Biology subjects

Duffy, F.

Publications and source records attributed to Duffy, F..

6 recordsLinked to original sources

bioRxiv2026

Modulation of Ferroptosis During Early Mycobacterium tuberculosis Infection Contributes to Beijing Lineage Strain SA161 Virulence

Although spread of internalized Mtb from the initial infected alveolar macrophages (AMs) is a crucial determinant of infection outcomes, the role of cell death in facilitating this spread, and how it is regulated by Mtb remains poorly understood. Ferroptosis, a lipid peroxidation-mediated form of necrotic cell death, contributes to pathology during later stages of infection. However, the role of ferroptosis in early AM cell death remains inadequately defined, and its induction during infection has been primarily studied with the laboratory strain, H37Rv. Using gene set variation analysis of single cell RNAseq data profiling Mtb-infected murine lungs, we found that the hypervirulent Beijing sublineage clinical strain SA161 is associated with an elevated pro-ferroptotic transcriptional response in AMs compared to H37Rv by 17 days post infection. Consistent with these transcriptional profiles, we found that SA161 induced increased lipid peroxidation in comparison to H37Rv during infection in vitro and in vivo. Administration of the lipid peroxidation inhibitor, ferrostatin-1 (Fer-1), reduces this Mtb-induced lipid peroxidation. Notably, we found that administration of Fer-1 to Mtb-infected mice significantly reduced bacterial burden for SA161 at 14 dpi while having no effect on H37Rv. Microscopic analysis of SA161-infected lung lesions at 14 dpi suggests that inhibition of ferroptosis-driving lipid peroxidation results in a greater proportion of AMs amongst infected cells and decreased neutrophil-associated IFN signaling. Collectively, these findings reveal that ferroptosis plays an important role during early infection with virulent clinical strains of Mtb by influencing bacterial spread and signaling of immune cell responders, potentially informing host-directed intervention strategies.

immunology↗

bioRxiv2025

Single-cell profiling reveals that dynamic lung immune responses distinguish protection from susceptibility to tuberculosis

The mechanisms that underlie protective immunity to Mycobacterium tuberculosis (Mtb) remain incompletely defined. To identify immune correlates associated with protection, we performed single-cell RNA sequencing of lung immune cells after aerosol Mtb infection of naive mice and mice with contained Mtb infection (CoMtb), a model of naturally acquired resistance, across multiple time points, mouse strains, and Mtb strains. Across conditions, protection was associated with distinct temporal patterns of immune activation, cell recruitment, and resolution. Early after challenge, CoMtb mice exhibited rapid, transient recruitment and activation of CD4 T cells, macrophages, NK, and NKT cells, accompanied by short-lived bursts of type I and II interferon signaling, increased oxidative phosphorylation, and enhanced chemokine-mediated cell-cell communication. In contrast, primary infection elicited delayed but sustained interferon and neutrophil responses and higher bacterial burdens. These data indicate that protection involves dynamically coordinated immune pathways rather than the magnitude of any single response. Transcriptional features of CoMtb overlapped with those observed in nonhuman primates following intravenous BCG vaccination, including enrichment of activated tissue-resident CD4 T cells and innate effector populations. Together, these findings support a model in which effective immunity to Mtb depends on the timing and coordination of immune activation, providing a framework for vaccine strategies that reproduce protective lung immune dynamics.

immunology↗

bioRxiv2023

Mycobacterium tuberculosis infection associated immune perturbations correlate with antiretroviral immunity

Infection with Mycobacterium tuberculosis (MTB) remains one of the most important opportunistic infections in people with HIV-1 (PWH). While active Tuberculosis (TB) leads to rapid progression of immunodeficiency in PWH, the interaction between MTB and HIV-1 during the asymptomatic phase of both infections remains poorly understood. In a cohort of individuals with HIV (PWH) with and without suppressed HIV-1 viral load, the transcriptomic profiles of peripheral blood mononuclear cells (PBMC) clustered in individuals infected with Mycobacterium tuberculosis (MTB) compared to carefully matched controls. Subsequent functional annotation analysis disclosed alterations in the IL-6, TNF, and KRAS pathways. Notably, MTB-associated genes demonstrated an inverse correlation with HIV-1 viremia, evident at both on individual gene level and when employed as a gene score. In sum, our data show that MTB infection in PWH is associated with a shift in the activation state of the immune system, displaying an inverse relationship with HIV-1 viral load. These results could provide an explanation for the observed increased antiretroviral control associated with MTB infection in PWH.

immunology↗

bioRxiv2022

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

Mycobacterium tuberculosis (M.tb) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Host immune responses have been implicated in driving the progression from infection to severe lung disease. We analyzed longitudinal RNA sequencing (RNAseq) data from the whole blood of 74 TB progressors whose samples were grouped into four six-month intervals preceding diagnosis (the GC6-74 study). We additionally analyzed RNAseq data from an independent cohort of 90 TB patients with positron emission tomography-computed tomography (PET-CT) scan results which were used to categorize them into groups with high and low levels of lung damage (the Catalysis TB Biomarker study). These groups were compared to non-TB controls to obtain a complete whole blood transcriptional profile for individuals spanning from early stages of M.tb infection to TB diagnosis. The results revealed a steady increase in the number of genes that were differentially expressed in progressors at time points closer to diagnosis with 278 genes at 13-18 months, 742 at 7-12 months and 5,131 detected 1-6 months before diagnosis and 9,205 detected in TB patients. A total of 2,144 differentially expressed genes were detected when comparing TB patients with high and low levels of lung damage. There was a large overlap in the genes upregulated in progressors 1-6 months before diagnosis (86%) with those in TB patients. A comprehensive pathway analysis revealed a potent activation of neutrophil and platelet mediated defenses including neutrophil and platelet degranulation, and NET formation at both time points. These pathways were also enriched in TB patients with high levels of lung damage compared to those with low. These findings suggest that neutrophils and platelets play a critical role in TB pathogenesis, and provide details of the timing of specific effector mechanisms that may contribute to TB lung pathology. Author summaryMycobacterium tuberculosis (M.tb) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Human immune responses must be balanced to inhibit disease progression while limiting self-damage, however in defense against M.tb host responses have been implicated in lung damage and in driving progression of M.tb infection to severe lung disease. The identification of immune responses that are activated during the development of TB could provide potential targets for interventions that might suppress disease progression, and possibly limit tissue damage. Here we identify a subset of genes that function in several biological processes that are strongly activated in the late stages of TB development and in TB patients. The proteins encoded by these genes are known to degrade lung tissue and contribute to severe lung disease.

genomics↗

bioRxiv2019

Latent Mycobacterium tuberculosis infection provides protection for the host by changing the activation state of the innate immune system

An efficacious vaccine against adult tuberculosis (TB) remains elusive. Progress is hampered by an incomplete understanding of the immune mechanisms that protect against infection with Mycobacterium tuberculosis (Mtb), the causative agent of TB1. Over 90% of people who become infected with Mtb mount an immune response that contains the bacteria indefinitely, leading to a state known as "latent TB infection" (LTBI)2. A significant body of epidemiologic evidence indicates that LTBI protects against active TB after re-exposure, offering an intriguing avenue to identifying protective mechanisms3, 4. We show that in a mouse model, LTBI is highly protective against infection with Mtb for up to 100 days following aerosol challenge. LTBI mice are also protected against heterologous bacterial challenge (Listeria monocytogenes) and disseminated melanoma suggesting that protection is in part mediated by alterations in the activation state of the innate immune system. Protection is associated with elevated activation of alveolar macrophages (AM), the first cells that respond to inhaled Mtb, and accelerated recruitment of Mtb-specific T cells to the lung parenchyma upon aerosol challenge. Systems approaches, including transcriptome analysis of both naive and infected AMs, as well as ex vivo functional assays, demonstrate that LTBI reconfigures the response of tissue resident AMs.. Furthermore, we demonstrate that both LTBI mice and latently infected humans show similar alterations in the relative proportions of circulating innate immune cells, suggesting that the same cellular changes observed in the LTBI mouse model are also occurring in humans. Therefore, we argue that under certain circumstances, LTBI could be beneficial to the host by providing protection against subsequent Mtb exposure.

immunology↗

bioRxiv2018

Multinomial modelling of TB/HIV co-infection yields a robust predictive signature and generates hypotheses about the HIV+TB+ disease state.

BackgroundCurrent diagnostics are inadequate to meet the challenges presented by coinfection with Mycobacterium tuberculosis (Mtb) and HIV, the leading cause of death for HIV-infected individuals. Improved characterisation of Mtb/HIV coinfection as a distinct disease state may lead to better identification and treatment of affected individuals.\n\nMethodsFour previously published TB and HIV co-infection related datasets were used to train and validate multinomial machine learning classifiers that simultaneously predict TB and HIV status. Classifier predictive performance was measured using leave-one-out cross validation on the training set and blind predictive performance on multiple test sets using area under the ROC curve (AUC) as the performance metric. Linear modelling of signature gene expression was applied to systematically classify genes as TB-only, HIV-only or combined TB/HIV.\n\nResultsThe optimal signature discovered was a single 10-gene random forest multinomial signature that robustly discriminates active tuberculosis (TB) from other non-TB disease states with improved performance compared with previously published signatures (AUC: 0. 87), and specifically discriminates active TB/HIV co-infection from all other conditions (AUC: 0.88). Signature genes exhibited a variety of transcriptional patterns including both TB-only and HIV-only response genes and genes with expression patterns driven by interactions between HIV and TB infection states, including the CD8+ T-cell receptor LAG3 and the apoptosis-related gene CERKL.\n\nConclusionsBy explicitly including distinct disease states within the machine learning analysis framework, we developed a compact and highly diagnostic signature that simultaneously discriminates multiple disease states associated with Mtb/HIV co-infection. Examination of the expression patterns of signature genes suggests mechanisms underlying the unique inflammatory conditions associated with active TB in the presence of HIV. In particular, we observed that disregulation of CD8+ effector T-cell and NK-cell associated genes may be an important feature of Mtb/HIV co-infection.

systems biology↗