Biology subjects

Beamer, G.

Publications and source records attributed to Beamer, G..

7 recordsLinked to original sources

bioRxiv2026

Deep Learning-Based Spatial Immunoprofiling of Multiplex Immunofluorescence Images Distinguishes Tuberculosis Disease States in Diversity Outbred Mice

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains a major global health challenge, with approximately 10.8 million new cases and 1.25 million deaths reported in 2023. Human responses to M.tb are heterogeneous with clinical outcomes including bacterial clearance, asymptomatic latent M.tb infection, and severe fatal pulmonary TB. Here, we aim to address knowledge gaps in the organization of M.tb granulomas by identifying cell-based spatial features indicating asymptomatic lung infection. To address this gap, which cannot be directly studied in humans, we used lung sections from M.tb infected Diversity Outbred mice with acute pulmonary TB, asymptomatic M.tb infection, or chronic pulmonary TB that were stained for T cells, B cells, macrophages, and bronchiolar epithelial cells by multiplexed immunofluorescence. We first developed a new, accurate model to automatically segment lung granulomas, detect/quantify the cell types within granulomas, and extract the location of immune cells in granulomas for each disease state. Analysis of model-derived results show that lung granulomas from asymptomatic mice have a characteristic spatial profile consisting of higher CD4+ and CD8a+ T cell densities, closer B cell proximity to bronchiolar epithelium, and increased T cell-macrophage proximity in asymptomatic M.tb infection. Next, we propose a second novel approach to utilize a large language model (LLM) to independently decode complex cellular patterns within granulomas, and distinguished key immunological signatures: balanced immune expression in asymptomatic M.tb mice, dysfunctional responses with low cellularity in acute TB, and highest immune cells in chronic TB. Overall, the results from this study show that lung granulomas in asymptomatic infection are characterized by increased T cell density, increased numbers of peribronchiolar B cells, and T cells closer to macrophages as compared to acute and chronic TB. These methods and results help establish an automated pipeline to extract and analyze data from multiplexed fluorescence images and provide a foundation to better understand how granuloma architecture varies by disease state.

immunology↗

bioRxiv2025

The ID93 + GLA-3M-052-LS vaccine candidate elicits mucosal and systemic immunogenicity and protective efficacy against Mycobacterium tuberculosis challenge in BCG-primed Collaborative Cross inbred mice

New vaccine approaches are needed against tuberculosis (TB). We sought to optimize mucosal immunogenicity and protective efficacy by modulating the adjuvant component and route of immunization of a next-generation TB vaccine using the recombinant TB vaccine antigen (Ag) ID93. ID93-specific mucosal and systemic immunogenicity and protective efficacy were assessed in the Collaborative Cross 004 mouse strain, a mouse strain susceptible to Mycobacterium tuberculosis (Mtb) infection, as a suitable model of Mtb susceptible populations. Immunogenicity data from various vaccine candidates were used to select lead vaccine candidates with the most preferred immunostimulatory profiles using a pre-determined desirability index. A liposomal adjuvant system containing synthetic TLR4 and TLR7/8 ligands (GLA-3M-052-LS), administered by a heterologous intramuscular-intranasal regimen, induced an optimal comprehensive immune response profile including high levels of mucosal antibody and Th1 CD4+ T cells in the lungs. In BCG-primed mice, immunization with intramuscular followed by intranasal ID93 + GLA-3M-052-LS boosts significantly reduced Mtb burden in the lungs after challenge vs. BCG vaccinated mice alone. Thus, ID93 + GLA-3M-052-LS represents a promising next-generation TB vaccine candidate suitable for testing in additional preclinical models.

immunology↗

bioRxiv2023

Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice.

Mycobacterium tuberculosis, the bacillus that causes tuberculosis (TB), infects 2 billion people across the globe, and results in 8-9 million new TB cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. We investigated the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using clinical indicators of disease, granuloma histopathological features, and immune response traits identified five new loci on mouse chromosomes 1, 2, 4, 16 and three previously identified loci on chromosomes 3 and 17. Quantitative trait loci (QTLs) on chromosomes 1, 16, and 17, associated with multiple correlated traits and had similar patterns of allele effects, suggesting these QTLs contain important genetic regulators of responses to M. tuberculosis. To narrow the list of candidate genes in QTLs, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks, generating functional scores. The scores were then used to rank candidates for each mapped trait in each locus, resulting in 11 candidates: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Importantly, all 11 candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling. Further, all candidates contain single nucleotide polymorphisms (SNPs), and some but not all SNPs were predicted to have deleterious consequences on protein functions. Multiple methods were used for validation including (i) a statistical method that showed Diversity Outbred mice carrying PWH/PhJ alleles on chromosome 17 QTL have shorter survival; (ii) quantification of S100A8 protein levels, confirming predicted allele effects; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and new functionally relevant gene candidates that may be major regulators of granuloma necrosis and acute inflammation in pulmonary TB.

genetics↗

bioRxiv2023

Perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell gene expression pathways identify asymptomatic Mycobacterium tuberculosis lung infection in Diversity Outbred mice{-}{-}{-}

Humans are highly genetically diverse, and most are resistant to Mycobacterium tuberculosis. However, lung tissue from genetically resistant humans is not readily available to identify potential mechanisms of resistance. To address this, we model M. tuberculosis infection in Diversity Outbred mice. Like humans, Diversity Outbred mice also exhibit genetically determined susceptibility to M. tuberculosis infection: Progressors who succumb within 60 days of a low dose aerosol infection due to acute necrotizing granulomas, and Controllers who maintain asymptomatic infection for at least 60 days, and then develop chronic pulmonary TB with occasional necrosis and cavitation, over months to greater than 1 year. Here, we identified specific regions of granuloma-associated lymphoid tissue (GrALT) and B-cell gene expression pathways as key features of asymptomatic lung infection using cytokine, antibody, granuloma image, and gene expression datasets. Cytokines and anti-M. tuberculosis cell wall antibodies discriminated acute vs chronic pulmonary TB but not asymptomatic lung infection. To find unique features of asymptomatic lung infection, we trained a weakly supervised, deep-learning neural network on lung histology images. The neural network accurately produced an interpretable imaging biomarker: perivascular and bronchiolar lymphocytic cuffs, a type of GrALT. We expected CD4 T cell genes would be highly expressed in asymptomatic lung infection. However, the significantly different, highly expressed genes in lungs of asymptomatically infected Diversity Outbred mice corresponded to B-cell activation, proliferation, and antigen-receptor signaling, including Fcrl1, Cd79, Pax5, Cr2, and Ms4a1. Overall, our results suggest that genetically controlled B-cell responses are important for establishing asymptomatic M. tuberculosis lung infection.

pathology↗

bioRxiv2022

Host genetic background is a barrier to vaccine-induced protection against infection

The heterogeneity of immune responses observed in humans is difficult to model in standard inbred laboratory mice. To capture the diversity inherent in mice and better understand how host variation affects BCG-induced immunity against Mycobacterium tuberculosis, 24 unique Collaborative Cross (CC) recombinant inbred mouse strains and the C57BL/6 reference strain were vaccinated with or without BCG, and then challenged with low-dose aerosolized virulent M. tuberculosis. In contrast to standard lab strains, BCG protected only half of the CC strains tested. Furthermore, BCG efficacy is dissociable from inherent susceptibility to TB. As these strains differed primarily in the genes and alleles they inherited from the CC founder strains, we conclude that the host genetic background has a major influence on whether BCG confers protection against M. tuberculosis infection and indicates that host genetics should be considered as an important barrier to vaccine-mediated protection. Importantly, we wished to identify the components of the immune response stimulated by BCG, which were subsequently recalled after Mtb infection and associated with protection. The T cell immune response following BCG vaccination and Mtb challenge was extensively characterized. Although considerable diversity was observed, BCG vaccination had little impact on the composition of T cells recruited and maintained in the lung after infection. Instead, the variability was largely shaped by the genetic background. We developed models to detect vaccine-induced differences, which identified immune signatures associated with BCG-elicited protection against TB. Importantly, even when categorized as susceptible vs. resistant, and protected vs. unprotected, many of the protected CC strains had unique flavors of immunity, indicating multiple paths to protection. Thus, CC mice can be used to define correlates of protection and to identify vaccine strategies that protect a larger fraction of genetically diverse individuals instead of optimizing protection for a single genotype.

immunology↗

bioRxiv2022

BCG vaccination of Diversity Outbred mice induces cross-reactive antibodies to SARS-CoV-2 spike protein

The Bacillus Calmette-Guerin (BCG) vaccine, the only vaccine against tuberculosis, induces cross-protection against pathogens unrelated to Mycobacterium, including viruses. Epidemiological studies have identified potential benefits of BCG vaccination against SARS-CoV-2 infection. While BCGs heterologous effects have been widely attributable to trained immunity, we hypothesized BCG vaccination could induce cross-reactive antibodies against the spike protein of SARS-CoV-2 Wuhan-Hu-1. The concentration of IgG reactive to SARS-CoV-2 spike protein from the sera of BCG-vaccinated, Diversity Outbred (DO) mice and C57BL/6J inbred mice was measured using ELISA. Sera from 10/15 BCG-vaccinated DO mice possessed more IgG reactive to recombinant spike protein than sera from BCG-vaccinated C57BL/6J mice and unvaccinated DO mice. Amino acid sequences common to BCG cell wall/membrane proteins and SARS-CoV-2 spike protein were identified as potential antigen candidates for future study. These results imply a humoral mechanism, influenced by genotype, by which BCG vaccination could confer immunity to SARS-CoV-2. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/488640v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1ff9d16org.highwire.dtl.DTLVardef@a2302dorg.highwire.dtl.DTLVardef@8ee2borg.highwire.dtl.DTLVardef@4c7b55_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2020

Recombinant Paraprobiotics as a New Paradigm for Treating Gastrointestinal Nematode Parasites of Humans

Gastrointestinal nematodes (GINs) of humans, e.g., hookworms, negatively impact childhood growth, cognition, nutrition, educational attainment, income, productivity, and pregnancy. Hundreds of millions of people are targeted with mass drug administration (MDA) of donated benzimidazole (BZ) anthelmintics. However, BZ efficacy against GINs is suboptimal, and reduced/low efficacy has been seen. Developing an anthelmintic for human MDA is daunting: it must be safe, effective, inexpensive, stable without a cold chain, and massively scalable. Bacillus thuringiensis (Bt) crystal protein 5B (Cry5B) has anthelmintic properties that could fill this void. Here we develop an API (Active Pharmaceutical Ingredient) form of Bt Cry5B compatible with MDA. We expressed Cry5B in asporogenous Bt during vegetative phase, forming cytosolic crystals. These Bacteria with Cytosolic Crystals (BaCC) were rendered inviable (inactivated BaCC or IBaCC) with food-grade essential oils. IBaCC potency was validated in vitro against nematodes. IBaCC was also potent in vivo against human hookworm infections in hamsters. IBaCC production was successfully scaled to 350 liters at a contract manufacturing facility. A simple fit-for-purpose formulation to protect against stomach digestion and powdered IBaCC were successfully made and used against GINS in hamsters and mice. A pilot histopathology study and blood chemistry workup showed that five daily consecutive doses of 200 mg/kg Cry5B IBaCC (the curative single dose is 40 mg/kg) was non-toxic and completely safe. IBaCC is a safe, inexpensive, highly effective, easy-to-manufacture, and scalable anthelmintic that is practical for MDA and represents a new paradigm for treating human GINs.

microbiology↗