise from finely balanced inflammatory and regulatory pathways, achieving pathogen control without immunopathology. We hypothesised that HIV-1 and antiretroviral therapy (ART) exert widespread changes to cell mediated immunity, which may compromise the optimal host protective response to TB and provide novel insights into the correlates of immune protection and pathogenesis. We sought to define these effects in patients with active TB by transcriptional profiling of tuberculin skin tests (TST) to make comprehensive molecular level assessments of in vivo human immune responses at the site of a standardised mycobacterial challenge. We showed that the TST transcriptome accurately reflects the molecular pathology at the site of human pulmonary TB, and used this approach to investigate immune dysregulation in HIV-1/TB co-infected patients with distinct clinical phenotypes associated with TST reactivity or anergy and unmasking TB immune reconstitution inflammatory syndrome (IRIS) after initiation of ART. HIV-1 infected patients with positive TSTs exhibited preserved Th1 responses but deficient immunoregulatory IL10-inducible responses. Those with clinically negative TSTs revealed profound anergy of innate as well as adaptive immune responses, except for preservation of type 1 interferon activity, implicated in impaired anti-mycobacterial immunity. Patients with unmasking TB IRIS showed recovery of Th1 immunity to normal levels, but exaggerated Th2-associated responses specifically. These mechanisms of immune dysregulation were localised to the tissue microenvironment and not evident in peripheral blood. TST molecular profiling categorised different mechanisms of immunological dysfunction in HIV-1 infection beyond the effects on CD4 T cells, each associated with increased risk of TB disease and amenable to host-directed therapies.

Partial Text

One and a half million deaths are attributed to nine million new cases of active tuberculosis (TB) per annum [1]. Most individuals infected with Mycobacterium tuberculosis (Mtb) do not develop disease, but co-infection with Human immunodeficiency virus (HIV)-1 substantially increases this risk, even before progression to advanced acquired immunodeficiency syndrome (AIDS) [2,3]. HIV-1 associated TB presents more frequently as primary infection and extrapulmonary or disseminated disease [4], suggesting inadequate immunological control of Mtb. In addition, rare genetic immunodeficiencies show unequivocally that interferon (IFN)γ responses and signalling pathways associated with CD4 T helper (Th)1 immunity are necessary for protection against mycobacterial infection generally [5]. However, most people with active TB typically exhibit robust Th1/IFNγ responses [6,7] that may even contribute to immunopathology [8,9]. Therefore, factors other than Th1 immunity must contribute to protection. Recent findings suggest that favourable outcomes following Mtb infection arise from finely balanced inflammatory and regulatory pathways, and point to a putative detrimental role for type 1 IFNs [10–13]. Investigation of HIV-1 associated TB has focussed on deficient CD4 T cell responses which are evident before severe depletion of circulating CD4 T cells in AIDS [14]. However, HIV-1 infection also causes persistent type 1 IFN responses and chronic immune activation by diverse mechanisms [15–17]. Therefore, increased TB disease in HIV-1 infected patients may arise as a result of inadequate inflammatory responses that are unable to control bacillary growth, or exaggerated inflammatory responses that lead to increased immunopathogenesis. The latter are widely implicated in the mechanism underlying TB immune reconstitution inflammatory syndrome (IRIS) which can occur after initiating treatment for HIV-1 with antiretroviral therapy (ART) [18,19]. We hypothesise that unbiased genome-wide assessments of anti-mycobacterial immune responses in HIV-1 patients with and without IRIS may identify deficient responses that contribute to host protection against TB, or exaggerated responses that drive its pathogenesis. These may also extend our general understanding of immunological correlates of protection and pathogenesis in TB, and thereby allow better stratification of the risk of disease after Mtb infection, rational design of novel vaccines and development of host-directed therapies to radically shorten duration of treatment or mitigate against increasing TB drug resistance [20,21].

Transcriptional profiling of the TST provides genome-wide assessments of in-situ human immune responses to a standardised challenge. Using this approach, we quantified Mtb specific innate responses, cellular recruitment and cytokine activity within the TST. We demonstrated that the same changes are evident in the transcriptome of human pulmonary TB granulomas, and were quantitatively correlated to the degree of immunopathology as measured by the MDH. Hence, the transcriptional profile of the TST provides an accurate model of the immune responses observed in TB lung granulomas, with better resolution than peripheral blood profiling. In order to undertake this analysis, we used the only five published transcriptional data sets from caseous pulmonary TB granuloma. More transcriptomic data comparing pathological lesions from the site of TB disease to normal tissue, and comparing TB granuloma at different stages of maturation, are necessary to consolidate our findings. In addition, we assessed the TST at 48 hours in line with clinical practice [28,56], but measurements at earlier and later time points may help build a dynamic molecular model of its initiation, amplification and resolution, each of which may contribute to differences in outcome.




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