Biology subjects

Naidoo, T.

Publications and source records attributed to Naidoo, T..

11 recordsLinked to original sources

bioRxiv2026

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

Tertiary lymphoid structures (TLSs) are sites of immune organization in peripheral tissues that arise from chronic inflammation. They play important roles in infection control and cancer but the mechanisms controlling their formation remain only partly understood. Here, we combine high-plex imaging, serial-section 3D reconstruction, and optimal transport trajectory modeling to reconstruct TLSs in human lungs infected with Mycobacterium tuberculosis. We find that the extended and irregular shape of TLSs is poorly captured by 2D histopathology or spatial profiling, making assessment of developmental stage (early, primary, or secondary) error prone. In contrast, modeling TLS development in 3D using optimal transport reveals two trajectories that differ in the timing and coordination of follicular dendritic cell association, germinal center consolidation, and position within the tissue. These findings highlight the value of volumetric analysis in understanding immune organization and provide new insights into TLS biology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/725201v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@11b4daorg.highwire.dtl.DTLVardef@7871feorg.highwire.dtl.DTLVardef@1840c2dorg.highwire.dtl.DTLVardef@3b6028_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI3D reconstruction of TB-infected lung reveals TLSs to be extended, heterogeneous structures that are frequently misclassified in 2D C_LIO_LITLS maturation follows continuous trajectories rather than discrete histological stages C_LIO_LIOptimal transport modeling identifies distinct maturation paths with divergent follicular dynamics C_LIO_LIGerminal center organization and Tfh-FDC interactions emerge along maturation trajectories C_LIO_LITLS maturation states are shaped by spatially localized microenvironmental niches. C_LI

immunology↗

bioRxiv2026

Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders

Light microscopy of tissue sections stained with hematoxylin and eosin (H&E) has been the foundation of histopathology for over 150 years and remains essential for diagnosis and research. The development of high-plex spatial profiling approaches able to measure protein and RNA expression at single-cell resolution augments but does not replace H&E imaging, even in research. Computational pathology (CPath) models based on deep learning promise to further increase the value of H&E imaging but interpreting these models in biological terms remains challenging. As a result, they are not widely used in spatial profiling studies. Here we describe a human-in-the-loop computational framework that leverages CPath foundation models (FMs) and sparse autoencoders (SAEs) to decompose FM embeddings and automatically identify diverse, human-interpretable histopathology features in H&E images. When FM-SAE modeling was applied to pulmonary diseases such as tuberculosis and lung cancer, human-machine interaction augmented and accelerated expert interpretation. Moreover, the resulting annotations provide a morphology-aware approach to integrating 2D and 3D mesoscale tissue architectures with molecular spatial profiling.

bioinformatics↗

bioRxiv2026

Glucose selectively drives a rapid oxidative burst and immunometabolic reprogramming in human neutrophils during Mycobacterium tuberculosis infection

Neutrophil functions have been linked to tuberculosis (TB)-associated tissue damage; however, the mechanisms driving immunopathology in the human TB lung remain poorly understood, due partly to the scarcity of human tissue for study. Here, we examine the metabolic and bioenergetic reprogramming of human neutrophils in response to Mycobacterium tuberculosis (Mtb) infection. In human necrotic TB granulomas, levels of NETosis-associated proteins are increased and co-localize with GLUT3, linking nutrient uptake to tissue damage. In vitro, Mtb elicits an immediate, contact-dependent oxidative burst in human neutrophils, and the magnitude of this response is carbon source-dependent. Glucose enables the most robust responses, indicating that glucose metabolism is a key driver of neutrophil-mediated inflammatory damage during TB. Mtb-induced responses are distinct from those induced by PMA, non-tuberculous mycobacteria, or other pathogenic intracellular bacteria, and are mediated through multiple neutrophil surface receptors. Notably, our data show that while the oxidative burst is carbon source-dependent, cytokine production is not. Further, Mtb infection reprograms neutrophil metabolism from glycolysis to the pentose phosphate pathway (PPP), generating NADPH required for the oxidative burst. Inhibiting G6PD, NADPH oxidase, or PAD4 significantly reduces this response, highlighting the PPP as a promising host target for mitigating TB immunopathology.

microbiology↗

bioRxiv2025

Targeting ALOX5/LTA4H driven granuloma caseation as a host-directed strategy for control of TB associated lung damage

Tuberculosis remains one of the major global health challenges with those previously exposed presenting persisting pulmonary dysfunction. Therefore, improved control measures are still required to prevent or reduce the TB-induced immunopathology in affected individuals. Host directed therapies that target host factors, have been suggested to improve on current treatments against TB. We previously reported a potential role for proteins which metabolize the arachidonic acids during TB immunopathogenesis. The study, therefore, sought to demonstrate the potential role of these proteins in TB-induced immunopathology. Using immune-histopathological assays, the association of macrophage driven ALOX5 signaling with severe pulmonary immunopathology during TB was demonstrated. Furthermore, using both in vitro and in vivo assays, the data demonstrated the contribution of ALOX5 signaling to TB-induced granulomatous inflammation. Interception of the signaling pathway through clinically approved pharmaceutical inhibitors, resulted in reduced lung damage during the disease. The resolution of TB-induced lung pathology further contributed to increased bactericidal activity. Taken together, our data strongly suggest a role for macrophage driven inflammation via ALOX5 signaling which can be targeted for the development of therapeutic treatment to prevent exacerbated TB-induced pulmonary immunopathology.

immunology↗

bioRxiv2024

A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment

Post-TB lung disease (PTLD) causes a significant burden of global disease. Fibrosis is a central component of many clinical features of PTLD. To date, we have a limited understanding of the mechanisms of TB-associated fibrosis and how these mechanisms are similar to or dissimilar from other fibrotic lung pathologies. We have adapted a mouse model of TB infection to facilitate the mechanistic study of TB-associated lung fibrosis. We find that the morphologies of fibrosis that develop in the mouse model are similar to the morphologies of fibrosis observed in human tissue samples. Using Second Harmonic Generation (SHG) microscopy, we are able to quantify a major component of fibrosis, fibrillar collagen, over time and with treatment. Inflammatory macrophage subpopulations persist during treatment; matrix remodeling enzymes and inflammatory gene signatures remain elevated. Our mouse model suggests that there is a therapeutic window during which adjunctive therapies could change matrix remodeling or inflammatory drivers of tissue pathology to improve functional outcomes after treatment for TB infection.

microbiology↗

bioRxiv2024

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

The possibility to obtain genome-wide ancient DNA data from multiple individuals has facilitated an unprecedented perspective into prehistoric societies. Studying biological relatedness in these groups requires tailored approaches for analyzing ancient DNA due to its low coverage, post-mortem damage, and potential ascertainment bias. Here we present READv2 (Relatedness Estimation from Ancient DNA version 2), an improved Python 3 re-implementation of the most widely used tool for this purpose. While providing increased portability and making the software future-proof, we are also able to show that READv2 (a) is orders of magnitude faster than its predecessor; (b) has increased power to detect pairs of relatives using optimized default parameters; and, when the number of overlapping SNPs is sufficient, (c) can differentiate between full-siblings and parent-offspring, and (d) can classify pairs of third-degree relatedness. We further use READv2 to analyze a large empirical dataset that has previously needed two separate tools to reconstruct complex pedigrees. We show that READv2 yields results and precision similar to the combined approach but is faster and simpler to run. READv2 will become a valuable part of the archaeogenomic toolkit in providing an efficient and user-friendly classification of biological relatedness from pseudohaploid ancient DNA data.

bioinformatics↗

bioRxiv2023

Detection of Mycobacterium tuberculosis in human tissue via RNA in situ hybridization

RationaleAccurate TB diagnosis is hampered by the variable efficacy of the widely-used Ziehl-Neelsen (ZN) staining method to identify Mycobacterium tuberculosis (Mtb) acid-fast bacilli (AFB). Here, we sought to circumvent this current limitation through direct detection of Mtb mRNA. ObjectivesTo employ RNAscope to determine the spatial distribution of Mtb mRNA within tuberculous human tissue, to appraise ZN-negative tissue from confirmed TB patients, and to provide proof-of-concept of RNAscope as a platform to inform TB diagnosis and Mtb biology. MethodsWe examined ante- and postmortem human TB tissue using RNAscope to detect Mtb mRNA and a dual ZN/immunohistochemistry staining approach to identify AFB and bacilli producing antigen 85B (Ag85B). Measurements and main resultsWe adapted RNAscope for Mtb and identified intact and disintegrated Mtb bacilli and intra- and extracellular Mtb mRNA. Mtb mRNA was distributed zonally within necrotic and non-necrotic granulomas. We also found Mtb mRNA within, and adjacent to, necrotic granulomas in ZN-negative lung tissue and in Ag85B-positive bronchial epithelium. Intriguingly, we observed accumulation of Mtb mRNA and Ag85B in the cytoplasm of host cells. Notably, many AFB were negative for Ag85B staining. Mtb mRNA was observed in ZN-negative antemortem lymph node biopsies. ConclusionsRNAscope has diagnostic potential and can guide therapeutic intervention as it detects Mtb mRNA and morphology in ZN-negative tissues from TB patients, and Mtb mRNA in ZN-negative antemortem biopsies, respectively. Lastly, our data provide evidence that at least two phenotypically distinct populations of Mtb bacilli exist in vivo.

microbiology↗

bioRxiv2022

aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a rapidly growing field with a great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been a long-standing challenge in ancient metagenomics analysis. This is also complicated by a limited choice of ancient microbiome specific computational frameworks that meet the growing computational demands of the field. Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements. Using simulated ancient metagenomic samples, we benchmark aMeta against a current state-of-the-art workflow, and demonstrate its superior sensitivity and specificity in both microbial detection and authentication, as well as substantially lower usage of computer memory. aMeta is implemented as a Snakemake workflow to facilitate use and reproducibility.

bioinformatics↗

bioRxiv2022

NAD(H) homeostasis is essential for host protection mediated by glycolytic myeloid cells in tuberculosis

Mycobacterium tuberculosis (Mtb) disrupts glycolytic flux in infected myeloid cells through an unclear mechanism. Flux through the glycolytic pathway in myeloid cells is inextricably linked to the availability of NAD+, which is maintained by NAD+ salvage and lactate metabolism. Using lung tissue from tuberculosis (TB) patients and myeloid deficient LDHA (LdhaLysM-/-) mice, we demonstrate that glycolysis in myeloid cells is essential for protective immunity in TB. Glycolytic myeloid cells are essential for the early recruitment of multiple classes of immune cells and the protective effects of IFN{gamma}. We identified NAD+ depletion as central to the glycolytic inhibition caused by Mtb. Lastly, we show that the NAD+ precursor nicotinamide exerts a host-directed, antimycobacterial effect, and that nicotinamide prophylaxis and treatment reduces Mtb lung burden in vivo. These findings provide new insight into how Mtb alters host metabolism through perturbation of NAD(H) homeostasis and reprogramming of glycolysis, highlighting this pathway as a potential therapeutic target.

microbiology↗

bioRxiv2020

3D microarchitecture of the human tuberculous granuloma

Our current understanding of the pathophysiology of human pulmonary TB is limited by the paucity of human TB lung tissue for study and reliance on 2D analytical methods. Here, to overcome the limitations of conventional 2D histopathology, we used high-resolution 3D X-ray imaging ({micro}CT/nCT) to characterize necrotic lesions within human tuberculous lung tissues in relation to the airways and vasculature. We observed marked heterogeneity in the 3D structure and volume of lesions. Also, 3D imaging of large human TB lung sections provides unanticipated new insight into the spatial organization of TB lesions in relation to airways and the vascular system. Contrary to the current dogma depicting granulomas as simple spherical structures, we show that TB lesions exhibit complex, cylindrical, branched-type morphologies, which are connected to, and shaped by, the small airways. Our results highlight the likelihood that a single structurally complex lesion could be wrongly viewed as multiple independent lesions when evaluated in 2D. These findings have strong implications for understanding the pathophysiology and evolution of TB disease and suggest that aerosolized drug delivery strategies for TB should be reconsidered.

microbiology↗

bioRxiv2019

Contrasting inflammatory signatures in peripheral blood and bronchoalveolar cells reveal compartment-specific effects of HIV infection.

The mechanisms by which HIV increases susceptibility to tuberculosis and other respiratory infections are incompletely understood. We used transcriptomics of paired whole bronchoalveolar lavage (BAL) fluid and peripheral blood mononuclear cells to compare the effect of HIV at the lung mucosal surface and in the peripheral blood. The large majority of HIV-induced differentially expressed genes (DEGs) were specific to either the peripheral or lung mucosa compartments (1,307/1,404, 93%). Type I interferon signaling was the dominant signature of DEGs in HIV-positive blood with a less dominant and qualitatively distinct type I interferon gene set expression pattern in HIV-positive BAL. DEGs in the HIV-positive BAL were significantly enriched for infiltration with cytotoxic CD8+ T cells. Higher expression of representative transcripts and proteins in BAL CD8+ T cells during HIV infection, including IFNG (IFN-{gamma}), GZMB (Granzyme B) and PDCD1 (PD-1), was confirmed by cell-subset specific transcriptional analysis and flow cytometry. Thus, we report that a whole transcriptomic approach revealed qualitatively distinct effects of HIV in blood and bronchoalveolar compartments. Further work exploring the impact of distinct type I interferon programs and CD8+ T cells infiltration of the lung mucosa during HIV infection may provide novel insights into HIV-induced susceptibility to respiratory pathogens.

immunology↗