Biology subjects

Bossel Ben-Moshe, N.

Publications and source records attributed to Bossel Ben-Moshe, N..

8 recordsLinked to original sources

bioRxiv2026

Antibiotics drive immunometabolic rewiring of human immune responses

Antibiotics are routinely evaluated for their antimicrobial activity, potential host toxicity, and disruption of the microbiome. Certain antibiotics can also impact cell-intrinsic host processes, including evolutionarily conserved processes in the mitochondria. These raise the possibility that antibiotics can directly impact host immunity, which relies on mitochondrial function for their immunometabolic activation. However, the immunological consequences of most antibiotics in current use have not been systematically examined. Here, we performed a comprehensive analysis of the effects of clinically used antibiotics on activation of primary human immune cells. We uncovered an underappreciated antibiotic-specific modulation of immune function in healthy individuals and infectious disease patients. Focusing on the immunomodulatory antibiotic ciprofloxacin, we found altered mitochondrial gene expression across multiple immune populations, driving distinct, lineage-specific responses and heightened sensitivity of T-cells. Ciprofloxacin impaired primary human T-cell expansion and activation and altered mitochondrial function and metabolism. We further demonstrated immunomodulatory effects of selected antibiotics in response to inactivated bacteria and during live viral infection. Finally, to test the implications of our findings in vivo, we showed that immune activation is altered shortly after a single dose of antibiotic administration in mice. This work established a widespread impact of antibiotics on immune-cell function, and identified mitochondrial perturbation as one underlying mechanism, with implications for host-pathogen interactions and antimicrobial therapy.

immunology↗

bioRxiv2026

Image-based transposon screening reveals a flavin reductase that restrains intracellular Salmonella replication in macrophages

Intracellular bacterial pathogens can survive and replicate within host cells, yet an isogenic population follows divergent fates: some bacteria are killed, some arrest growth, and others replicate to high numbers. Identifying the bacterial functions behind each fate requires recovering mutants from within the host cells displaying it. But systematic approaches, such as transposon insertion analysis, can only estimate fitness of mutants from the whole infected population. Here, we developed an approach that couples a genome-wide mutagenesis library to image-enabled cell sorting (ICS), sorting infected cells by the number of bacteria they contain and assigning mutants to defined replication outcomes. We applied this approach to Salmonella enterica serovar Typhimurium (S.Tm) in macrophages, and revealed genes required for replication from genes that restrain it, whose disruption increased replication. Among the latter we identified the cytosolic flavin reductase Fre, which supplies reduced flavins to a broad range of bacterial processes. We uncovered a mechanism whereby loss of fre protected S.Tm from oxidative and nitrosative damage and increased bacterial numbers. Inside macrophages this advantage was mediated by the upregulation of the iron-sulfur-independent cytochrome bd-I oxidase. By resolving a mutant library into phenotypically defined subpopulations, this framework can be applied to characterize bacterial or host genes that drive infection phenotypes in any infection model.

microbiology↗

bioRxiv2025

Learning the DNA syntax of human microbiomes to infer health and disease

The human microbiome is a key factor in human health and alterations in community structure are associated with diverse pathological conditions. However, defining universal criteria to distinguish healthy from altered microbiome configurations remains challenging due to inter- and intra-individual variability, database-dependent approaches, and the complexity of analyzing numerous microbial features simultaneously. Here, we developed an approach that learns the syntax of the entire DNA of human microbial communities, using Sequence-Informed GC-normalized 4-mers (SIG-mers) that feed into statistical and machine learning frameworks. We identified distinct SIG-mer signatures that differentiate microbiomes of body sites across diverse healthy human populations. These signatures reveal both global microbiome shifts and individual-specific dynamics in response to antibiotic treatments and in chronic inflammatory disease. Leveraging machine learning models, we inferred health- and disease-associated microbiome states from SIG-mer profiles, capturing the degree of perturbation and disease severity. Our findings highlight SIG-mer profiling as a robust, unbiased and broadly applicable approach for personalized microbiome diagnostics and guiding therapeutic interventions.

microbiology↗

bioRxiv2025

Hypoxia-related immune subsets induced by Salmonella Typhi infection link early bacterial gut invasion to human infection outcomes

Salmonella Typhi (S. Typhi), the causative agent of typhoid disease, remains a major public health concern. Owing to the human-restricted nature of S. Typhi, current studies of typhoid pathogenesis in animal models are limited to a murine non-typhoidal pathogen. Furthermore, human studies are limited to analyses of peripheral immune responses which are blind to tissue-specific immunity and do not allow perturbations. What is now needed is an integrative approach that will provide mechanistic insights into S. Typhi pathogenesis and immune correlates of infection outcome. Here, we performed an integrated single-cell analysis of immune responses from the human S. Typhi challenge model and mouse model of typhoid disease, to associate biological mechanism with human infection outcome. Most prominent, we revealed immune subsets with a hypoxia-related signature in circulating immune cells from individuals that develop disease in the human challenge model. This signature was also evident in the mouse model in activated macrophages infiltrating into the Peyers patches, but not during infection with a mutant strain impaired for gut invasion. We further identified hypoxia-related signature as a general immune correlate of disease outcome in other infection- and inflammatory-related diseases. Collectively, using integrated analysis of mouse and human infection models, we revealed a hypoxia-related signature that link immune responses during bacterial invasion to increased risk of developing typhoid disease in humans, suggesting a possible causative role during the development of typhoid disease.

immunology↗

bioRxiv2024

Early and Delayed STAT1-Dependent Responses Drive Local Trained Immunity of Macrophages in the Spleen

Trained immunity (TI) is the process wherein innate immune cells gain functional memory upon exposure to specific ligands or pathogens, leading to augmented inflammatory responses and pathogen clearance upon secondary exposure. While the differentiation of hematopoietic stem cells (HSCs) and reprogramming of bone marrow (BM) progenitors are well-established mechanisms underpinning durable TI protection, remodeling of the cellular architecture within the tissue during TI remains underexplored. Here, we study the effects of peritoneal Bacillus Calmette-Guerin (BCG) administration to find TI-mediated protection in the spleen against a subsequent heterologous infection by the Gram-negative pathogen Salmonella Typhimurium (S.Tm). Utilizing single cell RNA-sequencing and flow cytometry, we discerned STAT1-regulated genes in TI-associated resident and recruited splenic myeloid populations. The temporal dynamics of TI were further elucidated, revealing both early and delayed myeloid subsets with time-dependent, cell type-specific STAT1 signatures. Using lineage tracing, we find that tissue-resident red pulp macrophages (RPM), initially depleted by BCG exposure, are restored from both tissue-trained, self-renewing macrophages and from bone marrow-derived progenitors, fostering long lasting local defense. Early inhibition of STAT1 activation, using specific JAK-STAT inhibitors, reduces both RPM loss and recruitment of trained monocytes. Our study suggests a temporal window soon after BCG vaccination, in which STAT1-dependent activation of long-lived resident cells in the tissue mediates localized protection.

immunology↗

bioRxiv2023

Chemoresistome Mapping in Individual Breast Cancer Patients Unravels Diversity in Dynamic Transcriptional Adaptation

Emerging evidence reinforce the role of non-genetic adaptive resistance to chemotherapy, that involves rewiring of transcriptional programs in surviving tumors. We combined longitudinal transcriptomics with temporal pattern analysis to dissect patient-specific emergence of resistance in breast cancer. Matched triplets of tumor biopsies (pre-treatment, post-treatment and adjacent normal) were collected from breast cancer patients who received neo-adjuvant chemotherapy. Full transcriptome was analyzed by longitudinal pattern classification to follow patient-specific expression modulations. We found that dynamics of gene expression dictates resistance-related modulations. The results unraveled important principles in emergence of adaptive resistance: 1. Genes with resistance patterns are already dysregulated in the primary tumor, supporting a primed drug-tolerant state. 2. In each patient, multiple resistance-related genes are rewired but converge into few dysregulated modules. 3. Rewiring of diverse genes and pathway dysregulation vary among individuals who receive the same treatments. Patient-specific chemoresistome maps disclosed tumors acquired resistance and exposed their vulnerabilities. Mapping the complexity of dysregulated pathways in individual patients revealed important insights on adaptive resistance mechanisms. To survive the toxic drug effect, tumor cells either sustain a drug-tolerant state or intensify it, specifically bypassing the drugs interference. Depicting an individual road map to resistance can offer personalized therapeutic strategies.

cancer biology↗

bioRxiv2022

Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks

Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA-sequencing (scRNA-seq) are increasingly used to study the host factors underlying diverse cellular phenotypes. But current approaches do not permit the simultaneous unbiased study of both host and bacterial factors during infection. Here, we developed scPAIR-seq, an approach to analyze both host and pathogen factors during infection by combining multiplex-tagged mutant bacterial library with scRNA-seq to identify mutant-specific changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We developed a pipeline to independently analyze redundancy between effectors and mutant-specific unique fingerprints, and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.

microbiology↗

bioRxiv2021

scRNA-seq Reveals A Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella

Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population defined by unique molecular features, but the implications to their function during infection is unknown. Here, we applied high resolution kinetic analysis using microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe an eclipse like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue resident red pulp macrophages. A second phase involved bacterial growth mediated by intracellular replication within a macrophage population we termed CD9 macrophages, that originate from non-classical monocytes. Nr4a1e2-/- mice, specifically depleted of non-classical monocytes but not other mononuclear cells, are more resistant to S.Tm infection. Our study underscores a cell-type specific host-pathogen interaction that determines early infection growth dynamics and has implications to the infection outcome of the entire organism.

immunology↗