ScnasRNA-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection [small intestine]
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ABSTRACT: The immune response against pathogens involves multiple cell state transitions and complex gene expression changes. Here we established an in vivo single-cell nascent RNA labeling sequencing method (scnasRNA-seq) and applied it to survey time-resolved RNA dynamics during immune response to acute enteric infection with Salmonella. We showed that detection of nascent RNA synthesis reflects more realistic information on cell activation and gene transcription than total RNA level. Interplay of nascent RNA synthesis and RNA degradation together modulate dynamics of total RNA. We found that bone marrow macrophages are first primed at very early stage upon Salmonella infection. In contrast, the innate immune response of macrophages in intestine is limited. Notably, intestinal CD8+ T cells and plasma cells are rapidly and specifically activated at early stage post infection. Intestinal late enterocytes quickly express MHC-I molecules and present Salmonella antigen to CD8+ T cells for their activation, serving as antigen presenting cells for initiation of adaptive immunity. Our findings unveil novel RNA control strategies of immune cells and dynamic time course of immune response activation upon Salmonella infection, challenging the doctrine boundary between innate immunity and adaptive immunity against bacterial infection.
Project description:The immune response against pathogens involves multiple cell state transitions and complex gene expression changes. Here we established an in vivo single-cell nascent RNA labeling sequencing method (scnasRNA-seq) and applied it to survey time-resolved RNA dynamics during immune response to acute enteric infection with Salmonella. We showed that detection of nascent RNA synthesis reflects more realistic information on cell activation and gene transcription than total RNA level. Interplay of nascent RNA synthesis and RNA degradation together modulate dynamics of total RNA. We found that bone marrow macrophages are first primed at very early stage upon Salmonella infection. In contrast, the innate immune response of macrophages in intestine is limited. Notably, intestinal CD8+ T cells and plasma cells are rapidly and specifically activated at early stage post infection. Intestinal late enterocytes quickly express MHC-I molecules and present Salmonella antigen to CD8+ T cells for their activation, serving as antigen presenting cells for initiation of adaptive immunity. Our findings unveil novel RNA control strategies of immune cells and dynamic time course of immune response activation upon Salmonella infection, challenging the doctrine boundary between innate immunity and adaptive immunity against bacterial infection.
Project description:This is a dynamic mathematical model describing the development of the cellular branch of the intestinal immune system of poultry during the first 42 days of life, and of its response towards an oral infection with Salmonella enterica serovar Enteritidis.
Project description:BACKGROUND & AIMS: The immune system comprises an innate and an adaptive immune response to combat pathogenic agents. The human enteropathogen Salmonella enterica serovar Typhimurium invades the intestinal mucosa and triggers an early innate pro-inflammatory host gene response, which results in diarrheal disease. Several host factors are involved in the acute early response to Salmonella infection. Transcription factors and transcription co-regulators have an especially important function, because they are required for the expression and synthesis of pro-inflammatory cytokines, chemokines and adhesion molecules. A central transcription factor involved in inflammation is NF-κB, which requires the nuclear protein PARP1 as co-factor for the expression of some of its target genes. Here, we investigated the role of PARP1 during Salmonella infection using a mouse model for Salmonella-induced colitis. METHODS: To study enterocolitis by Salmonella Typhimurium, an established mouse model system, which relies on streptomycin-pretreatment prior to Salmonella infection, was employed. Histopathologic signs of inflammation and cecum colonization at various time-points after infection of wild type and PARP1 knockout mice were analyzed. PARP1 expression in the gut mucosa was studied by quantitative RT-PCR, Western blot and immunofluorescence. Gene expression profiles of infected and control infected mice in the wild type or PARP1 knockout background were obtained by whole mouse genome arrays and confirmed by quantitative RT-PCR. 2 genotypes (wildtype, PARP1 knockout), 2 treatments (Salmonella SB300 infection, Salmonella SB161 control infection), 2 time-points (6h, 10h). 2-3 replicates/condition.
Project description:Immune protection of the body cavities depends on the swift activation of innate and adaptive immune responses in non-classical secondary lymphoid organs known as fat-associated lymphoid clusters (FALCs). While it is well-established that fibroblastic reticular cells (FRCs) are an integral component of the immune-stimulating infrastructure of lymph nodes and other classical secondary lymphoid organs, it has remained elusive whether and how FRCs in FALCs contribute to peritoneal immunity. Using FRC-specific gene targeting, we found that FALCs are underpinned by an elaborated FRC network and that initiation of peritoneal immunity was governed through FRC activation via MyD88-dependent innate immunological sensing. FRC-specific ablation of Myd88 expression blocked recruitment of inflammatory monocytes into FALCs and subsequent CD4+ T cell-dependent B-cell activation. Moreover, containment of Salmonella infection was compromised in conditionally Myd88-deficient mice indicating that FRCs in FALCs function as initial checkpoint in the orchestration of protective immune responses in the peritoneal cavity.
Project description:Baris Hancioglu, David Swigon & Gilles Clermont. A dynamical model of human immune response to influenza A virus infection. Journal of Theoretical Biology 246, 1 (2007).
We present a simplified dynamical model of immune response to uncomplicated influenza A virus (IAV) infection, which focuses on the control of the infection by the innate and adaptive immunity. Innate immunity is represented by interferon-induced resistance to infection of respiratory epithelial cells and by removal of infected cells by effector cells (cytotoxic T-cells and natural killer cells). Adaptive immunity is represented by virus-specific antibodies. Similar in spirit to the recent model of Bocharov and Romanyukha [1994. Mathematical model of antiviral immune response. III. Influenza A virus infection. J. Theor. Biol. 167, 323-360], the model is constructed as a system of 10 ordinary differential equations with 27 parameters characterizing the rates of various processes contributing to the course of disease. The parameters are derived from published experimental data or estimated so as to reproduce available data about the time course of IAV infection in a naïve host. We explore the effect of initial viral load on the severity and duration of the disease, construct a phase diagram that sheds insight into the dynamics of the disease, and perform sensitivity analysis on the model parameters to explore which ones influence the most the onset, duration and severity of infection. To account for the variability and speed of adaptation of the adaptive response to a particular virus strain, we introduce a variable that quantifies the antigenic compatibility between the virus and the antibodies currently produced by the organism. We find that for small initial viral load the disease progresses through an asymptomatic course, for intermediate value it takes a typical course with constant duration and severity of infection but variable onset, and for large initial viral load the disease becomes severe. This behavior is robust to a wide range of parameter values. The absence of antibody response leads to recurrence of disease and appearance of a chronic state with nontrivial constant viral load.
Project description:Consecutive exposures to different pathogens are very common and often alter host immune responses. Yet, it remains unknown how a secondary bacterial infection interferes with an ongoing adaptive immune response elicited against primary invading pathogens. Here, we demonstrate that pre-existing germinal center (GC) B cells are incapable of enduring radical metabolic changes induced by recruited Sca-1+ monocytes during Salmonella Typhimurium (STm) infection. GCs-induced by influenza, plasmodium and commensals deteriorated upon STm infection. GC collapse was independent of direct bacterial interactions with B cells, but rather, was induced through recruitment of CCR2-dependent Sca-1+ monocytes. GC collapse was dependent on non-B cell TLR-4, TNFα and IFNγ, which was essential for Sca-1+ monocyte differentiation in the bone-marrow. Monocyte recruitment and GC disruption also occurred during LPS-supplemented vaccination and Listeria monocytogenes infection. Thus, systemic activation of the innate immune response upon lethal bacterial infection is induced at the expense of antibody-mediated immunity.
Project description:Consecutive exposures to different pathogens are very common and often alter host immune responses. Yet, it remains unknown how a secondary bacterial infection interferes with an ongoing adaptive immune response elicited against primary invading pathogens. Here, we demonstrate that pre-existing germinal center (GC) B cells are incapable of enduring radical metabolic changes induced by recruited Sca-1+ monocytes during Salmonella Typhimurium (STm) infection. GCs-induced by influenza, plasmodium and commensals deteriorated upon STm infection. GC collapse was independent of direct bacterial interactions with B cells, but rather, was induced through recruitment of CCR2-dependent Sca-1+ monocytes. GC collapse was dependent on non-B cell TLR-4, TNFα and IFNγ, which was essential for Sca-1+ monocyte differentiation in the bone-marrow. Monocyte recruitment and GC disruption also occurred during LPS-supplemented vaccination and Listeria monocytogenes infection. Thus, systemic activation of the innate immune response upon lethal bacterial infection is induced at the expense of antibody-mediated immunity.
Project description:BACKGROUND & AIMS: The immune system comprises an innate and an adaptive immune response to combat pathogenic agents. The human enteropathogen Salmonella enterica serovar Typhimurium invades the intestinal mucosa and triggers an early innate pro-inflammatory host gene response, which results in diarrheal disease. Several host factors are involved in the acute early response to Salmonella infection. Transcription factors and transcription co-regulators have an especially important function, because they are required for the expression and synthesis of pro-inflammatory cytokines, chemokines and adhesion molecules. A central transcription factor involved in inflammation is NF-κB, which requires the nuclear protein PARP1 as co-factor for the expression of some of its target genes. Here, we investigated the role of PARP1 during Salmonella infection using a mouse model for Salmonella-induced colitis. METHODS: To study enterocolitis by Salmonella Typhimurium, an established mouse model system, which relies on streptomycin-pretreatment prior to Salmonella infection, was employed. Histopathologic signs of inflammation and cecum colonization at various time-points after infection of wild type and PARP1 knockout mice were analyzed. PARP1 expression in the gut mucosa was studied by quantitative RT-PCR, Western blot and immunofluorescence. Gene expression profiles of infected and control infected mice in the wild type or PARP1 knockout background were obtained by whole mouse genome arrays and confirmed by quantitative RT-PCR.
Project description:Using DropSeq single cell RNA sequencing, we report that neuronal derived-IL-18 is required for goblet cell expression of intestinal antimicrobial protein expression Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the anti-microbial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA-hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron derived IL-18 signaling controls tissue wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.
Project description:Using RNA sequencing, we report that neuron derived-IL-18 is required for intestinal antimicrobial protein expression Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the anti-microbial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA-hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron derived IL-18 signaling controls tissue wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.