Interferon Gene Signature Research Articles

Step-dose IL-7 treatment promotes systemic expansion of T cells and alters immune cell landscape in blood and lymph nodes

We employed a dose-escalation regimen in rhesus macaques to deliver glycosylated IL-7, a cytokine critical for development and maintenance of T lymphocytes. IL-7 increased proliferation and survival of Tcells and triggered several chemokines and cytokines. Induction of CXCL13 in lymph nodes (LNs) led to a remarkable increase of B cells in the LNs, proliferation of germinal center follicular T helper cells and elevated IL-21 levels suggesting an increase in follicle activity. Transcriptomics analysis showed induction of IRF-7 and Flt3L, which was linked to increased frequency of circulating plasmacytoid dendritic cells (pDCs) on IL-7 treatment. These pDCs expressed higher levels of CCR7, homed to LNs, and were associated with upregulation of type-1 interferon gene signature and increased production of IFN-α2a on TLR stimulation. Superior effects and dose-sparing advantage was observed by the step-dose regimen. Thus, IL-7 treatment leads to systemic effects involving both lymphoid and myeloid compartments.

The meningeal transcriptional response to traumatic brain injury and aging.

Emerging evidence suggests that the meningeal compartment plays instrumental roles in various neurological disorders, however, we still lack fundamental knowledge about meningeal biology. Here, we utilized high-throughput RNA sequencing (RNA-seq) techniques to investigate the transcriptional response of the meninges to traumatic brain injury (TBI) and aging in the sub-acute and chronic time frames. Using single-cell RNA sequencing (scRNA-seq), we first explored how mild TBI affects the cellular and transcriptional landscape in the meninges in young mice at one-week post-injury. Then, using bulk RNA-seq, we assessed the differential long-term outcomes between young and aged mice following TBI. In our scRNA-seq studies, we highlight injury-related changes in differential gene expression seen in major meningeal cell populations including macrophages, fibroblasts, and adaptive immune cells. We found that TBI leads to an upregulation of type I interferon (IFN) signature genes in macrophages and a controlled upregulation of inflammatory-related genes in the fibroblast and adaptive immune cell populations. For reasons that remain poorly understood, even mild injuries in the elderly can lead to cognitive decline and devastating neuropathology. To better understand the differential outcomes between the young and the elderly following brain injury, we performed bulk RNA-seq on young and aged meninges 1.5 months after TBI. Notably, we found that aging alone induced upregulation of meningeal genes involved in antibody production by B cells and type I IFN signaling. Following injury, the meningeal transcriptome had largely returned to its pre-injury signature in young mice. In stark contrast, aged TBI mice still exhibited upregulation of immune-related genes and downregulation of genes involved in extracellular matrix remodeling. Overall, these findings illustrate the dynamic transcriptional response of the meninges to mild head trauma in youth and aging.

Interferon signaling and hypercytokinemia-related gene expression in the blood of antidepressant non-responders

Only 50% of patients with depression respond to the first antidepressant drug administered. Thus, biomarkers for prediction of antidepressant responses are needed, as predicting which patients will not respond to antidepressants can optimize selection of alternative therapies. We aimed to identify biomarkers that could predict antidepressant responsiveness using a novel data-driven approach based on statistical pattern recognition. We retrospectively divided patients with major depressive disorder into antidepressant responder and non-responder groups. Comprehensive gene expression analysis was performed using peripheral blood without narrowing the genes. We designed a classifier according to our own discrete Bayes decision rule that can handle categorical data. Nineteen genes showed differential expression in the antidepressant non-responder group (n = 15) compared to the antidepressant responder group (n = 15). In the training sample of 30 individuals, eight candidate genes had significantly altered expression according to quantitative real-time polymerase chain reaction. The expression of these genes was examined in an independent test sample of antidepressant responders (n = 22) and non-responders (n = 12). Using the discrete Bayes classifier with the HERC5, IFI6, and IFI44 genes identified in the training set yielded 85% discrimination accuracy for antidepressant responsiveness in the 34 test samples. Pathway analysis of the RNA sequencing data for antidepressant responsiveness identified that hypercytokinemia- and interferon-related genes were increased in non-responders. Disease and biofunction analysis identified changes in genes related to inflammatory and infectious diseases, including coronavirus disease. These results strongly suggest an association between antidepressant responsiveness and inflammation, which may be useful for future treatment strategies for depression.

The effect of the cyclic GMP-AMP synthase-stimulator of interferon genes signaling pathway on organ inflammatory injury and fibrosis.

The cyclic GMP-AMP synthase-stimulator of interferon genes signal transduction pathway is critical in innate immunity, infection, and inflammation. In response to pathogenic microbial infections and other conditions, cyclic GMP-AMP synthase (cGAS) recognizes abnormal DNA and initiates a downstream type I interferon response. This paper reviews the pathogenic mechanisms of stimulator of interferon genes (STING) in different organs, including changes in fibrosis-related biomarkers, intending to systematically investigate the effect of the cyclic GMP-AMP synthase-stimulator of interferon genes signal transduction in inflammation and fibrosis processes. The effects of stimulator of interferon genes in related auto-inflammatory and neurodegenerative diseases are described in this article, in addition to the application of stimulator of interferon genes-related drugs in treating fibrosis.

Translational potential of JAX humanized APOE mice: Peripheral interferon gamma induces systemic immuno‐metabolic dysfunction

AbstractBackgroundInflammation is a well‐documented feature of Alzheimer’s disease (AD) in human brain. Previous findings from our group demonstrated upregulated immune transcripts in the AD brain as well as sex differences in immune transcript levels during pre‐clinical midlife aging. Using our humanized APOE mouse model, we identified elevated immune transcripts in the female brain including interferon signaling genes, CD3, CD4, and MHCII. We hypothesized that activation via increased interferon gamma (IFN‐γ) during endocrine aging may disrupt the immune‐metabolic balance in the brain and therefore advance changes in grey and white matter. With this study, we test the hypothesis that increased levels of peripheral IFN‐γ induces genotype dependent immuno‐metabolic changes in the JAX humanized APOE (hAPOE) mouse model.MethodTo determine the role of IFN‐γ in female midlife aging and AD risk, pre‐menopausal and peri‐menopausal hAPOE mice were intraperitoneally treated with recombinant IFN‐γ for 9 days. Immunophenotyping using multi‐color flow cytometry was conducted microglial reactivity, phagocytosis, neutral lipid content, oxidative stress, and the presence of lymphocytes were determined. Structural and diffusion weighted analysis using MRI was conducted to evaluate grey and white matter structural integrity in the brain. ELISA assays were conducted to assess the presence of beta amyloid 40 and 42 and levels of pro‐inflammatory cytokines.ResultIFN‐γ treated animals exhibited upregulation of markers that perpetuate neuroinflammation and white matter catabolism including MHCII, CD8, pHrodo, and BODIPY. Peripheral immune effects were genotype dependent while immune signaling in brain largely exhibited treatment‐dependent effects. Fasting blood glucose levels were significantly increased by IFN‐γ consistent with an accelerated aging profile. Diffusion metrics including mean and radial kurtosis in addition to mean, axial, and radial diffusivity were greater in IFN‐treated animals.ConclusionPeripheral increase of interferon gamma signaling during female endocrine aging in hAPOE mice induced 1) dysfunction of metabolic systems and neuroinflammatory response and 2) decreases in white and grey matter microstructural integrity throughout the brain. These outcomes support the investigation of therapeutic strategies targeting interferon signaling pathways at the earliest stages of midlife aging to reduce risk of AD or delay AD onset.

Interferons and systemic lupus erythematosus: Pathogenesis, clinical features, and treatments in interferon-driven disease.

Type I interferons (IFNs) have recently received a lot of attention with the elucidation of the pathogenesis of systemic lupus erythematosus (SLE). Type I IFNs are associated with many SLE symptoms and play a role in the pathogenesis of autoimmune diseases that may occur concurrently with SLE, such as Sjögren's syndrome, antiphospholipid syndrome, myositis, scleroderma, and interferonopathy. Type I IFNs could be the link between these diseases. However, direct measurement of type I IFN levels and the IFN gene signature is currently unavailable in clinical practice. This review discusses type I IFN signalling in SLE, investigates the role of type I IFN in the clinical manifestations and symptoms associated with SLE and other IFN-related diseases, and discusses the clinical tests that can be used to diagnose SLE and measure disease activity. In addition, the role of type I IFN-blocking therapies as potential treatments for SLE is discussed.

Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size.

Prior genomewide association studies have identified variation in major histocompatibility complex (MHC) class I alleles and C-C chemokine receptor type 5 gene (CCR5Δ32) as genetic predictors of viral control, especially in 'elite' controllers, individuals who remain virally suppressed in the absence of therapy. Cross-sectional genomewide association study. We analyzed custom whole exome sequencing and direct human leukocyte antigen (HLA) typing from 202 antiretroviral therapy (ART)-suppressed HIV+ noncontrollers in relation to four measures of the peripheral CD4+ T-cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T-cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. Previously reported 'protective' host genetic mutations related to viral setpoint (e.g. among elite controllers) were found to predict smaller HIV reservoir size. The HLA 'protective' B∗57:01 was associated with significantly lower HIV usRNA (q = 3.3 × 10-3), and among the largest subgroup, European ancestry individuals, the CCR5Δ32 deletion was associated with smaller HIV tDNA (P = 4.3 × 10-3) and usRNA (P = 8.7 × 10-3). In addition, genomewide analysis identified several single nucleotide polymorphisms in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q = 0.02), and the direction of these associations paralleled MX1 gene eQTL expression. We observed a significant association between previously reported 'protective' MHC class I alleles and CCR5Δ32 with the HIV reservoir size in noncontrollers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.

Characterization and Clinical Impact of the Tumor Microenvironment of Post-Transplant Large B-Cell Lymphoma

Post-transplant lymphoproliferative disorders (PTLDs) arise after solid organ or allogeneic hematopoietic stem cell transplantation. They are characterized by abnormal proliferation of lymphoid cells associated with immunosuppression and comprise three histological categories (non-destructive, polymorphic, monomorphic) entailing a heterogeneous clinical behavior. The majority of monomorphic PTLDs fulfill the criteria of aggressive large B-cell lymphomas and are often associated with Epstein-Barr virus (EBV) positivity. The composition and function of the tumor microenvironment (TME) has a major impact on lymphoma development and survival, but to date, only few studies investigating the TME in PTLD have been reported. We used digital gene expression profiling and in silico immunophenotyping to characterize the TME of 75 post-transplant monomorphic aggressive B-cell lymphomas from three Nordic countries and correlated the findings with patient demographics (Table 1) and survival. Unsupervised clustering demonstrated a high degree of heterogeneity and variation in the immune response profile among the PTLDs. EBV+ PTLDs clustered closely together and were enriched for type I interferon signaling and antiviral response genes. In addition, a signature for cytotoxicity associated with EBV-positivity and better overall survival (OS; HR 0.61, 95%CI 0.40-0.92, P=0.019). In silico immunophenotyping utilizing CIBERSORTx suggested that the PTLDs can be divided into two subgroups with distinct immune cell compositions (Figure 1). The patients in the inflamed subgroup with high proportions of T cells and NK cells, as well as high T cell/macrophage ratio, had significantly better OS and PFS compared to the patients in the non-inflamed subgroup (median OS >200.0 vs. 15.2 months, P=0.006; median PFS 89.0 vs. 14.4 months, P=0.049). In multivariable analysis with the EBV-status, International Prognostic Index (IPI) and rituximab-containing treatment, the inflamed TME remained as an independent predictor for favorable OS and PFS. The inflamed subgroup was associated with EBV-positivity (P=0.008) and earlier onset of the disease (P=0.004). We also compared the TME composition between post-transplant and de novo diffuse large B-cell lymphomas (DLBCLs, n=82) and discovered that the PTLD TME was enriched in dendritic cells, NK cells, and activated mast cells, whereas the proportion of T cells, memory B cells and resting mast cells was lower compared to the de novo DLBCL. In conclusion, we provide a comprehensive phenotypic characterization of PTLD, highlighting the importance of TME biology, and in particular T cell infiltration, in the clinical behavior and prognosis of PTLD. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Single-Cell RNA-Seq Reveals an Interferon-Driven Inflammatory CD4 Naïve T Cell Subpopulation at Day 100 in Hematopoietic Stem Cell Transplant Patients That Ultimately Develop Chronic Gvhd

Background: Chronic GVHD (cGVHD) is the most significant cause of long-term morbidity and mortality after hematopoietic stem cell transplant (HCT). Improving patient outcomes requires a better understanding of biological mechanisms that underly disease, in order to develop novel risk-assignment biomarkers and therapeutic strategies. Naïve T cells (TN) are a prevailing risk factor for cGVHD, with mouse studies and clinical trial data demonstrating that graft depletion of TN cells decreases the frequency of cGVHD. Nevertheless, little is known about how TN cells progress to alloreactivity and, ultimately, to clinical cGVHD. In this study, we compared single-cell RNA sequencing (scRNA-Seq) from patients receiving unrelated donor transplantation (URD HCT) who developed mod-severe cGVHD, versus patients who were free from cGVHD, to identify disease-specific subpopulations of T cells that preceded disease. Methods: This analysis was designed to identify immune profiles in blood at Day 100 that could distinguish patients who ultimately developed cGVHD from those who remained free of this disease. Blood was drawn from patients with hematologic malignancies undergoing 8/8 HLA-matched URD HCT after myeloablative conditioning, and who received CNI/MTX GVHD prophylaxis. We focused on Day 100 samples from patients with Gr 0-2 acute GVHD who did not require systemic steroids as our starting population, and then divided these patients into those who subsequently developed moderate-severe cGVHD ('cGVHD' group, n=8; median cGVHD onset = 181 days) and patients who never developed mod-severe cGVHD through at least 2 years post-HCT (termed 'operationally tolerant' patients, 'OpTol', n = 24). Flow cytometry of longitudinal samples was performed using 16 ten-color panels, characterizing T cell reconstitution, activation, exhaustion, and naïve/memory subpopulations. Bulk RNA sequencing was performed on flow-sorted CD4 T cells (within 3h of collection) at Day 100 on patients from two central lab sites (cGVHD = 7, OpTol = 9). Statistical modeling was performed using DESeq2, followed by differential expression and Gene Set Enrichment Analysis (GSEA) with clusterProfiler. scRNA-Seq was performed on flow-sorted CD4 T cells using the 10X platform (cGVHD = 7, OpTol = 5). scRNA-Seq data was batch corrected with Harmony, annotated with SignacX and analyzed with Seurat. Results: Flow cytometry identified a higher proportion of CD4TN but not CD8TN cells in cGVHD patients that persisted longitudinally through Day 100 (25.9% vs. 10.0% at Day 100, p=0.03). Bulk transcriptome GSEA of Day 100 CD4 T cells confirmed enrichment of TN cells in cGVHD patients, but also revealed additional gene sets relating to interferon signaling (Fig. 1A). In contrast, OpTol patients revealed gene signatures relating to memory T cells and quiescence. scRNA-Seq enabled the discovery of CD4 T cell types/states enriched in patients who would develop mod-severe cGVHD. We profiled >100,000 CD4 T cells from Day 100 samples from cGVHD and OpTol patients. Unsupervised clustering identified two populations that were enriched in cGVHD vs. OpTol patients (Fig. 1B): interferon-stimulated CD4TN cells and interferon-stimulated CD4 memory cells. Both subsets show significantly higher expression of an interferon-response signature relative to all other cells (TN = 0.93, Tmem = 1.61, others = 0.14, p < 0.0001). The CD4TN subset possessed a signature for IFN-α-related stimulation (including IFI6, ISG15, IFI44L, EPSTI1) as well as IFN-γ-related genes (including STAT1, MX1). These findings further substantiate the IFN gene signature identified by bulk RNA-Seq at day 100 in cGVHD vs. OpTol patients. Conclusions: These data identified an inflammatory CD4TN cell subpopulation at day 100 in patients that go on to develop cGVHD, and suggest that CD4TN cells may harbor pathogenic cells that could predispose patients to allo-inflammatory complications. scRNA-Seq revealed a strong type I and type II interferon signaling signature in this CD4TN subset, and also identified a novel population of interferon-stimulated memory cells which may indicate a more differentiated population of alloreactive cells. These data highlight an interferon-driven transcriptome signature preceding the onset of cGVHD. Continued exploration of these cells may yield new risk-assignment biomarkers and nominate therapeutic approaches to prevent cGVHD in high-risk patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

RAD21 amplification epigenetically suppresses interferon signaling to promote immune evasion in ovarian cancer.

Prevalent copy number alteration is the most prominent genetic characteristic associated with ovarian cancer (OV) development, but its role in immune evasion has not been fully elucidated. In this study, we identified RAD21, a key component of the cohesin complex, as a frequently amplified oncogene that could modulate immune response in OV. Through interrogating the RAD21-regulated transcriptional program, we found that RAD21 directly interacts with YAP/TEAD4 transcriptional corepressors and recruits the NuRD complex to suppress interferon (IFN) signaling. In multiple clinical cohorts, RAD21 overexpression is inversely correlated with IFN signature gene expression in OV. We further demonstrated in murine syngeneic tumor models that RAD21 ablation potentiated anti-PD-1 efficacy with increased intratumoral CD8+ T cell effector activity. Our study identifies a RAD21-YAP/TEAD4-NuRD corepressor complex in immune modulation, and thus provides a potential target and biomarker for precision immunotherapy in OV.

Identification of Galectin-7 as a crucial metastatic enhancer of squamous cell carcinoma associated with immunosuppression.

Metastasis predicts poor prognosis in cancer patients. It has been recognized that specific tumor microenvironment defines cancer cell metastasis, whereas the underlying mechanisms remain elusive. Here we show that Galectin-7 is a crucial mediator of metastasis associated with immunosuppression. In a syngeneic mouse squamous cell carcinoma (SCC) model of NR-S1M cells, we isolated metastasized NR-S1M cells from lymph nodes in tumor-bearing mice and established metastatic NR-S1M cells in in vitro culture. RNA-seq analysis revealed that interferon gene signature was markedly downregulated in metastatic NR-S1M cells compared with parental cells, and in vivo NR-S1M tumors heterogeneously developed focal immunosuppressive areas featured by deficiency of anti-tumor immune cells. Spatial transcriptome analysis (Visium) for the NR-S1M tumors revealed that various pro-metastatic genes were significantly upregulated in immunosuppressive areas when compared to immunocompetent areas. Notably, Galectin-7 was identified as a novel metastasis-driving factor. Galectin-7 expression was induced during tumorigenesis particularly in the microenvironment of immunosuppression, and extracellularly released at later stage of tumor progression. Deletion of Galectin-7 in NR-S1M cells significantly suppressed lymph node and lung metastasis without affecting primary tumor growth. Therefore, Galectin-7 is a crucial mediator of tumor metastasis of SCC, which is educated in the immune-suppressed tumor areas, and may be a potential target of cancer immunotherapy.

MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling

The limited efficacy of immune checkpoint inhibitor treatment in triple-negative breast cancer (TNBC) patients is attributed to sparse or unresponsive tumor-infiltrating lymphocytes, but the mechanisms that lead to a therapy resistant tumor immune microenvironment are incompletely known. Here we show a strong correlation between MYC expression and loss of immune signatures in human TNBC. In mouse models of TNBC proficient or deficient of breast cancer type 1 susceptibility gene (BRCA1), MYC overexpression dramatically decreases lymphocyte infiltration in tumors, along with immune signature remodelling. MYC-mediated suppression of inflammatory signalling induced by BRCA1/2 inactivation is confirmed in human TNBC cell lines. Moreover, MYC overexpression prevents the recruitment and activation of lymphocytes in both human and mouse TNBC co-culture models. Chromatin-immunoprecipitation-sequencing reveals that MYC, together with its co-repressor MIZ1, directly binds promoters of multiple interferon-signalling genes, resulting in their downregulation. MYC overexpression thus counters tumor growth inhibition by a Stimulator of Interferon Genes (STING) agonist via suppressing induction of interferon signalling. Together, our data reveal that MYC suppresses innate immunity and facilitates tumor immune escape, explaining the poor immunogenicity of MYC-overexpressing TNBCs.

FIVE INTERFERON RECEPTOR TRIPLICATES: A UNIQUE CASE OF HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS IN A DOWN SYNDROME PATIENT

<h3>Introduction</h3> Down Syndrome (DS) is recognized as a mild interferonopathy with features of autoimmunity, developmental delays and brain calcifications explained by triplicates of four of the six interferon receptors (IFNAR1, IFNAR2, IFNGR2, and IL10RB) found on chromosome 21. We describe hemophagocytic lymphohistiocytosis (HLH) in a DS patient who was found to have a second copy number gain encompassing IFNGR1. <h3>Case Description</h3> An ex 35-week male with a history of DS and transient abnormal myelopoiesis in the newborn period presented at 10 months of age with recurrent fever, lymphadenopathy and splenomegaly. He met criteria for HLH with anemia, hyperferritinemia, elevated soluble CD25, elevated fibrinogen and a cervical lymph node biopsy showing evidence of hemophagocytosis. Evaluation for underlying triggers was unremarkable. Given a disproportionately elevated interleukin-18 (148,566pg/mL) and S100A12 (26,911ng/mL) compared to CXCL9 (161pg/mL), targeted treatment with anakinra was initiated. The patient defervesced and laboratory findings improved. A primary immunodeficiency gene panel revealed copy number variants consistent with chromosome 21, along with a duplication of <i>IFNGR1</i> gene located on chromosome 6. A post-natal microarray confirmed trisomy 21 and revealed a duplication on chromosome 6p23.3 involving the <i>IFNGR1</i> gene. His type I interferon gene signature (IGS) was only slightly elevated while on therapy. <h3>Discussion</h3> DS has been established to have both elevated Type I and II IGS in the setting of 4/6 interferon receptor gene triplicates. Our patient has the unique overexpression of the IFNGR1 gene as well, likely contributing to his HLH-like presentation.

SARS-CoV-2 mRNA-based vaccines in the Aicardi Goutières Syndrome.

Aicardi Goutières Syndrome (AGS) is an autoinflammatory disorder resulting in sustained interferon activation through defects in nucleic acid modification and sensing pathways. Thus, mRNA-based vaccination used against SARS-CoV-2, raise disease-specific safety concerns. To assess interferon signaling, we tested mRNA SARS-CoV-2 vaccines in AGS whole blood samples. Interferon activation is measured through quantitation of interferon signaling gene (ISG) expression and is increased in AGS patients. There was no increase in ISG scores from baseline following treatment with the nucleoside modified mRNA formulation compared to an increase with unmodified. A patient-family survey reported that the vaccines were well tolerated. These findings suggest that COVID vaccination using nucleoside-modified forms of mRNA vaccines are unlikely to directly stimulate ISG expression in response to mRNA internalization in AGS tissues. With continued community spread, we recommend vaccination using nucleoside-modified mRNA vaccines in this rare disease group in individuals for whom vaccines were previously well tolerated.

Increased Type I interferon signaling and brain endothelial barrier dysfunction in an experimental model of Alzheimer’s disease

Blood–brain barrier (BBB) dysfunction is emerging as a key pathogenic factor in the progression of Alzheimer’s disease (AD), where increased microvascular endothelial permeability has been proposed to play an important role. However, the molecular mechanisms leading to increased brain microvascular permeability in AD are not fully understood. We studied brain endothelial permeability in female APPswe/PS1∆E9 (APP/PS1) mice which constitute a transgenic mouse model of amyloid-beta (Aβ) amyloidosis and found that permeability increases with aging in the areas showing the greatest amyloid plaque deposition. We performed an unbiased bulk RNA-sequencing analysis of brain endothelial cells (BECs) in female APP/PS1 transgenic mice. We observed that upregulation of interferon signaling gene expression pathways in BECs was among the most prominent transcriptomic signatures in the brain endothelium. Immunofluorescence analysis of isolated BECs from female APP/PS1 mice demonstrated higher levels of the Type I interferon-stimulated gene IFIT2. Immunoblotting of APP/PS1 BECs showed downregulation of the adherens junction protein VE-cadherin. Stimulation of human brain endothelial cells with interferon-β decreased the levels of the adherens junction protein VE-cadherin as well as tight junction proteins Occludin and Claudin-5 and increased barrier leakiness. Depletion of the Type I interferon receptor in human brain endothelial cells prevented interferon-β-induced VE-cadherin downregulation and restored endothelial barrier integrity. Our study suggests that Type I interferon signaling contributes to brain endothelial dysfunction in AD.

COVID-19 patients exhibit unique transcriptional signatures indicative of disease severity.

COVID-19 manifests a spectrum of respiratory symptoms, with the more severe often requiring hospitalization. To identify markers for disease progression, we analyzed longitudinal gene expression data from patients with confirmed SARS-CoV-2 infection admitted to the intensive care unit (ICU) for acute hypoxic respiratory failure (AHRF) as well as other ICU patients with or without AHRF and correlated results of gene set enrichment analysis with clinical features. The results were then compared with a second dataset of COVID-19 patients separated by disease stage and severity. Transcriptomic analysis revealed that enrichment of plasma cells (PCs) was characteristic of all COVID-19 patients whereas enrichment of interferon (IFN) and neutrophil gene signatures was specific to patients requiring hospitalization. Furthermore, gene expression results were used to divide AHRF COVID-19 patients into 2 groups with differences in immune profiles and clinical features indicative of severe disease. Thus, transcriptomic analysis reveals gene signatures unique to COVID-19 patients and provides opportunities for identification of the most at-risk individuals.

Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells

BackgroundBats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN.ResultsWe found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN.ConclusionCollectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.

ADAR1 Prevents Autoinflammatory Processes in the Heart Mediated by IRF7.

ADAR1 (adenosine deaminase acting on RNA-1)-mediated adenosine to inosine (A-to-I) RNA editing plays an essential role for distinguishing endogenous from exogenous RNAs, preventing autoinflammatory ADAR1 also regulates cellular processes by recoding specific mRNAs, thereby altering protein functions, but may also act in an editing-independent manner. The specific role of ADAR1 in cardiomyocytes and its mode of action in the heart is not fully understood. To determine the role of ADAR1 in the heart, we used different mutant mouse strains, which allows to distinguish immunogenic, editing-dependent, and editing-independent functions of ADAR1. Different Adar1-mutant mouse strains were employed for gene deletion or specific inactivation of ADAR1 enzymatic activity in cardiomyocytes, either alone or in combination with Ifih1 (interferon induced with helicase C domain 1) or Irf7 (interferon regulatory factor 7) gene inactivation. Mutant mice were investigated by immunofluorescence, Western blot, RNAseq, proteomics, and functional MRI analysis. Inactivation of Adar1 in cardiomyocytes resulted in late-onset autoinflammatory myocarditis progressing into dilated cardiomyopathy and heart failure at 6 months of age. Adar1 depletion activated interferon signaling genes but not NFκB (nuclear factor kappa B) signaling or apoptosis and reduced cardiac hypertrophy during pressure overload via induction of Irf7. Additional inactivation of the cytosolic RNA sensor MDA5 (melanoma differentiation-associated gene 5; encoded by the Ifih1 gene) in Adar1 mutant mice prevented activation of interferon signaling gene and delayed heart failure but did not prevent lethality after 8.5 months. In contrast, compound mutants only expressing catalytically inactive ADAR1 in an Ifih1-mutant background were completely normal. Inactivation of Irf7 attenuated the phenotype of Adar1-deficient cardiomyocytes to a similar extent as Ifih1 depletion, identifying IRF7 as the main mediator of autoinflammatory responses caused by the absence of ADAR1 in cardiomyocytes. Enzymatically active ADAR1 prevents IRF7-mediated autoinflammatory reactions in the heart triggered by endogenous nonedited RNAs. In addition to RNA editing, ADAR1 also serves editing-independent roles in the heart required for long-term cardiac function and survival.

DDX58 Is Associated With Susceptibility to Severe Influenza Virus Infection in Children and Adolescents.

Seasonal influenza virus infection causes a range of disease severity, including lower respiratory tract infection with respiratory failure. We evaluated the association of common variants in interferon (IFN) regulatory genes with susceptibility to critical influenza infection in children. We performed targeted sequencing of 69 influenza-associated candidate genes in 348 children from 24 US centers admitted to the intensive care unit with influenza infection and lacking risk factors for severe influenza infection (PICFlu cohort, 59.4% male). As controls, whole genome sequencing from 675 children with asthma (CAMP cohort, 62.5% male) was compared. We assessed functional relevance using PICFlu whole blood gene expression levels for the gene and calculated IFN gene signature score. Common variants in DDX58, encoding the retinoic acid-inducible gene I (RIG-I) receptor, demonstrated association above or around the Bonferroni-corrected threshold (synonymous variant rs3205166; intronic variant rs4487862). The intronic single-nucleotide polymorphism rs4487862 minor allele was associated with decreased DDX58 expression and IFN signature (P < .05 and P = .0009, respectively) which provided evidence supporting the genetic variants' impact on RIG-I and IFN immunity. We provide evidence associating common gene variants in DDX58 with susceptibility to severe influenza infection in children. RIG-I may be essential for preventing life-threatening influenza-associated disease.

Identifying key genes in CD4+ T cells of systemic lupus erythematosus by integrated bioinformatics analysis.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by excessive activation of T and B lymphocytes and breakdown of immune tolerance to autoantigens. Despite several mechanisms including the genetic alterations and inflammatory responses have been reported, the overall signature genes in CD4+ T cells and how they affect the pathological process of SLE remain to be elucidated. This study aimed to identify the crucial genes, potential biological processes and pathways underlying SLE pathogenesis by integrated bioinformatics. The gene expression profiles of isolated peripheral CD4+ T cells from SLE patients with different disease activity and healthy controls (GSE97263) were analyzed, and 14 co-expression modules were identified using weighted gene co-expression network analysis (WGCNA). Some of these modules showed significantly positive or negative correlations with SLE disease activity, and primarily enriched in the regulation of type I interferon and immune responses. Next, combining time course sequencing (TCseq) with differentially expressed gene (DEG) analysis, crucial genes in lupus CD4+ T cells were revealed, including some interferon signature genes (ISGs). Among these genes, we identified 4 upregulated genes (PLSCR1, IFI35, BATF2 and CLDN5) and 2 downregulated genes (GDF7 and DERL3) as newfound key genes. The elevated genes showed close relationship with the SLE disease activity. In general, our study identified 6 novel biomarkers in CD4+ T cells that might contribute to the diagnosis and treatment of SLE.