scRNA-seq in TB/HIV


We have showed that initiation of antiretroviral therapy (cART) at peak viremia led to i) better control of viral replication, ii) significantly reduced immune activation in the lung vasculature and iii) reduced macrophage turnover in the lung of macaques. However, skewed CD4+ T effector memory responses persisted and new TB lesions formed despite cART initiation as early as 2 weeks post-SIV. Understanding why skewed effector responses persist despite the control of viral replication by cART is critical to forming a causal link between immune activation and T cell function. Similar to humans, SIV differentially impacts alveolar macrophages (in BAL) and interstitial macrophages in lungs. We hypothesize that cART is unable to rescue the impaired T- effector function in the lungs of Mtb/SIV co-infected macaques despite reducing the macrophage turnover resulting in worsening of disease condition and LTBI reactivation. Our research utilizes scRNA-seq technology to identify the specific lineage markers in the interplay between macrophages and CD4+ T cells that remain impaired despite cART. This is critical to developing interventions to control immune activation and prevent LTBI reactivation upon HIV co-infection.

Figure 1:_scRNA-seq review

Highlighted Publications

  • Sharan, Riti, Dhiraj Kumar Singh, Jyothi Rengarajan, and Deepak Kaushal. (2021) 2021. “Characterizing Early T Cell Responses in Nonhuman Primate Model of Tuberculosis”. Frontiers in Immunology 12: 706723.

    Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a leading infectious disease killer worldwide with 1.4 million TB deaths in 2019. While the majority of infected population maintain an active control of the bacteria, a subset develops active disease leading to mortality. Effective T cell responses are critical to TB immunity with CD4+ and CD8+ T cells being key players of defense. These early cellular responses to TB infection have not yet been studied in-depth in either humans or preclinical animal models. Characterizing early T cell responses in a physiologically relevant preclinical model can provide valuable understanding of the factors that control disease development. We studied Mtb-specific T cell responses in the lung compartment of rhesus macaques infected with either a low- or a high-dose of Mtb CDC1551 via aerosol. Relative to baseline, significantly higher Mtb-specific CD4+IFN-γ+ and TNF-α+ T cell responses were observed in the BAL of low dose infected macaques as early as week 1 post TB infection. The IFN-γ and TNF-a response was delayed to week 3 post infection in Mtb-specific CD4+ and CD8+T cells in the high dose group. The manifestation of earlier T cell responses in the group exposed to the lower Mtb dose suggested a critical role of these cytokines in the antimycobacterial immune cascade, and specifically in the granuloma formation to contain the bacteria. However, a similar increase was not reflected in the CD4+ and CD8+IL-17+ T cells at week 1 post infection in the low dose group. This could be attributed to either a suppression of the IL-17 response or a lack of induction at this early stage of infection. On the contrary, there was a significantly higher IL-17+ response in Mtb-specific CD4+ and CD8+T cells at week 3 in the high dose group. The results clearly demonstrate an early differentiation in the immunity following low dose and high dose infection, largely represented by differences in the IFN-γ and TNF-α response by Mtb-specific T cells in the BAL. This early response to antigen expression by the bacteria could be critical for both bacterial growth control and bacterial containment.