Identification of miRNAs that target Fcγ receptor-mediated phagocytosis during macrophage activation syndrome

Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile arthritis, accompanied by cytokine storm and hemophagocytosis. In addition, COVID-19-related hyperinflammation shares clinical features of MAS. Mechanisms that activate macrophages in MAS remain unclear. Here, we identify the role of miRNA in increased phagocytosis and interleukin-12 (IL-12) production by macrophages in a murine model of MAS. MAS significantly increased F4/80+ macrophages and phagocytosis in the mouse liver. Gene expression profile revealed the induction of Fcγ receptor-mediated phagocytosis (FGRP) and IL-12 production in the liver. Phagocytosis pathways such as High-affinity IgE receptor is known as Fc epsilon RI -signaling and pattern recognition receptors involved in the recognition of bacteria and viruses and phagosome formation were also significantly upregulated. In MAS, miR-136-5p and miR-501-3p targeted and caused increased expression of Fcgr3, Fcgr4, and Fcgr1 genes in FGRP pathway and consequent increase in phagocytosis by macrophages, whereas miR-129-1-3p and miR-150-3p targeted and induced Il-12. Transcriptome analysis of patients with MAS revealed the upregulation of FGRP and FCGR gene expression. A target analysis of gene expression data from a patient with MAS discovered that miR-136-5p targets FCGR2A and FCGR3A/3B, the human orthologs of mouse Fcgr3 and Fcgr4, and miR-501-3p targets FCGR1A, the human ortholog of mouse Fcgr1. Together, we demonstrate the novel role of miRNAs during MAS pathogenesis, thereby suggesting miRNA mimic-based therapy to control the hyperactivation of macrophages in patients with MAS as well as use overexpression of FCGR genes as a marker for MAS classification.

6-Formylindolo[3,2-b]carbazole, a potent ligand for the aryl hydrocarbon receptor, attenuates concanavalin-induced hepatitis by limiting T-cell activation and infiltration of proinflammatory CD11b+ Kupffer cells

FICZ (6-formylindolo[3,2-b]carbazole) is a potent aryl hydrocarbon receptor agonist that has a poorly understood function in the regulation of inflammation. In this study, we investigated the effect of aryl hydrocarbon receptor activation by FICZ in a murine model of autoimmune hepatitis induced by concanavalin A. High-throughput sequencing techniques such as single-cell RNA sequencing and assay for transposase accessible chromatin sequencing were used to explore the mechanisms through which FICZ induces its effects. FICZ treatment attenuated concanavalin A-induced hepatitis, evidenced by decreased T-cell infiltration, decreased circulating alanine transaminase levels, and suppression of proinflammatory cytokines. Concanavalin A revealed an increase in natural killer T cells, T cells, and mature B cells upon concanavalin A injection while FICZ treatment reversed the presence of these subsets. Surprisingly, concanavalin A depleted a subset of CD55+ B cells, while FICZ partially protected this subset. The immune cells showed significant dysregulation in the gene expression profiles, including diverse expression of migratory markers such as CCL4, CCL5, and CXCL2 and critical regulatory markers such as Junb. Assay for transposase accessible chromatin sequencing showed more accessible chromatin in the CD3e promoter in the concanavalin A-only group as compared to the naive and concanavalin A-exposed, FICZ-treated group. While there was overall more accessible chromatin of the Adgre1 (F4/80) promoter in the FICZ-treated group, we observed less open chromatin in the Itgam (CD11b) promoter in Kupffer cells, supporting the ability of FICZ to reduce the infiltration of proinflammatory cytokine producing CD11b+ Kupffer cells. Taken together, these data demonstrate that aryl hydrocarbon receptor activation by FICZ suppresses liver injury through the limitation of CD3+ T-cell activation and CD11b+ Kupffer cell infiltration.

Protocol for analyzing transforming growth factor β signaling in dextran-sulfate-sodium-induced colitic mice using flow cytometry and western blotting

Transforming growth factor β (TGF-β) is critical to the maintenance of intestinal immune homeostasis. Here, we present techniques for analyzing Smad molecules downstream of TGF-β receptor signaling in dextran-sulfate-sodium-induced colitic mice. We describe colitis induction, cell isolation, and flow cytometric cell sorting of dendritic cells and T cells. We then detail intracellular staining of phosphorylated Smad2/3 and western blotting analysis of Smad7. This protocol can be performed on a limited number of cells from many sources. For complete details on the use and execution of this protocol, please refer to Garo et al.¹.

AhR Activation Leads to Attenuation of Murine Autoimmune Hepatitis: Single-Cell RNA-Seq Analysis Reveals Unique Immune Cell Phenotypes and Gene Expression Changes in the Liver

The aryl hydrocarbon receptor (AhR) is a ubiquitously expressed ligand-activated transcription factor. While initially identified as an environmental sensor, this receptor has been shown more recently to regulate a variety of immune functions. AhR ligands vary in structure and source from environmental chemicals such as 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and indoles found in cruciferous vegetables to endogenous ligands derived from tryptophan metabolism. In the current study, we used TCDD, a high affinity AhR ligand to study the impact of AhR activation in the murine model of autoimmune hepatitis (AIH). Primarily, we used single-cell RNA-sequencing (scRNA-seq) technology to study the nature of changes occurring in the immune cells in the liver at the cellular and molecular level. We found that AhR activation attenuated concanavalin A (ConA)-induced AIH by limiting chemotaxis of pro-inflammatory immune cell subsets, promoting anti-inflammatory cytokine production, and suppressing pro-inflammatory cytokine production. scRNA-seq analysis showed some unusual events upon ConA injection such as increased presence of mature B cells, natural killer (NK) T cells, CD4+ or CD8+ T cells, Kupffer cells, memory CD8+ T cells, and activated T cells while TCDD treatment led to the reversal of most of these events. Additionally, the immune cells showed significant alterations in the gene expression profiles. Specifically, we observed downregulation of inflammation-associated genes including Ptma, Hspe1, and CD52 in TCDD-treated AIH mice as well as alterations in the expression of migratory markers such as CXCR2. Together, the current study characterizes the nature of inflammatory changes occurring in the liver during AIH, and sheds light on how AhR activation during AIH attenuates liver inflammation by inducing phenotypic and genotypic changes in immune cells found in the liver.

Ameliorative role of AhR ligands in concanavalin-induced liver injury is due to increased miR-100 expression leading to mTOR downregulation and promoter hydroxymethylation

The promiscuous aryl hydrocarbon receptor (AhR) has long been the target of immunological studies due to its expression on many immune cells. However, the specific mechanisms underlying the role of AhR activation in inflammatory disease has not been elucidated. We employed a murine model of immune cell-mediated liver injury, comparable to autoimmune hepatitis (AIH) in humans, by intravenously injecting 12.5 mg/kg of Concanavalin A (ConA) and treating one hour later via intraperitoneal injection with an AhR ligand: 10 μg/kg 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or 50 μg/kg 6-formylindolo[3,2-b] carbazole (FICZ). Our studies showed that both ligands improved the clinical parameters of AIH in this model. 24 hours after challenge, liver mononuclear cells were harvested, and total RNA and DNA were isolated. We examined the underlying mechanisms by conducting small RNA-sequencing and discovered dysregulation of many miRNAs. Of note, miR-100 was significantly upregulated, and we found this molecule to contain a dioxin-responsive element (DRE) in its promoter region. Further, we conducted methylated and hydroxymethylated DNA immunoprecipitation sequencing on CD45+ cells in this model and found distinct methylation profiles between each of the groups. Specifically, we observed increased hydroxymethylation in both treatment groups as compared to the ConA+Vehicle group in the promoter of mTOR, a direct target of miR-100. These data suggest that AhR activation reduces liver injury by upregulating miR-100 and reducing mTOR activity. Additionally, hydroxymethylation of the mTOR promoter may contribute to the changes observed upon AhR activation, thus lending credence for a role of hydroxymethylation in cell differentiation.

Supported by NIH grants P01AT003961, P20GM103641, R01ES030144, R01AI129788 and R01AI123947, R01AI160896 and R01AI123947-04S1

Targeting AhR as a Novel Therapeutic Modality against Inflammatory Diseases

For decades, activation of Aryl Hydrocarbon Receptor (AhR) was excluded from consideration as a therapeutic approach due to the potential toxic effects of AhR ligands and the induction of the cytochrome P450 enzyme, Cyp1a1, following AhR activation. However, it is now understood that AhR activation not only serves as an environmental sensor that regulates the effects of environmental toxins, but also as a key immunomodulator where ligands induce a variety of cellular and epigenetic mechanisms to attenuate inflammation. Thus, the emergence of further in-depth research into diverse groups of compounds capable of activating this receptor has prompted reconsideration of its use therapeutically. The aim of this review is to summarize the body of research surrounding AhR and its role in regulating inflammation. Specifically, evidence supporting the potential of targeting this receptor to modulate the immune response in inflammatory and autoimmune diseases will be highlighted. Additionally, the opportunities and challenges of developing AhR-based therapies to suppress inflammation will be discussed.

Downregulation of AW112010 upon treatment with 6-formylindolo[3,2-b] carbazole protects mice from fulminant Concanavalin-induced T cell-mediated liver injury

Upregulation of long noncoding RNA (lncRNA) AW112010 has been observed in multiple inflammatory disease models. In line with implication of this lncRNA as a regulator of inflammation, it has also been shown that AW112010 expression decreases upon treatment with anti-inflammatory compounds. Since lncRNAs show abnormal expression in many inflammatory diseases and reactions, elucidating their role in such ailments is necessary. Data from our lab has shown that treatment with aryl hydrocarbon receptor (AhR) ligands induce epigenetic pathway dysregulation, so this study aimed to determine inflammatory genes dysregulated upon treatment with the endogenous AhR ligand, 6-formylindolo[3,2-b] carbazole (FICZ). A murine model of immune cell-mediated liver injury was employed by intravenously injecting 12.5 mg/kg Concanavalin A (ConA). One hour after challenge, mice were treated with 50 μg/kg FICZ via an intraperitoneal injection. Interestingly, analysis of serum collected twenty-four hours after challenge showed that FICZ was able to reduce the level of alanine transaminase (ALT) suggesting a decrease in disease severity. Single cell RNA sequencing was conducted on infiltrating liver mononuclear cells enriched via a percoll gradient. We observed a reduced percentage of T cells upon FICZ treatment and an increase in the percentage of neutrophils. Overall, we observed downregulation of AW112010 in the FICZ-treated group. Specifically, AW112010 was identified as one of the top 20 genes dysregulated in the NK cell cluster and was downregulated in the B cell, CD8+ T cell, and Kupffer cell clusters. Together, these data suggest AW112010 downregulation as a potential mechanism through which FICZ protects mice from severe liver injury.

A single-cell atlas of the lung mononuclear cell response in Staphylococcus Enterotoxin B-induced Acute Respiratory Distress Syndrome

The emergence of SARS-CoV-2 variants will change the landscape of what we already know about COVID-19, making it important to understand the immunological and molecular mechanism of this illness. The virulent nature of the virus, disease outcomes and lack of suitable facilities for studying virus-infected samples has made the need for small animal models urgent. Staphylococcus enterotoxin B (SEB)-induced Acute Respiratory Distress Syndrome (ARDS) mimics the cytokine storm presented in patients with severe COVID-19 and is a safer alternative than working with infected samples. To identify pathways in pulmonary cells that potentially cause ARDS, we utilized single-cell RNA sequencing (scRNASeq) to profile the whole lung cells of C3H/HeJ mice treated with SEB and healthy controls. While it is well established that SEB induces robust proliferation of CD4+ T cells with the receptor Vβ8.2 by binding of these cells with antigen presenting cells, effects in other cell types is not well described. We found that intranasal administration of SEB induced the proliferation of three subsets of macrophages, neutrophils, and cytotoxic T cells in the lungs. Our data also illustrated a loss of multiple cell types including resident macrophages, multiple subsets of B cells, and club cells. Macrophage subsets displayed increased expression of genes related to interferon signaling and lipid metabolism. This data emphasizes the importance of understanding the role of macrophages in ARDS, and can further provide insights into elucidating the mechanisms not only in SEB-induced ARDS but also in severe COVID-19. This may serve as a model for severe case of the disease. (Supported by NIH P01AT003961, P20GM103641, R01AI129788, R01 ES030144 and R01AI123947)

2,3,7,8-Tetrachlorodibenzo-p-dioxin Induces Gimap5 Expression to Ameliorate Concanavalin-Induced T Cell-Mediated Liver Injury

GTPase of the immune-associated protein 5 (Gimap5) has been implicated in immune cell maintenance and development. A mouse model comparable to autoimmune hepatitis in humans was used to study the alterations induced in the gene expression profile of immune cells upon administration of environmental toxin 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD). In this study, we tested the hypothesis that TCDD is capable of modulating gene expression to ameliorate autoimmune hepatitis severity. Mice were injected intravenously with 12.5 mg/kg concanavalin A (ConA) and treated intraperitoneally one hour after challenge with vehicle or 10 μg/kg TCDD. TCDD-treated mice showed lower levels of liver injury enzymes, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), as compared to vehicle-treated mice. Histopathological analysis revealed a reduction in liver damage in the TCDD-treated group as compared to the vehicle-treated control. Furthermore, flow cytometric analysis of liver-infiltrating mononuclear cells demonstrated that following treatment with TCDD, there was an increase in FoxP3+CD4+ Tregs as well as a decrease in proinflammatory Tbet+ Th1 and RORγt+ Th17 T helper cell subtypes after induction of the disease. Single cell RNA-sequencing was conducted on liver mononuclear cells to further assess the changes induced by TCDD. The gene expression profile showed that TCDD treatment significantly upregulated the expression of vital genes such as Gimap5, a maintenance gene for normal liver function and survival of T cells. In summary, our data suggests that TCDD is capable of inducing Gimap5 expression in autoimmune hepatitis, which in turn modulates the progression of this disease.