Host-directed therapies for tuberculosis: quantitative systems pharmacology approaches

Phagosomal RNA sensing through TLR8 controls susceptibility to tuberculosis

Genetic determinants of susceptibility to Mycobacterium tuberculosis (Mtb) remain poorly understood but could provide insights into critical pathways involved in infection, informing host-directed therapies and enabling risk stratification at individual and population levels. Through a genome-wide forward genetic screen, we identify Toll-like receptor 8 (TLR8) as a key regulator of intracellular killing of Mtb. Pharmacological TLR8 activation enhances the killing of phylogenetically diverse clinical isolates of drug-susceptible and multidrug-resistant Mtb by macrophages and during in vivo infection in mice. TLR8 is activated by phagosomal mycobacterial RNA released by extracellular membrane vesicles and enhances xenophagy-dependent Mtb killing. We find that the TLR8 variant M1V, common in Far Eastern populations, enhances intracellular killing of Mtb through preferential signal-dependent trafficking to phagosomes. TLR8 signaling may, therefore, both regulate susceptibility to tuberculosis and provide novel drug targets.

Unraveling the role of the immune landscape in tuberculosis granuloma

Despite significant advances in research over the past century, Tuberculosis (TB) remains a formidable global health concern. TB granulomas are organized structures composed of immune cells, that serve as the body's primary defense against the spread of Mycobacterium tuberculosis (Mtb). The immune landscape of TB granulomas involves a complex array of immune cells, including CD4+ and CD8+ T cells, B cells, NK cells, and others, which collectively influence the fate of the granuloma. B cells contribute to the formation of the granuloma's germinal center, while the functional state of T cells-particularly their ability to control infection-dictates whether the granuloma is controlling or proliferative. The intricate interplay between T cells and the dynamic microenvironment of the granuloma plays a pivotal role in determining the outcome of the infection. However, several aspects of the immunological basis of tuberculosis are still unknown. This review delves into the immunological landscape of TB granuloma, focusing on the dynamic cellular interplay within the granuloma and its profound influence on disease pathogenesis.

Post-tuberculosis lung disease: towards prevention, diagnosis, and care

There is a growing body of data describing the high burden of respiratory sequelae seen among tuberculosis survivors, including children, adolescents, and adults. This group of sequelae are known as post-tuberculosis lung disease and include parenchymal damage, airway disease, and pulmonary vascular disease. It is thought that approximately half of pulmonary tuberculosis survivors have ongoing structural pathology, lung function impairment, or respiratory symptoms after the resolution of active disease. Post-tuberculosis lung disease has been associated with adverse patient outcomes, including persistent symptoms and functional impairment, ongoing health seeking, and impacts on income and employment. There is still much to understand about the epidemiology and nature of post-tuberculosis lung disease, but in this Review we focus on strategies for prevention, diagnosis, and care to inform the ongoing work of tuberculosis-affected communities, health-care providers, researchers, and policy makers. We summarise recent data, highlight evidence gaps, and suggest key research priorities for those working in the field.

Chemokine CXCL14 Inhibits the Survival of Mycobacterium smegmatis inside Macrophages by Upregulating A20 to Promote ROS Production

Tuberculosis remains a major global health threat, with traditional antibiotic treatments facing challenges such as drug resistance. Host-directed therapy (HDT) has emerged as a promising approach to combat tuberculosis by enhancing the host immune response. CXCL14, a chemokine family member, plays a crucial role in regulating host antipathogenic immune responses. To elucidate the role of CXCL14 and its key regulatory molecules in mycobacterial infections, we identified new targets for host-directed therapy. RAW264.7 macrophages were pretreated with CXCL14 and infected with Mycobacterium smegmatis. CFU, ROS levels, and apoptosis were assessed. Cell RNA was extracted for high-throughput sequencing, and significantly differentially expressed genes were screened and identified. The effects of candidate genes were verified using knockdown and overexpression techniques. A mouse model of mycobacterial infection was established to validate the role of CXCL14 in vivo. CXCL14 pretreatment significantly reduced intracellular mycobacteria and increased ROS levels in macrophages without affecting apoptosis. Transcriptome analysis identified A20 as a key differentially expressed gene. A20 overexpression promoted ROS production and decreased intracellular mycobacteria, while A20 knockdown reversed these effects. The combination of CXCL14 and A20 overexpression effectively inhibited mycobacterial survival in macrophages. CXCL14 significantly inhibited mycobacterial survival in mice and reduced organ damage in vivo. CXCL14 promoted ROS production in macrophages by upregulating A20 expression, thereby inhibiting mycobacterial survival. In the mouse model, CXCL14 alleviated inflammatory responses and histopathological damage caused by mycobacterial infection. These findings suggest that CXCL14 is a promising new HDT molecule for the treatment of mycobacterial infections.

Timing matters in macrophage/CD4+ T cell interactions: an agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant health challenge. Clinical manifestations of TB exist across a spectrum with a majority of infected individuals remaining asymptomatic, commonly referred to as latent TB infection (LTBI). In vitro models have demonstrated that cells from individuals with LTBI can better control Mtb growth and form granuloma-like structures more quickly, compared to cells from uninfected (Mtb-naïve) individuals. These in vitro results agree with animal and clinical evidence that LTBI protects, to some degree, against reinfection. However, the mechanisms by which LTBI might offer protection against reinfection remain unclear, and quantifying the relative contributions of multiple control mechanisms is challenging using experimental methods alone. To complement in vitro models, we have developed an in silico agent-based model to help elucidate host responses that might contribute to protection against reinfection. Our simulations indicate that earlier contact between macrophages and CD4+ T cells leads to LTBI simulations having more activated CD4+ T cells and, in turn, more activated infected macrophages, all of which contribute to a decreased bacterial load early on. Our simulations also demonstrate that granuloma-like structures support this early macrophage activation in LTBI simulations. We find that differences between LTBI and Mtb-naïve simulations are driven by TNFα and IFNγ-associated mechanisms as well as macrophage phagocytosis and killing mechanisms. Together, our simulations show how important the timing of the first interactions between innate and adaptive immune cells is, how this impacts infection progression, and why cells from LTBI individuals might be faster to respond to reinfection.IMPORTANCETuberculosis (TB) remains a significant global health challenge, with millions of new infections and deaths annually. Despite extensive research, the mechanisms by which latent TB infection (LTBI) confers protection against reinfection remain unclear. In this study, we developed an in silico agent-based model to simulate early immune responses to Mycobacterium tuberculosis infection based on experimental in vitro infection of human donor cells. Our simulations reveal that early interactions between macrophages and CD4+ T cells, driven by TNFα and IFNγ, are critical for bacterial control and granuloma formation in LTBI. These findings offer new insights into the immune processes involved in TB, which could inform the development of targeted vaccines and host-directed therapies. By integrating experimental data with computational predictions, our research provides a robust framework for understanding TB immunity and guiding future interventions to mitigate the global TB burden.

Tinosporae Radix attenuates acute pharyngitis by regulating glycerophospholipid metabolism and inflammatory responses through PI3K-Akt signaling pathway

Introduction

With the onset of the COVID-19 pandemic, the incidence and prevalence of acute pharyngitis (AP) have increased significantly. Tinosporae Radix (TR) is a vital medication utilized in the treatment of pharyngeal and laryngeal ailments, especially AP. The study endeavors to explore unclear molecular mechanisms of TR in addressing AP.

Methods

Network pharmacology and metabolomics analyses of effect of TR on AP were conducted, and apossible pathway was validated both in vivo using the acute pharyngitis rat model and in vitro using the LPS-induced RAW264.7 cells model, through techniques such as histopathological examinations, immunohistochemical technology, ELISA, RT-qPCR, and Western blotting to systematically explore the possible mechanisms underlying the inhibition of AP by TR.

Results and discussion

Network pharmacology analysis identified several key targets, including PIK3CA, IL6, AKT1, TNF, and PTGS2, alongside pivotal signaling pathways such as IL-17, TNF, Hepatitis B, nuclear factor kappa B (NF-κB), Influenza A, and the PI3K-Akt pathway. Most of them are closely associated with inflammation. Then, wide-target metabolomics analysis showed that TR downregulated substances within the glycerophospholipid metabolic pathway, and modulated the PI3K-Akt pathway. The integrated findings from network pharmacology and metabolomics underscored the pivotal role of the PI3K-Akt signaling pathway and the attenuation of inflammatory responses. Finally, in vitro and in vivo experiments have shown that TR can inhibit inflammatory factors such as IL-6, TNF - α, and COX-2, downregulate targets such as PI3K and AKT on the PI3K-Akt signaling pathway, and thereby alleviate the inflammatory response of AP. Our study demonstrated that TR exerts an anti-AP effect through suppression of release of inflammatory factors and modulation of glycerophospholipid metabolism via suppressing the PI3K-Akt signaling pathway.

Monitoring host-pathogen interactions using chemical proteomics

With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.

Push forward LC-MS-based therapeutic drug monitoring and pharmacometabolomics for anti-tuberculosis precision dosing and comprehensive clinical management

The spread of tuberculosis (TB), especially multidrug-resistant TB and extensively drug-resistant TB, has strongly motivated the research and development of new anti-TB drugs. New strategies to facilitate drug combinations, including pharmacokinetics-guided dose optimization and toxicology studies of first- and second-line anti-TB drugs have also been introduced and recommended. Liquid chromatography-mass spectrometry (LC-MS) has arguably become the gold standard in the analysis of both endo- and exo-genous compounds. This technique has been applied successfully not only for therapeutic drug monitoring (TDM) but also for pharmacometabolomics analysis. TDM improves the effectiveness of treatment, reduces adverse drug reactions, and the likelihood of drug resistance development in TB patients by determining dosage regimens that produce concentrations within the therapeutic target window. Based on TDM, the dose would be optimized individually to achieve favorable outcomes. Pharmacometabolomics is essential in generating and validating hypotheses regarding the metabolism of anti-TB drugs, aiding in the discovery of potential biomarkers for TB diagnostics, treatment monitoring, and outcome evaluation. This article highlighted the current progresses in TDM of anti-TB drugs based on LC-MS bioassay in the last two decades. Besides, we discussed the advantages and disadvantages of this technique in practical use. The pressing need for non-invasive sampling approaches and stability studies of anti-TB drugs was highlighted. Lastly, we provided perspectives on the prospects of combining LC-MS-based TDM and pharmacometabolomics with other advanced strategies (pharmacometrics, drug and vaccine developments, machine learning/artificial intelligence, among others) to encapsulate in an all-inclusive approach to improve treatment outcomes of TB patients.

Nanocarriers in Tuberculosis Treatment: Challenges and Delivery Strategies

The World Health Organization identifies tuberculosis (TB), caused by Mycobacterium tuberculosis, as a leading infectious killer. Although conventional treatments for TB exist, they come with challenges such as a heavy pill regimen, prolonged treatment duration, and a strict schedule, leading to multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. The rise of MDR strains endangers future TB control. Despite these concerns, the hunt for an efficient treatment continues. One breakthrough has been the use of nanotechnology in medicines, presenting a novel approach for TB treatment. Nanocarriers, such as lipid nanoparticles, nanosuspensions, liposomes, and polymeric micelles, facilitate targeted delivery of anti-TB drugs. The benefits of nanocarriers include reduced drug doses, fewer side effects, improved drug solubility, better bioavailability, and improved patient compliance, speeding up recovery. Additionally, nanocarriers can be made even more targeted by linking them with ligands such as mannose or hyaluronic acid. This review explores these innovative TB treatments, including studies on nanocarriers containing anti-TB drugs and related patents.

Beyond the Clinic: The Activation of Diverse Cellular and Humoral Factors Shapes the Immunological Status of Patients with Active Tuberculosis

Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis (TB), has killed nearly one billion people in the last two centuries. Nowadays, TB remains a major global health problem, ranking among the thirteen leading causes of death worldwide. Human TB infection spans different levels of stages: incipient, subclinical, latent and active TB, all of them with varying symptoms, microbiological characteristics, immune responses and pathologies profiles. After infection, Mtb interacts with diverse cells of both innate and adaptive immune compartments, playing a crucial role in the modulation and development of the pathology. Underlying TB clinical manifestations, individual immunological profiles can be identified in patients with active TB according to the strength of their immune responses to Mtb infection, defining diverse endotypes. Those different endotypes are regulated by a complex interaction of the patient's cellular metabolism, genetic background, epigenetics, and gene transcriptional regulation. Here, we review immunological categorizations of TB patients based on the activation of different cellular populations (both myeloid and lymphocytic subsets) and humoral mediators (such as cytokines and lipid mediators). The analysis of the participating factors that operate during active Mtb infection shaping the immunological status or immune endotypes of TB patients could contribute to the development of Host Directed Therapy.

Reconstructed Genome-Scale Metabolic Model Characterizes Adaptive Metabolic Flux Changes in Peripheral Blood Mononuclear Cells in Severe COVID-19 Patients

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a mortal threat to human health. The elucidation of the relationship between peripheral immune cells and the development of inflammation is essential for revealing the pathogenic mechanism of COVID-19 and developing related antiviral drugs. The immune cell metabolism-targeting therapies exhibit a desirable anti-inflammatory effect in some treatment cases. In this study, based on differentially expressed gene (DEG) analysis, a genome-scale metabolic model (GSMM) was reconstructed by integrating transcriptome data to characterize the adaptive metabolic changes in peripheral blood mononuclear cells (PBMCs) in severe COVID-19 patients. Differential flux analysis revealed that metabolic changes such as enhanced aerobic glycolysis, impaired oxidative phosphorylation, fluctuating biogenesis of lipids, vitamins (folate and retinol), and nucleotides played important roles in the inflammation adaptation of PBMCs. Moreover, the main metabolic enzymes such as the solute carrier (SLC) family 2 member 3 (SLC2A3) and fatty acid synthase (FASN), responsible for the reactions with large differential fluxes, were identified as potential therapeutic targets. Our results revealed the inflammation regulation potentials of partial metabolic reactions with differential fluxes and their metabolites. This study provides a reference for developing potential PBMC metabolism-targeting therapy strategies against COVID-19.

Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy

Quantitative systems pharmacology (QSP) modeling of the host immune response against Mycobacterium tuberculosis can inform the rational design of host-directed therapies (HDTs). We aimed to develop a QSP framework to evaluate the effects of metformin-associated autophagy induction in combination with antibiotics. A QSP framework for autophagy was developed by extending a model for host immune response to include adenosine monophosphate-activated protein kinase (AMPK)-mTOR-autophagy signaling. This model was combined with pharmacokinetic-pharmacodynamic models for metformin and antibiotics against M. tuberculosis. We compared the model predictions to mice infection experiments and derived predictions for the pathogen- and host-associated dynamics in humans treated with metformin in combination with antibiotics. The model adequately captured the observed bacterial load dynamics in mice M. tuberculosis infection models treated with metformin. Simulations for adjunctive metformin therapy in newly diagnosed patients suggested a limited yet dose-dependent effect of metformin on reduction of the intracellular bacterial load when the overall bacterial load is low, late during antibiotic treatment. We present the first QSP framework for HDTs against M. tuberculosis, linking cellular-level autophagy effects to disease progression and adjunctive HDT treatment response. This framework may be extended to guide the design of HDTs against M. tuberculosis.