Interferon-inducible antiviral effectors

Development and Validation of a Predictive Nomogram for Myelosuppression Risk in Chronic Hepatitis B Patients Treated with Peginterferon

Purpose

Peginterferon (Peg-IFN) is a common treatment for chronic hepatitis B (CHB); however, some patients developing myelosuppression as a side-effect. In this study, we identified risk factors associated with increased myelosuppression, and incorporated them into a predictive nomogram.

Patients and Methods

This study is designed as a case-control study. A total of 312 CHB patients treated with Peg-IFN from two medical centers were retrospectively enrolled between December 2019 and December 2022. Patients from the First Affiliated Hospital of Nanchang University were randomly divided into a training cohort (n=153) and a test cohort (n=55) at a 3:1 ratio. Patients from the Jiangxi Provincial People's Hospital composed the validation cohort (n= 104). In the training cohort, based on the blood routine results of patients 1 week after Peg-IFN treatment, patients were further divided into Normal (myelosuppression grades 0-I) and Myelosuppression (grades II-IV) groups. Then uni- and multivariate logistic regression analyses were carried out to identify myelosuppression risk factors, which were subsequently incorporated into a predictive nomogram. The capability of the predictive nomogram was validated using an area under the curve (AUC) of the receiver operating characteristic (ROC) curve. The Hosmer-Lemeshow test, calibration curves, and decision curve analysis (DCA) were used to evaluate the nomogram. Finally, the developed predictive nomogram was validated both internally and externally using separate test and validation cohorts.

Results

Body mass index (BMI; odds ratio [OR]=0.841, 95% confidence interval [CI] 0.738-0.959, P=0.010), white blood cell counts (WBC; OR=0.657, 95% CI 0.497-0.868, P=0.003), globulin (GLB; OR=0.796, 95% CI 0.713-0.889, P<0.001) and serum creatinine levels (SCR; OR=1.029, 95% CI 1.002-1.058, P=0.038) are independent risk factors for myelosuppression in Peg-IFN-treated CHB patients. A predictive nomogram was constructed by incorporating the above independent risk factors, and its performance was assessed across the training, test, and validation cohorts. The model demonstrated AUC values of 0.824 (95% CI 0.757-0.891), 0.812 (95% CI 0.701-0.923), and 0.870 (95% CI 0.802-0.940), respectively, highlighting its good predictive accuracy. As for Hosmer-Lemeshow, it was P=0.351, (χ2= 8.898) for training, P=0.514 (χ2=6.226) for the test, and P=0.442 (χ2=7.918) for the validation cohort. The results of the calibration curves and DCA demonstrated good concordance between predicted probabilities and observed outcomes, with the model showing higher clinical net benefit.

Conclusion

Lower BMI, WBC counts, GLB, and higher SCR levels are independent risk factors for myelosuppression among Peg-IFN-treated CHB patients. The predictive nomogram, based on those factors, is able to identify high-risk individuals for myelosuppression, thereby aiding in early alleviation of this side-effect.

Omics analyses uncover host networks defining virus-permissive and -hostile cellular states

The capacity of host cells to sustain or restrict virus infection is influenced by their proteome. Understanding the compendium of proteins defining cellular permissiveness is key to many questions in fundamental virology. Here, we apply a multiomic approach to determine the proteins that are associated with highly permissive, intermediate, and hostile cellular states. We observed two groups of differentially regulated genes: i) with robust changes in mRNA and protein levels, and ii) with protein/RNA discordances. Whereas many of the latter are classified as interferon stimulated genes (ISGs), most exhibit no antiviral effects in overexpression screens. This suggest that IFN-dependent protein changes can be better indicators of antiviral function than mRNA levels. Phosphoproteomics revealed an additional regulatory layer involving non-signalling proteins with altered phosphorylation. Indeed, we confirmed that several permissiveness-associated proteins with changes in abundance or phosphorylation regulate infection fitness. Altogether, our study provides a comprehensive and systematic map of the cellular alterations driving virus susceptibility.

Interferon-I modulation and natural products: Unraveling mechanisms and therapeutic potential in severe COVID-19

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a significant global public health threat, particularly to older adults, pregnant women, and individuals with underlying chronic conditions. Dysregulated immune responses to SARS-CoV-2 infection are believed to contribute to the progression of COVID-19 in severe cases. Previous studies indicates that a deficiency in type I interferon (IFN-I) immunity accounts for approximately 15 %-20 % of patients with severe pneumonia caused by COVID-19, highlighting the potential therapeutic importance of modulating IFN-I signals. Natural products and their derivatives, due to their structural diversity and novel scaffolds, play a crucial role in drug discovery. Some of these natural products targeting IFN-I have demonstrated applications in infectious diseases and inflammatory conditions. However, the immunomodulatory potential of IFN-I in critical COVID-19 pneumonia and the natural compounds regulating the related signal pathway remain not fully understood. In this review, we offer a comprehensive assessment of the association between IFN-I and severe COVID-19, exploring its mechanisms and integrating information on natural compounds effective for IFN-I regulation. Focusing on the primary targets of IFN-I, we also summarize the regulatory mechanisms of natural products, their impact on IFNs, and their therapeutic roles in viral infections. Collectively, by synthesizing these findings, our goal is to provide a valuable reference for future research and to inspire innovative treatment strategies for COVID-19.

Unveiling the prevalence and impact of silent rhinovirus infection in chronic rhinosinusitis with nasal polyps

BACKGROUND

Chronic rhinosinusitis with nasal polyps (CRSwNPs) involves persistent sinus inflammation, with emerging evidence suggesting a potential role of rhinovirus (RV) in its pathophysiology. However, whether RV exists in nasal tissues and affects the nasal mucosa after the resolution of infection symptoms remains unknown.

OBJECTIVE

To investigate the prevalence and impact of silent RV infection in nasal tissues.

METHODS

RV loads were detected in the nasal tissues of 47 controls and 101 patients with CRSwNP without respiratory infection. Participants were categorized into RV-positive (+), RV-negative (-), and the "gray zone" groups. Quantitative polymerase chain reaction, Western blotting, and immunofluorescence assays were used to analyze the impact of silent RV infection on the immune status of nasal tissues.

RESULTS

Silent RV infection was prevalent in both control (34%) and CRSwNP (30.7%) tissues, with higher viral loads observed in the nasal polyps. In controls, it was associated with high expression of types 1 and 2 interferon (IFN), type 2 inflammation, interleukin (IL)-17A, and IL-10. In patients with CRSwNP, silent RV infection was associated with lower levels of type 1 IFN, IL-17A, type 2 inflammation, and IL-10 but higher levels of type 2 IFN compared with those without RV infection. Meanwhile, RV (+) nasal polyps exhibited fewer tissue eosinophils and neutrophils than RV (-) nasal polyps.

CONCLUSION

Silent RV infection was prevalent in the nasal tissues, with a higher viral load detected in the nasal polyps. This silent RV infection is associated with distinct immune responses in healthy controls and patients with CRSwNP, involving differential modulation of IFNs, TH2 cytokines, IL-17A, IL-10, and eosinophil and neutrophil levels.

A tissue-scale strategy for sensing threats in barrier organs

Barrier organs rely on a limited set of pattern recognition receptors (PRRs) to detect diverse immunogenic challenges. How organs assess threats and adjust immune responses to balance host protection with collateral tissue damage remains unclear. Here, by analyzing influenza infection in the lung using single-molecule imaging and spatial transcriptomics, we discovered a tiered threat-sensing strategy at the tissue scale, where the probability of detecting and responding to infection is lowest in the outermost epithelia and highest in the inner stroma. This strategy emerges from spatially graded PRR expression that results in cell-type-specific probabilities of threat-sensing across the tissue, a design broadly adopted by barrier organs. Selectively increasing PRR expression in lung epithelia in vivo exacerbated tissue damage upon inflammatory challenge. These results reveal a spatially tiered strategy to tolerate threats restricted within the epithelia, and yet enable progressively potent immune responses as threats invade deeper into the tissue.

Harnessing immunotherapeutic molecules and diagnostic biomarkers as human-derived adjuvants for MERS-CoV vaccine development

The pandemic potential of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) highlights the critical need for effective vaccines due to its high fatality rate of around 36%. In this review, we identified a variety of immunotherapeutic molecules and diagnostic biomarkers that could be used in MERS vaccine development as human-derived adjuvants. We identified immune molecules that have been incorporated into standard clinical diagnostics such as CXCL10/IP10, CXCL8/IL-8, CCL5/RANTES, IL-6, and the complement proteins Ca3 and Ca5. Utilization of different human monoclonal antibodies in the treatment of MERS-CoV patients demonstrates promising outcomes in combatting MERS-CoV infections in vivo, such as hMS-1, 4C2H, 3B11-N, NBMS10-FC, HR2P-M2, SAB-301, M336, LCA60, REGN3051, REGN3048, MCA1, MERs-4, MERs-27, MERs-gd27, and MERs-gd33. Host-derived adjuvants such as CCL28, CCL27, RANTES, TCA3, and GM-CSF have shown significant improvements in immune responses, underscoring their potential to bolster both systemic and mucosal immunity. In conclusion, we believe that host-derived adjuvants like HBD-2, CD40L, and LL-37 offer significant advantages over synthetic options in vaccine development, underscoring the need for clinical trials to validate their efficacy.

Identification of novel antiviral host factors by functional gene expression analysis using in vitro HBV infection assay systems

To cure hepatitis B virus (HBV) infection, it is essential to elucidate the function of hepatocyte host factors in regulating the viral life cycle. Signaling and transcription activator of transcription (STAT)1 play important roles in immune responses, but STAT1-independent pathways have also been shown to have important biological reactivity. Using an in vitro HBV infection assay system, the current study aimed to investigate the STAT1-independent host factors that contribute to the control of viral infection by comprehensive functional screening. The in vitro HBV infection system was established using primary human hepatocytes (PXB cells) infected with HBV derived from a plasmid containing the 1.3-mer HBV genome. Comprehensive functional studies were performed using small interfering RNA (siRNA) and vector transfection and analyzed using microarrays. Knockdown of STAT1 increased viral products in HBV-transfected HepG2 cells, but decreased in HBV-infected PXB cells. RNA microarray was performed using HBV-infected PXB cells with STAT1 knockdown. Fumarylacetoacetate hydrolase (FAH) was extracted by siRNA of genes in PXB cells altered by STAT1 knockdown. Transfection of FAH inhibited HBV replication. Dimethyl fumarate (DMF), the methyl ester of FAH metabolite, showed antiviral effects by inducing autophagy and anti-HBV-related genes. Independently of STAT1, FAH was identified as a host factor that contributes to the control of viral infection, and its metabolite, DMF, exhibited antiviral activity. These results suggest that the novel host factor FAH and its metabolites may be an innovative therapeutic strategy to control the HBV life cycle.

Switching of OAS1 splicing isoforms overcomes SNP-derived vulnerability to SARS-CoV-2 infection

BACKGROUND

The SARS-CoV-2 pandemic provided important insights into the relationship between infectious diseases and the human genome. A genomic region encoding the 2'-5'-oligoadenylate synthetase (OAS) family proteins that sense viral genomic RNAs and trigger an antiviral response contains single nucleotide polymorphisms (SNPs) associated with SARS-CoV-2 infection susceptibility. A high-risk SNP identified at the splice acceptor site of OAS1 exon 6-a terminal exon-alters the proportion of various splicing isoforms of OAS1 and its activity. However, the actual causality of this SNP or splicing to infection susceptibility remains unknown.

RESULTS

In this study, it was found that serine-arginine-rich splicing factor 6 (SRSF6) binds to the splice donor site of the human OAS1 exon 5. SRSF6 determines the selected alternative terminal exon when the risk allele disrupts the splice acceptor site. Subsequently, an inhibitor for CDC-like kinase was rationally selected as a candidate splicing modulator. RNA-Seq and RT-PCR analyses revealed that this inhibitor can induce splice switching of OAS1 mRNAs in the human lung adenocarcinoma cell line Calu-3. Under the inhibitor treatment, the cells exhibited reduced SARS-CoV-2 infection rates. Meanwhile, the colonic epithelial cell line Caco-2 expressed non-risk type OAS1 mRNA isoforms that did not undergo splice-switching or demonstrate altered SARS-CoV-2 sensitivity following treatment with the inhibitor.

CONCLUSIONS

These results indicate that a high-risk SNP in OAS1 influences cell susceptibility to SARS-CoV-2 infection by inducing splice-switching at its terminal exon. Additionally, chemical splicing modifiers may prove beneficial in overcoming this genomic vulnerability.

Downregulation of RSAD2 ameliorates keratinocyte hyperproliferation and skin inflammation in psoriasis via the TAK1/NF-κB axis

Immune cell infiltration and keratinocyte (KC) hyperproliferation are characteristics of psoriasis. Radical S-adenosyl methionine domain-containing 2 (RSAD2) plays an integral role in the innate immune response and is associated with various immune-related diseases. However, RSAD2's expression and role in modulating immune responses in psoriasis remain unexplored. In this study, we demonstrated a significant upregulation of RSAD2 expression in both psoriatic lesions and psoriasis-like mouse epidermis, with its expression positively correlated with psoriasis severity. In psoriatic cell models, RSAD2 was shown to promote the proliferation and secretion of pro-inflammatory cytokines by activating the transforming growth factor-β-activated kinase 1 (TAK1)-mediated nuclear factor kappa-B (NF-κB) signaling pathway. Additionally, it was found that the expression of RSAD2 is increased by the action of interferon regulatory factor-1 (IRF1), which binds to the promoter region of RSAD2. Therefore, the function of RSAD2 in psoriasis is regulated by IRF1. Notably, RSAD2 inhibition decreased epidermal hyperplasia and alleviated imiquimod (IMQ)-induced psoriatic dermatitis. In summary, our study highlights the modulation of the IRF1-RSAD2-TAK1 axis as a potential innovative therapeutic approach for psoriasis, offering new insights into the molecular mechanisms by which KCs drive inflammation in psoriasis.

Heterogeneity of OAS family expression in tuberculosis and the impact of different sample selection: a comprehensive analysis

The 2'-5' oligoadenylate synthetase (OAS)family, comprising OAS1, OAS2, OAS3, and OASL, has been shown to participate in the host immune response against Mycobacterium tuberculosis (Mtb). However, their expression profiles in tuberculosis (TB) remain inconsistent. In two TB-related datasets, the OAS family exhibits contrasting expression trends. To further investigate, we examined the expression of the OAS family in whole blood, peripheral blood mononuclear cells (PBMC), and pleural fluid mononuclear cells (PFMC) as study samples, focusing on pulmonary tuberculosis (PTB) and tuberculous pleuritis (TPE). The results revealed differing expression patterns of the OAS family in the two diseases. In PFMC samples from TPE patients, the OAS family showed overall upregulation. Additionally, matched samples from nine TPE patients indicated overlapping expression of the OAS family in both PBMC and PFMC samples.

ISGylation: is our genome yearning for such a modification?

ISGylation is the post-translational modification of protein substrates covalently conjugated with the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15). Although initially linked to antiviral immunity, recent evidence highlights important roles for ISGylation in various biological processes, such as maintaining genomic stability, promoting tumourigenesis, and being involved in other pathological conditions. In this review, we examine the molecular mechanisms underlying ISGylation, its interplay with other post-translational modifications, and its involvement in diverse biological and pathological processes. We propose future research directions to advance the field and discuss how ISGylation might be harnessed to ensure human health, particularly genome instability-associated diseases.

iPSC-derived human cortical organoids display profound alterations of cellular homeostasis following SARS-CoV-2 infection and Spike protein exposure

COVID-19 commonly leads to respiratory issues, yet numerous patients also exhibit a diverse range of neurological conditions, suggesting a detrimental impact of SARS-CoV-2 or the viral Spike protein on the central nervous system. Nonetheless, the molecular pathway behind neurological pathology and the presumed neurotropism of SARS-CoV-2 remains largely unexplored. We generated human cortical organoids (HCOs) derived from human induced pluripotent stem cells (hiPSC) to assess: (1) the expression of SARS-CoV-2 main entry factors; (2) their vulnerability to SARS-CoV-2 infection; and (3) the impact of SARS-CoV-2 infection and exposure to the Spike protein on their transcriptome. Results proved that (1) HCOs express the main SARS-CoV-2 receptors and co-receptors; (2) HCOs may be productively infected by SARS-CoV-2; (3) the viral particles released by SARS-CoV-2-infected HCOs are able to re-infect another cellular line; and (4) the infection resulted in the activation of apoptotic and stress pathways, along with inflammatory processes. Notably, these effects were recapitulated when HCOs were exposed to the Spike protein alone. The data obtained demonstrate that SARS-CoV-2 likely infects HCOs probably through the binding of ACE2, CD147, and NRP1 entry factors. Furthermore, exposure to the Spike protein alone proved sufficient to disrupt their homeostasis and induce neurotoxic effects, potentially contributing to the onset of long-COVID symptoms.

Homeostatic antiviral protection of the neonatal gut epithelium by interferon lambda

Cell-intrinsic antiviral gene expression by intestinal epithelial cells (IECs) limits infection by enteric viral pathogens. Here, we find that neonatal IECs express antiviral genes at homeostasis that depend on interferon lambda (IFN-λ) and are required for early control of mouse rotavirus (mRV) infection. Neonatal homeostatic IFN-λ responses are independent of microbiota and pervasively distributed among IECs, distinguishing them from the homeostatic responses of adult mice. Developmental differences in homeostatic IFN-stimulated gene signatures of the intestine are regulated by maturation during the suckling-to-weanling transition, which includes reduced expression of Prdm1 by mature IECs. These studies identify developmental regulation of the homeostatic IFN-λ response, which is present in the neonatal intestine from birth, stimulated independent of microbiota, and preemptively protects IECs from viral infection. This intrinsically programmed antiviral response in early life is particularly important due to the absence of a robust microbiota or protective immune memory at birth, when the risk of enteric infection is high.

Diffuse Traumatic Brain Injury Induced Stimulator of Interferons (STING) Signaling in Microglia Drives Cortical Neuroinflammation, Neuronal Dysfunction, and Impaired Cognition

Neuropsychiatric complications including depression and cognitive impairment develop, persist, and worsen in the years after traumatic brain injury (TBI), negatively affecting life and lifespan. Inflammatory responses mediated by microglia are associated with the transition from acute to chronic neuroinflammation after TBI. Moreover, type I interferon (IFN-I) signaling is a key mediator of inflammation during this transition. Thus, the purpose of this study was to determine the degree to which a microglia-specific knockout of the stimulator of interferons (STING) influenced TBI-induced neuroinflammation, neuronal dysfunction, and cognitive impairment. Here, microglial inducible STING knockout (CX₃CR1Cre/ERT2 x STING fl/fl ) mice were created and validated (mSTING -/- ). Diffuse brain injury (midline fluid percussion) in male and female mice increased STING expression in microglia, promoted microglial morphological restructuring, and induced robust cortical inflammation and pathology 7 days post injury (dpi). These TBI-associated responses were attenuated in mSTING -/- mice. Increased cortical astrogliosis and rod-shaped microglia induced by TBI were independent of mSTING -/- . 7 dpi, TBI induced 237 differentially expressed genes (DEG) in the cortex of functionally wildtype (STING +/+ ) associated with STING, NF- κB, and Interferon Alpha signaling and 85% were attenuated by mSTING -/- . Components of neuronal injury including reduced NeuN expression, increased cortical lipofuscin, and increased neurofilament light chain in plasma were increased by TBI and dependent on mSTING. TBI-associated cognitive tasks (novel object recognition/location, NOR/NOL) at 7 dpi were dependent on mSTING. Notably, the TBI-induced cognitive deficits in NOR/NOL and increased cortical inflammation 7 dpi were unaffected in global interferon-α/β receptor 1 knockout (IFNAR1) mice. In the final study, the RNA profile of neurons after TBI in STING +/+ and mSTING -/- mice was assessed 7 dpi by single nucleus RNA-sequencing. There was a TBI-dependent suppression of cortical neuronal homeostasis with reductions in CREB signaling, synaptogenesis, and oxytocin signaling and increases in cilium assembly and PTEN signaling. Overall, mSTING -/- prevented 50% of TBI-induced DEGs in cortical neurons. Collectively, ablation of STING in microglia attenuates TBI-induced IFN-dependent responses, cortical inflammation, neuronal dysfunction, neuronal pathology, and cognitive impairment.

Gene regulatory logic of the interferon-β enhancer contains multiple selectively deployed modes of transcription factor synergy

Type I interferon IFNβ is a key regulator of the immune response, and its dysregulated expression causes disease. The regulation of IFNβ promoter activity has been a touchpoint of mammalian gene control research since the discovery of functional synergy between two stimulus-responsive transcription factors (TFs) nuclear factor kappa B (NFκB) and interferon regulatory factors (IRF). However, subsequent gene knockout studies revealed that this synergy is condition-dependent such that either NFκB or IRF activation can be dispensable, leaving the precise regulatory logic of IFNβ transcription an open question. Here, we developed a series of quantitative enhancer states models of IFNβ expression control and evaluated them with stimulus-response data from TF knockouts. Our analysis confirmed that TF synergy is a hallmark of the regulatory logic but that it need not involve NFκB, as synergy between two adjacent IRF dimers is sufficient. We found that a sigmoidal binding curve at the distal site renders the dual IRF synergy mode ultrasensitive, allowing it only in conditions of high IRF activity upon viral infection. In contrast, the proximal site has high affinity and enables expression in response to bacterial exposure through synergy with NFκB. However, its accessibility is controlled by the competitive repressor p50:p50, which prevents basal IRF levels from synergizing with NFκB, such that NFκB-only stimuli do not activate IFNβ expression. The enhancer states model identifies multiple synergy modes that are accessed differentially in response to different immune threats, enabling a highly stimulus-specific but also versatile regulatory logic for stimulus-specific IFNβ expression.

Influence of Viral Re-Infection on Head Kidney Transcriptome of Nervous Necrosis Virus-Resistant and -Susceptible European Sea Bass (Dicentrarchus labrax, L.)

Fish viral infections have great environmental and economic implications in aquaculture. Nervous necrosis virus (NNV) is a pathogen affecting more than 120 different species, causing high mortality and morbidity. Herein, we study how NNV re-infection affects the European sea bass (Dicentrarchus labrax, L.) head kidney transcriptome in disease-resistant and -susceptible sea bass families. To determine how each family responds to re-infection, we performed the RNA-sequencing analysis of experimentally NNV-infected D. labrax. Fish were experimentally infected in a long-term study, and one month after the last recorded death, all surviving fish were re-infected by the same NNV strain. Fish tissues were sampled 7 days upon re-infection. The transcriptome profiles of infected vs. non-infected fish revealed 103 differentially expressed genes (DEGs) for the resistant family and 336 DEGs for the susceptible family. Only a few pathways were commonly enriched in the two families, further indicating that the resistant and susceptible families utilize completely different mechanisms to fight the NNV re-infection. Protein-protein interaction analysis identified a variety of hub genes for the resistant and the susceptible families, quite distinct in their function on NNV resistance. In conclusion, NNV-resistant and -sensitive sea bass transcriptomes were analyzed following NNV survivors' viral re-infection, offering a glimpse into how host attempts to control the infection depending on its genetic background in relation with virus resistance.

Multi-Omics Study Reveals Nc886/vtRNA2-1 as a Positive Regulator of Prostate Cancer Cell Immunity

Noncoding RNA 886 has emerged as a pivotal regulatory RNA with distinct functions across tissues, acting as a regulator of protein activity by directly binding to protein partners. While it is well recognized as a tumor suppressor in prostate cancer, the underlying molecular mechanisms remain elusive. To discover the principal pathways regulated by nc886 in prostate cancer, we used a transcriptomic and proteomic approach analyzing malignant DU145, LNCaP, PC3, and benign RWPE-1 prostate cell line models transiently transfected with in vitro transcribed nc886 or antisense oligonucleotides. Multiomics revelead a significant enrichment of immune system-related pathways across the cell lines, including cytokines and interferon signaling. The interferon response provoked by nc886 was validated by functional assays. The invariability of PKR phosphorylation and NF-κB activity in the gain/loss of nc886 function experiments and the positive regulation of innate immunity suggest a PKR-independent mechanism of nc886 action. Accordingly, the GSEA of the PRAD-TCGA data set revealed immune stimulation as the nc886 most associated node also in the clinical setting. Our study showed that the reduction of nc886 leads to a blunted immune response in prostate cancer.

Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states

Functional regeneration of the lung's gas exchange surface following injury requires the coordination of a complex series of cell behaviors within the alveolar niche. Using single-cell transcriptomics combined with lineage tracing of proliferating progenitors, we examined mouse lung regeneration after influenza injury, demonstrating an asynchronously phased response across different cellular compartments. This longitudinal atlas of injury responses has produced a catalog of transient and persistent transcriptional alterations in cells as they transit across axes of differentiation. These cell states include an injury-induced capillary endothelial cell (iCAP) that arises after injury, persists indefinitely, and shares hallmarks with developing lung endothelium and endothelial aberrations found in degenerative human lung diseases. This dataset provides a foundational resource to understand the complexity of cellular and molecular responses to injury and correlations to responses found in human development and disease.

Advances in antiviral strategies targeting mosquito-borne viruses: cellular, viral, and immune-related approaches

Mosquito-borne viruses (MBVs) are a major global health threat, causing significant morbidity and mortality. MBVs belong to several distinct viral families, each with unique characteristics. The primary families include Flaviviridae (e.g., Dengue, Zika, West Nile, Yellow Fever, Japanese Encephalitis), transmitted predominantly by Aedes and Culex mosquitoes; Togaviridae, which consists of the genus Alphavirus (e.g., Chikungunya, Eastern and Western Equine Encephalitis viruses), also transmitted by Aedes and Culex; Bunyaviridae (recently reorganized), containing viruses like Rift Valley Fever and Oropouche virus, transmitted by mosquitoes and sometimes sandflies; and Reoviridae, which includes the genus Orbivirus (e.g., West Nile and Bluetongue viruses), primarily affecting animals and transmitted by mosquitoes and sandflies. Despite extensive research, effective antiviral treatments for MBVs remain scarce, and current therapies mainly provide symptomatic relief and supportive care. This review examines the viral components and cellular and immune factors involved in the life cycle of MBVs. It also highlights recent advances in antiviral strategies targeting host factors such as lipid metabolism, ion channels, and proteasomes, as well as viral targets like NS2B-NS3 proteases and nonstructural proteins. Additionally, it explores immunomodulatory therapies to enhance antiviral responses and emphasizes the potential of drug repurposing, bioinformatics, artificial intelligence, and deep learning in identifying novel antiviral candidates. Continued research is crucial in mitigating MBVs' impact and preventing future outbreaks.

Update on the treatment navigation for functional cure of chronic hepatitis B: Expert consensus 2.0

As new evidence emerges, treatment strategies toward the functional cure of chronic hepatitis B are evolving. In 2019, a panel of national hepatologists published a Consensus Statement on the functional cure of chronic hepatitis B. Currently, an international group of hepatologists has been assembled to evaluate research since the publication of the original consensus, and to collaboratively develop the updated statements. The 2.0 Consensus was aimed to update the original consensus with the latest available studies, and provide a comprehensive overview of the current relevant scientific literatures regarding functional cure of hepatitis B, with a particular focus on issues that are not yet fully clarified. These cover the definition of functional cure of hepatitis B, its mechanisms and barriers, the effective strategies and treatment roadmap to achieve this endpoint, in particular new surrogate biomarkers used to measure efficacy or to predict response, and the appropriate approach to pursuing a functional cure in special populations, the development of emerging antivirals and immunomodulators with potential for curing hepatitis B. The statements are primarily intended to offer international guidance for clinicians in their practice to enhance the functional cure rate of chronic hepatitis B.

Diet-induced changes in metabolism influence immune response and viral shedding in Jamaican fruit bats

Land-use change may drive viral spillover from bats into humans, partly through dietary shifts caused by decreased availability of native foods and increased availability of cultivated foods. We experimentally manipulated diets of Jamaican fruit bats to investigate whether diet influences viral shedding. To reflect dietary changes experienced by wild bats during periods of nutritional stress, Jamaican fruit bats were fed either a standard diet or a putative suboptimal diet, which was deprived of protein (suboptimal-sugar diet) and/or supplemented with fat (suboptimal-fat diet). Upon H18N11 influenza A-virus infection, bats fed on the suboptimal-sugar diet shed the most viral RNA for the longest period, but bats fed the suboptimal-fat diet shed the least viral RNA for the shortest period. Bats on both suboptimal diets ate more food than the standard diet, suggesting nutritional changes may alter foraging behaviour. This study serves as an initial step in understanding whether and how dietary shifts may influence viral dynamics in bats, which alters the risk of spillover to humans.

Long Non-Coding RNA THRIL Promotes Influenza Virus Replication by Inhibiting the Antiviral Innate Immune Response

Long non-coding RNAs (lncRNAs) have been recognized for their crucial roles in the replication processes of various viruses. However, the specific functions and regulatory mechanisms of many lncRNAs in influenza A virus (IAV) pathogenesis remain poorly understood. In this study, we identified lncRNA THRIL and observed a significant reduction in its expression following IAV infection in A549 cells. The treatment of cells with the viral mimic poly (I:C), or with type I and type III interferons, resulted in a substantial decrease in THRIL expression. Furthermore, THRIL overexpression significantly enhanced IAV replication, while its silencing markedly reduced IAV replication. Additionally, IAV infection led to notable reductions in the expression levels of type I and type III interferons in cell lines overexpressing THRIL compared to control groups; conversely, cell lines with THRIL knockdown exhibited significantly higher interferon levels than control groups. Moreover, THRIL was found to inhibit the expression of several critical interferon-stimulated genes (ISGs), which are essential for an effective antiviral response. Notably, our findings demonstrated that THRIL impaired the activation of IRF3, a key transcription factor in the interferon signaling pathway, thereby suppressing host innate immunity. These results highlight THRIL's potential as a therapeutic target for antiviral strategies.

Pyrimidine synthesis enzyme CTP synthetase 1 suppresses antiviral interferon induction by deamidating IRF3

Metabolism is typically contextualized in conjunction with proliferation and growth. The roles of metabolic enzymes beyond metabolism-such as in innate immune responses-are underexplored. Using a focused short hairpin RNA (shRNA)-mediated screen, we identified CTP synthetase 1 (CTPS1), a rate-limiting enzyme of pyrimidine synthesis, as a negative regulator of interferon induction. Mechanistically, CTPS1 interacts with and deamidates interferon regulatory factor 3 (IRF3). Deamidation at N85 impairs IRF3 binding to promoters containing IRF3-responsive elements, thus muting interferon (IFN) induction. Employing CTPS1 conditional deletion and IRF3 deamidated or deamidation-resistant knockin mice, we demonstrated that CTPS1-driven IRF3 deamidation restricts IFN induction in response to viral infection in vivo. However, during immune activation, IRF3 deamidation by CTPS1 is inhibited by glycogen synthase kinase 3 beta (GSK3β) to promote IFN induction. This work demonstrates how CTPS1 tames innate immunity independent of its role in pyrimidine synthesis, thus expanding the functional repertoire of metabolic enzymes into immune regulation.

Human DBR1 deficiency impairs stress granule-dependent PKR antiviral immunity

The molecular mechanism by which inborn errors of the human RNA lariat-debranching enzyme 1 (DBR1) underlie brainstem viral encephalitis is unknown. We show here that the accumulation of RNA lariats in human DBR1-deficient cells interferes with stress granule (SG) assembly, promoting the proteasome degradation of at least G3BP1 and G3BP2, two key components of SGs. In turn, impaired assembly of SGs, which normally recruit PKR, impairs PKR activation and activity against viruses, including HSV-1. Remarkably, the genetic ablation of PKR abolishes the corresponding antiviral effect of DBR1 in vitro. We also show that Dbr1Y17H/Y17H mice are susceptible to similar viral infections in vivo. Moreover, cells and brain samples from Dbr1Y17H/Y17H mice exhibit decreased G3BP1/2 expression and PKR phosphorylation. Thus, the debranching of RNA lariats by DBR1 permits G3BP1/2- and SG assembly-mediated PKR activation and cell-intrinsic antiviral immunity in mice and humans. DBR1-deficient patients are prone to viral disease because of intracellular lariat accumulation, which impairs G3BP1/2- and SG assembly-dependent PKR activation.

Host-derived Bacillus antagonistic novel duck reovirus infection by regulating gut microbiota-mediated immune responses

The Novel Duck Reovirus (NDRV) infection poses a significant health risk to ducks, primarily attributed to the absence of efficacious preventive measures. This research aimed to investigate whether the administration of isolated Bacillus could protect antagonistic NDRV infection in a Cherry Valley duck model. Four indigenous Bacillus strains from the feces of healthy ducks demonstrated promising biosafety profiles. One-day-old ducklings were inoculated intramuscularly with NDRV and subsequently subjected to a 28-day regimen of mixed Bacillus (Bac) treatment. The effects of Bac on pathological symptoms, immune response and intestinal flora were analyzed. The results showed that Bac significantly reduced weight loss, clinical symptoms, and viral loading. Moreover, Bac treatment significantly decreased neutrophils, monocytes proportion, the TNF-α, IL-1β and IL-6 expression, increased platelets, lymphocytes proportion, the IFN-β and IL-10 expression, and restored immune dysfunction. In addition, Bac has increased the relative abundance of Enterococcaceae, Lactobacillales, Bacilli, Ruminococcaceae, Clostridium and Phascolarctobacterium. Moreover, the metabolism of short-chain fatty acids (SCFAs) was further regulated, thereby enhancing the acetate content. The correlation analysis showed that a positive association between acetate levels and IFN-β expression, while a negative correlation was observed with viral loading. In conclusion, the results suggest that the anti-NDRV mechanism of Bac may involve the modulation of gut microbiota to elicit an immune response that inhibits viral infection. This study presents a novel approach for the prevention and treatment of NDRV, thereby establishing a theoretical foundation for the future development of probiotics in the prevention and treatment of NDRV.

Machine learning models to further identify advantaged populations that can achieve functional cure of chronic hepatitis B virus infection after receiving Peg-IFN alpha treatment

OBJECTIVE

Functional cure is currently the highest goal of hepatitis B virus(HBV) treatment.Pegylated interferon(Peg-IFN) alpha is an important drug for this purpose,but even in the hepatitis B e antigen(HBeAg)-negative population,there is still a portion of the population respond poorly to it.Therefore,it is important to explore the influencing factors affecting the response rate of Peg-IFN alpha and establish a prediction model to further identify advantaged populations.

METHODS

We retrospectively analyzed 382 patients.297 patients were in the training set and 85 patients from another hospital were in the test set.The intersect features were extracted from all variables using the recursive feature elimination(RFE) algorithm, Boruta algorithm, and least absolute shrinkage and selection operator(LASSO) regression algorithm in the training dataset.Then,we employed six machine learning(ML) algorithms-Logistic Regression(LR),Random Forest(RF),Support Vector Machines(SVM),K Nearest Neighbors(KNN),Light Gradient Boosting Machine(LightGBM) and Extreme Gradient Boosting(XGBoost)-to develop the model.Internal 10-fold cross-validation helped determine the best-performing model,which was then tested externally.Model performance was assessed using metrics such as area under the curve(AUC) and other metrics.SHapley Additive exPlanations(SHAP) plots were used to interpret variable significance.

RESULTS

138/382(36.13 %) patients achieved functional cure.HBsAg at baseline,HBsAg decline at week12,non-alcoholic fatty liver disease(NAFLD) and age were identified as significant variables.RF performed the best,with AUC value of 0.988,and maintained good performance in test set.The SHapley Additive exPlanations(SHAP) plot highlighted HBsAg at baseline and HBsAg decline at week 12 are the top two predictors.The web-calculator was designed to predict functional cure more conveniently(https://www.xsmartanalysis.com/model/list/predict/model/html?mid = 17054&symbol = 317ad245Hx628ko3uW51).

CONCLUSION

We developed a prediction model,which can be used to not only accurately identifies advantageous populations with Peg-IFN alpha,but also determines whether to continue subsequent Peg-IFN alpha.

Application of myxovirus resistance protein A in the etiological diagnosis of infections in adults

BACKGROUND

Inappropriate antibiotic treatment for patients with viral infections has led to a surge in antimicrobial resistance, increasing mortality and healthcare costs. Viral and bacterial infections are often difficult to distinguish. Myxovirus resistance protein A (MxA), an essential antiviral factor induced by interferon after viral infection, holds promise for distinguishing between viral and bacterial infections. This study aimed to determine the ability of MxA to distinguish viral from bacterial infections.

METHODS

We quantified MxA in 121 infected patients via dry immunofluorescence chromatography. The Kruskal-Wallis test and receiver operating characteristic (ROC) curve analysis were used to determine the diagnostic value of MxA, either alone or in combination with C-reactive protein (CRP) or procalcitonin (PCT), in patients with viral, bacterial, or co-infections.

RESULTS

The value of MxA (ng/mL) was significantly higher in patients with viral infections than in those with bacterial and co-infections (82.3 [24.5-182.9] vs. 16.4 [10.8-26.5], P<0.0001) (82.3 [24.5-182.9] vs. 28.5 [10.2-106.8], P=0.0237). The area under the curve (AUC) of the ROC curve for distinguishing between viral and bacterial infections was 0.799 (95% confidence interval [95% CI] 0.696-0.903), with a sensitivity of 68.9% (95% CI 54.3%-80.5%) and specificity of 90.0% (95% CI 74.4%-96.5%) at the threshold of 50.3 ng/mL. Combining the MxA level with the CRP or PCT level improved its ability. MxA expression was low in cytomegalovirus (15.8 [9.6-47.6] ng/mL) and Epstein-Barr virus (12.9 [8.5-21.0] ng/mL) infections.

CONCLUSION

Our study showed the diagnostic efficacy of MxA in distinguishing between viral and bacterial infections, with further enhancement when it was combined with CRP or PCT. Moreover, Epstein-Barr virus and human cytomegalovirus infections did not elicit elevated MxA expression.

Sterile activation of RNA-sensing pathways in autoimmunity

RNA-sensing pathways play a pivotal role in host defense against pathogenic infections to maintain cellular homeostasis. However, in the absence of infection, certain endogenous RNAs can serve as the activators of RNA-sensing pathways as well. The inappropriate activation of RNA-sensing pathways by self-ligands leads to systemic inflammation and autoimmune diseases. In this review, we summarize current findings on the sterile activation of RNA sensors, as well as its implications in autoimmunity, inflammatory diseases, and therapeutics.

Integrating Whole Genome and Transcriptome Sequencing to Characterize the Genetic Architecture of Isoform Variation and its Implications for Health and Disease

We created a comprehensive whole blood splice variation quantitative trait locus (sQTL) resource by analyzing isoform expression ratio (isoform-to-gene) in Framingham Heart Study (FHS) participants (discovery: n=2,622; validation: n=1,094) with whole genome (WGS) and transcriptome sequencing (RNA-seq) data. External replication was conducted using WGS and RNA-seq from the Jackson Heart Study (JHS, n=1,020). We identified over 3.5 million cis -sQTL-isoform pairs ( p <5e-8), comprising 1,176,624 cis -sQTL variants and 10,883 isoform transcripts from 4,971 sGenes, with significant change in isoform-to-gene ratio due to allelic variation. We validated 61% of these pairs in the FHS validation sample ( p <1e-4). External validation ( p <1e-4) in JHS for the top 10,000 and 100,000 most significant cis -sQTL-isoform pairs was 88% and 69%, respectively, while overall pairs validated at 23%. For 20% of cis -sQTLs in the FHS discovery sample, allelic variation did not significantly correlate with overall gene expression. sQTLs are enriched in splice donor and acceptor sites, as well as in GWAS SNPs, methylation QTLs, and protein QTLs. We detailed several sentinel cis -sQTLs influencing alternative splicing, with potential causal effects on cardiovascular disease risk. Notably, rs12898397 (T>C) affects splicing of ULK3 , lowering levels of the full-length transcript ENST00000440863.7 and increasing levels of the truncated transcript ENST00000569437.5, encoding proteins of different lengths. Mendelian randomization analysis demonstrated that a lower ratio of the full-length isoform is causally associated with lower diastolic blood pressure and reduced lymphocyte percentages. This sQTL resource provides valuable insights into how transcriptomic variation may influence health outcomes.

MDA5 Is a Major Determinant of Developing Symptoms in Critically Ill COVID-19 Patients

Apart from the skin and mucosal immune barrier, the first line of defense of the human immune system includes MDA5 (ifih1 gene) which acts as a cellular sensor protein for certain viruses including SARS-CoV-2. Upon binding with viral RNA, MDA5 activates cell-intrinsic innate immunity, humoral responses, and MAVS (mitochondrial antiviral signaling). MAVS signaling induces type I and III interferon (IFN) expressions that further induce ISGs (interferon stimulatory genes) expressions to initiate human cell-mediated immune responses and attenuate viral replication. SARS-CoV-2 counteracts by producing NSP1, NSP2, NSP3, NSP5, NSP7, NSP12, ORF3A, ORF9, N, and M protein and directs anti-MDA5 antibody production presumably to antagonize IFN signaling. Furthermore, COVID-19 resembles several diseases that carry anti-MDA5 antibodies and the current COVID-19 vaccines induced anti-MDA5 phenotypes in healthy individuals. GWAS (genome-wide association studies) identified several polymorphisms (SNPs) in the ifih1-ifn pathway genes including rs1990760 in ifih1 that are strongly associated with COVID-19, and the associated risk allele is correlated with reduced IFN production. The genetic association of SNPs in ifih1 and ifih1-ifn pathway genes reinforces the molecular findings of the critical roles of MDA5 in sensing SARS-CoV-2 and subsequently the IFN responses to inhibit viral replication and host immune evasion. Thus, MDA5 or its pathway genes could be targeted for therapeutic development of COVID-19.

Cryptic phosphoribosylase activity of NAMPT restricts the virion incorporation of viral proteins

As obligate intracellular pathogens, viruses activate host metabolic enzymes to supply intermediates that support progeny production. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of salvage nicotinamide adenine dinucleotide (NAD+) synthesis, is an interferon-inducible protein that inhibits the replication of several RNA and DNA viruses through unknown mechanisms. Here, we show that NAMPT restricts herpes simplex virus type 1 (HSV-1) replication by impeding the virion incorporation of viral proteins owing to its phosphoribosyl-hydrolase (phosphoribosylase) activity, which is independent of the role of NAMPT in NAD+ synthesis. Proteomics analysis of HSV-1-infected cells identifies phosphoribosylated viral structural proteins, particularly glycoproteins and tegument proteins, which are de-phosphoribosylated by NAMPT in vitro and in cells. Chimeric and recombinant HSV-1 carrying phosphoribosylation-resistant mutations show that phosphoribosylation promotes the incorporation of structural proteins into HSV-1 virions and subsequent virus entry. Loss of NAMPT renders mice highly susceptible to HSV-1 infection. Our work describes an additional enzymatic activity of a metabolic enzyme in viral infection and host defence, offering a system to interrogate the roles of protein phosphoribosylation in metazoans.

Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex

Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman is a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact double-stranded DNA (dsDNA). When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating "phantom" cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and enzymes from eukaryotes and archaea suggest deep functional symmetries with other important helicases across domains of life.

The Generation of Genetically Engineered Human Induced Pluripotent Stem Cells Overexpressing IFN-β for Future Experimental and Clinically Oriented Studies

Induced pluripotent stem cells (iPSCs) can be generated from various adult cells, genetically modified and differentiated into diverse cell populations. Type I interferons (IFN-Is) have multiple immunotherapeutic applications; however, their systemic administration can lead to severe adverse outcomes. One way of overcoming the limitation is to introduce cells able to enter the site of pathology and to produce IFN-Is locally. As a first step towards the generation of such cells, here, we aimed to generate human iPSCs overexpressing interferon-beta (IFNB, IFNB-iPSCs). IFNB-iPSCs were obtained by CRISPR/Cas9 editing of the previously generated iPSC line K7-4Lf. IFNB-iPSCs overexpressed IFNB RNA and produced a functionally active IFN-β. The cells displayed typical iPSC morphology and expressed pluripotency markers. Following spontaneous differentiation, IFNB-iPSCs formed embryoid bodies and upregulated endoderm, mesoderm, and some ectoderm markers. However, an upregulation of key neuroectoderm markers, PAX6 and LHX2, was compromised. A negative effect of IFN-β on iPSC neuroectoderm differentiation was confirmed in parental iPSCs differentiated in the presence of a recombinant IFN-β. The study describes new IFN-β-producing iPSC lines suitable for the generation of various types of IFN-β-producing cells for future experimental and clinical applications, and it unravels an inhibitory effect of IFN-β on stem cell neuroectoderm differentiation.

Sangju Cold Granule exerts anti-viral and anti-inflammatory activities against influenza A virus in vitro and in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Sangju Cold Granule (SJCG) is a classical traditional Chinese medicine (TCM) prescription described in "Item Differentiation of Warm Febrile Diseases". Historically, SJCG was employed to treat respiratory illnesses. Despite its popular usage, the alleviating effect of SJCG on influenza A virus infection and its mechanisms have not been fully elucidated.

AIM OF THE STUDY

Influenza is a severe respiratory disease that threatens human health. This study aims to assess the therapeutic potential of SJCG and the possible molecular mechanism underlying its activity against influenza A virus in vitro and in vivo.

MATERIALS AND METHODS

Ultrahigh-performance liquid chromatography (UPLC)-Q-Exactive was used to identify the components of SJCG. The 50% cytotoxic concentration of SJCG in MDCK and A549 cells were determined using the CCK-8 assay. The activity of SJCG against influenza A virus H1N1 was evaluated in vitro using plaque reduction and progeny virus titer reduction assays. RT-qPCR was performed to obtain the expression levels of inflammatory mediators and the transcriptional regulation of RIG-I and MDA5 in H1N1-infected A549 cells. Then, the mechanism of SJCG effect on viral replication and inflammation was further explored by measuring the expressions of proteins of the RIG-I/NF-kB/IFN(I/III) signaling pathway by Western blot. The impact of SJCG was explored in vivo in an intranasally H1N1-infected BALB/c mouse pneumonia model treated with varying doses of SJCG. The protective role of SJCG in this model was evaluated by survival, body weight monitoring, lung viral titers, lung index, lung histological changes, lung inflammatory mediators, and peripheral blood leukocyte count.

RESULTS

The main SJCG chemical constituents were flavonoids, carbohydrates and glycosides, amino acids, peptides, and derivatives, organic acids and derivatives, alkaloids, fatty acyls, and terpenes. The CC50 of SJCG were 24.43 mg/mL on MDCK cells and 20.54 mg/mL on A549 cells, respectively. In vitro, SJCG significantly inhibited H1N1 replication and reduced the production of TNF-α, IFN-β, IL-6, IL-8, IL-13, IP-10, RANTES, TRAIL, and SOCS1 in infected A549 cells. Intracellularly, SJCG reduced the expression of RIG-I, MDA5, P-NF-κB P65 (P-P65), P-IκBα, P-STAT1, P-STAT2, and IRF9. In vivo, SJCG enhanced the survival rate and decreased body weight loss in H1N1-infected mice. Mice with H1N1-induced pneumonia treated with SJCG showed a lower lung viral load and lung index than untreated mice. SJCG effectively alleviated lung damage and reduced the levels of TNF-α, IFN-β, IL-6, IP-10, RANTES, and SOCS1 in lung tissue. Moreover, SJCG significantly ameliorated H1N1-induced leukocyte changes in peripheral blood.

CONCLUSIONS

SJCG significantly reduced influenza A virus and virus-mediated inflammation through inhibiting the RIG-I/NF-kB/IFN(I/III) signaling pathway. Thus, SJCG could provide an effective TCM for influenza treatment.

Porcine reproductive and respiratory syndrome virus degrades TANK-binding kinase 1 via chaperon-mediated autophagy to suppress type I interferon production and facilitate viral proliferation

Porcine reproductive and respiratory syndrome virus (PRRSV) has led to significant economic losses in the global swine industry. Type I interferon (IFN-I) plays a crucial role in the host's resistance to PRRSV infection. Despite extensive research showing that PRRSV employs multiple strategies to antagonise IFN-I induction, the underlying mechanisms remain to be fully elucidated. In this study, we have discovered that PRRSV inhibits the production of IFN-I by degrading TANK-binding kinase 1 (TBK1) through chaperon-mediated autophagy (CMA). From a mechanistic standpoint, PRRSV nonstructural protein 2 (Nsp2) increases the interaction between the heat shock protein member 8 (HSPA8) and TBK1. This interaction leads to the translocation of TBK1 into lysosomes for degradation, mediated by lysosomal-associated membrane protein 2A (LAMP2A). As a result, the downstream activation of IFN regulatory factor 3 (IRF3) and the production of IFN-I are hindered. Together, these results reveal a new mechanism by which PRRSV suppresses host innate immunity and contribute to the development of new antiviral strategies against the virus.

A multi-trait epigenome-wide association study identified DNA methylation signature of inflammation among men with HIV

Inflammation underlies many conditions causing excess morbidity and mortality among people with HIV (PWH). A handful of single-trait epigenome-wide association studies (EWAS) have suggested that inflammation is associated with DNA methylation (DNAm) among PWH. Multi-trait EWAS may further improve statistical power and reveal pathways in common between different inflammatory markers. We conducted single-trait EWAS of three inflammatory markers (soluble CD14, D-dimers and interleukin-6) in the Veterans Aging Cohort Study (n = 920). The study population was all male PWH with an average age of 51 years, and 82.3% self-reported as Black. We then applied two multi-trait EWAS methods-CPASSOC and OmniTest-to combine single-trait EWAS results. CPASSOC and OmniTest identified 189 and 157 inflammation-associated DNAm sites, respectively, of which 112 overlapped. Among the identified sites, 56% were not significant in any single-trait EWAS. Top sites were mapped to inflammation-related genes including IFITM1, PARP9 and STAT1. These genes were significantly enriched in pathways such as "type I interferon signaling" and "immune response to virus." We demonstrate that multi-trait EWAS can improve the discovery of inflammation-associated DNAm sites, genes and pathways. These DNAm sites might hold the key to addressing persistent inflammation in PWH.

Biologically informed machine learning modeling of immune cells to reveal physiological and pathological aging process

The immune system undergoes progressive functional remodeling from neonatal stages to old age. Therefore, understanding how aging shapes immune cell function is vital for precise treatment of patients at different life stages. Here, we constructed the first transcriptomic atlas of immune cells encompassing human lifespan, ranging from newborns to supercentenarians, and comprehensively examined gene expression signatures involving cell signaling, metabolism, differentiation, and functions in all cell types to investigate immune aging changes. By comparing immune cell composition among different age groups, HLA highly expressing NK cells and CD83 positive B cells were identified with high percentages exclusively in the teenager (Tg) group, whereas unknown_T cells were exclusively enriched in the supercentenarian (Sc) group. Notably, we found that the biological age (BA) of pediatric COVID-19 patients with multisystem inflammatory syndrome accelerated aging according to their chronological age (CA). Besides, we proved that inflammatory shift- myeloid abundance and signature correlate with the progression of complications in Kawasaki disease (KD). The shift- myeloid signature was also found to be associated with KD treatment resistance, and effective therapies improve treatment outcomes by reducing this signaling. Finally, based on those age-related immune cell compositions, we developed a novel BA prediction model PHARE ( https://xiazlab.org/phare/ ), which can apply to both scRNA-seq and bulk RNA-seq data. Using this model, we found patients with coronary artery disease (CAD) also exhibit accelerated aging compared to healthy individuals. Overall, our study revealed changes in immune cell proportions and function associated with aging, both in health and disease, and provided a novel tool for successfully capturing features that accelerate or delay aging.

Interferon Epsilon-Mediated Antiviral Activity Against Human Metapneumovirus and Respiratory Syncytial Virus

BACKGROUND

Interferon epsilon (IFN-ε) is a type I IFN that plays a critical role in the host immune response against pathogens. Despite having demonstrated antiviral activity in macrophages and mucosal tissues such as the female reproductive tract and the constitutive expression in mucosal tissues such as the lung, the relevance of IFN-ε against respiratory viral infections remains elusive.

RESULTS

We present, for the first time, the expression of IFN-ε in alveolar epithelial cells and primary human bronchial epithelial cells grown in an air-liquid interface (ALI) in response to human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) infection. The molecular characterization of the IFN-ε induction by the viruses indicates that the expression of RIG-I is necessary for an optimal IFN-ε expression. Furthermore, treatment of the airway epithelial cells with rhIFN-ε induced the expression of IFN-stimulated genes (ISGs) and significantly restricted the viral replication of HMPV and RSV.

CONCLUSIONS

These findings underscore the relevance of IFN-ε against viral infections in the respiratory tract.

A plant-based oligomeric CD2v extracellular domain antigen exhibits equivalent immunogenicity to the live attenuated vaccine ASFV-G-∆I177L

African swine fever (ASF), caused by the African swine fever virus (ASFV), is a deadly, highly contagious disease in both domestic pigs and wild boar. With mortality up to 100%, the disease has been making a serious impact on the swine industry worldwide. Because no effective antiviral treatment has been observed, proactive prevention such as vaccination remains the key to controlling the outbreak. In the pursuit of expediting vaccine development, our current work has made the first report for heterologous production of the viral outer envelope glycoprotein CD2v extracellular domain (CD2v ED), a proposed promising vaccine antigen candidate in the "green" synthetic host Nicotiana benthamiana. Protein oligomerization strategies were implemented to increase the immunogenicity of the target antigen. Herein, the protein was expressed in oligomeric forms based on the C-terminally fused GCN4pII trimerization motif and GCN4pII_TP oligomerization motif. Quantitative western blot analysis showed significantly higher expression of trimeric CD2v ED_GCN4pII with a yield of about 12 mg/100 g of fresh weight, in comparison to oligomeric CD2v ED_GCN4pII_TP, revealing the former is the better choice for further studies. The results of purification and size determination by size exclusion chromatography (SEC) illustrated that CD2v ED_GCN4pII was successfully produced in stable oligomeric forms throughout the extraction, purification, and analysis process. Most importantly, purified CD2v ED_GCN4pII was demonstrated to induce both humoral and cellular immunity responses in mice to extents equivalent to those of the live attenuated vaccine ASFV-G-∆I177L, suggesting it as the potential subunit vaccine candidate for preventing ASFV.

Herpes Simplex Virus Type 2 Blocks IFN-β Production through the Viral UL24 N-Terminal Domain-Mediated Inhibition of IRF-3 Phosphorylation

Herpes simplex virus type 2 (HSV-2) is a sexually transmitted virus, the cause of genital herpes, and its infection can increase the risk of HIV-1 infection. After initial infection, HSV-2 can establish lifelong latency within the nervous system, which is likely associated with the virus-mediated immune evasion. In this study, we found that HSV-2 UL24 significantly inhibited the activation of the IFN-β promoter and the production of IFN-β at both mRNA and protein levels. Of importance, the inhibitory effect of HSV-2 on IFN-β production was significantly impaired in the context of HSV-2 infection when UL24 was knocked down. Additional studies revealed that, although the full-length HSV-2 UL24 affected cell cycle and viability to some extent, its N-terminal 1-202AA domain showed no obvious cytotoxicity while its C-terminal 201-281 AA domain had a minimal impact on cell viability. Further studies showed that the N-terminal 1-202 AA domain of HSV-2 UL24 (HSV-2 UL24-N) was the main functional region responsible for the inhibition of IFN-β production mediated by HSV-2 UL24. This domain significantly suppressed the activity of RIG-IN, MAVS, TBK-1, IKK-ε, or the IRF-3/5D-activated IFN-β promoter. Mechanistically, HSV-2 UL24-N suppressed IRF-3 phosphorylation, resulting in the inhibition of IFN-β production. The findings of this study highlight the significance of HSV-2 UL24 in inhibiting IFN-β production, revealing two potential roles of UL24 during HSV-2 infection: facilitating immune evasion and inducing cell cycle arrest.

The effects of GCRV on various tissues of grass carp (Ctenopharyngodon idella) and identification of differential interferon-stimulating genes (ISGs) through muscle transcriptome analysis

Grass carp hemorrhagic disease is caused by the grass carp reovirus (GCRV). The disease spreads rapidly and has a high fatality rate, which seriously affects grass carp culture. Moreover, the molecular mechanisms underlying grass carp hemorrhagic disease remain unclear. To decipher the effects of GCRV on grass carp tissues, resistant grass carp A (GA) and susceptible grass carp B (GB) were selected through GCRV treatment, and control grass carp C (GC) was also established. The gill, liver, and muscle tissues exhibited different onset symptoms under the influence of GCRV by histological observation. We selected muscle samples with significant differences in symptoms for Illumina RNA sequencing. Analyses using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed 3512, 3074, and 1853 differentially expressed genes between "GC vs. GB," "GC vs. GA," and "GA vs. GB," respectively. Additionally, 40 differential immune-related genes and 28 differential interferon-stimulating genes (ISGs) related to the interferon (IFN) pathway were identified. The expression of immunogene-related genes of GB and GA, such as MDA5, IL-34, NF-KB, TRIM25, SOCS3, CEBPB, and BCL2, and genes associated with the JAK-STAT signaling pathway, such as IRF4, STAT1, STAT3, JAK 1, and JAK 2, was significantly upregulated. The IFN and JAK-STAT signaling pathways were closely related to anti-GCRV infection. The transcriptome data and predicted immune genes and ISGs in this study provide novel insights into the treatment of GCRV.

Swine NONO promotes IRF3-mediated antiviral immune response by Detecting PRRSV N protein

Non-POU domain-containing octamer-binding protein (NONO) is a multi-functional nuclear protein which belongs to the Drosophila behavior/human splicing (DBHS) protein family. NONO is known to regulate multiple important biological processes including host antiviral immune response. However, whether NONO can inhibit porcine reproductive and respiratory syndrome virus (PRRSV) replication is less well understood. In this study, we demonstrated that swine NONO (sNONO) inhibited PRRSV replication, via increasing expression of IFN-β, whereas NONO knockdown or knockout in PAM-KNU cells was more susceptible to PRRSV infection. As an IRF3 positive regulation factor, NONO promoted IFN-β expression by enhancing activation of IRF3. During PRRSV infection, NONO further up-regulated IRF3-mediated IFN-β expression by interacting with PRRSV N protein. Mechanistically, NONO functioned as a scaffold protein to detect PRRSV N protein and formed N-NONO-IRF3 complex in the nucleus. Interestingly, it was found that the NONO protein reversed the inhibitory effect of PRRSV N protein on type I IFN signaling pathway. Taken together, our study provides a novel mechanism for NONO to increase the IRF3-mediated IFN-β activation by interacting with the viral N protein to inhibit PRRSV infection.

Assessing the antiviral activity of antimicrobial peptides Caerin1.1 against PRRSV in Vitro and in Vivo

The Porcine reproductive and respiratory syndrome (PRRS) causes severe financial losses to the global swine industry. Due to continuous virus evolution, the protection against the PRRS provided by current vaccines is limited. In order to find new antiviral strategies, this study investigated the antiviral potential of antimicrobial peptides (AMPs) against PRRSV. Given the diversity of PRRSV strains and the limited effectiveness of existing vaccines in controlling PRRSV, this study evaluated the inhibitory effects of KLAK, Cecropin B, Piscidin1, and Caerin1.1 on 3 strains of PRRSV (lineage 5 classical strain, lineage 8 highly pathogenic strain, and lineage 1 NADC30-like strain). Caerin1.1 exhibited significant dose-dependent antiviral activity, with an effective concentration (EC50) of 7.5 μM. Caerin1.1 effectively inhibited PRRSV replication when added before or in early infection but showed reduced effectiveness when added in late infection, indicating its potential involvement in targeting early transcription mechanisms of viral RNA polymerase and significantly upregulating cytokine gene expression. In the NADC30 strain-based animal infection model, Caerin1.1 treatment significantly reduced lung viral loads and inflammation in the lungs of PRRSV-infected pigs, with a mortality rate of 0 % (0/5) in the treated group compared to 66.67 % (4/6) in the untreated group, indicating a reduction in the mortality rate. Additionally, compared with the untreated group, the Caerin1.1-treated group showed significant improvements, such as lighter fever, more daily weight gain, less clinical symptoms, less viral load in blood, and less virus oral shedding (P < 0.05). These findings reveal the potential of antimicrobial peptides as PRRSV therapeutic agents and suggest that Caerin1.1 is a promising candidate for a novel anti-PRRSV drug.

Recombinant VSVs: A Promising Tool for Virotherapy

Cancer is one of the leading causes of death worldwide. Traditional cancer treatments include surgery, radiotherapy, and chemotherapy, as well as combinations of these treatments. Despite significant advances in these fields, the search for innovative ways to treat malignant tumors, including the application of oncolytic viruses, remains relevant. One such virus is the vesicular stomatitis virus (VSV), which possess a number of useful oncolytic properties. However, VSV-based drugs are still in their infancy and are yet to be approved for clinical use. This review discusses the mechanisms of oncogenesis, the antiviral response of tumor and normal cells, and markers of tumor cell resistance to VSV virotherapy. In addition, it examines methods for producing and arming recombinant VSV and provides examples of clinical trials. The data presented will allow better assessment of the prospects of using VSV as an oncolytic.

An evolutionary perspective to innate antiviral immunity in animals

Viruses pose a significant threat to cellular organisms. Innate antiviral immunity encompasses both RNA- and protein-based mechanisms designed to sense and respond to infections, a fundamental aspect present in all living organisms. A potent RNA-based antiviral mechanism is RNA interference, where small RNA-programmed nucleases target viral RNAs. Protein-based mechanisms often rely on the induction of transcriptional responses triggered by the recognition of viral infections through innate immune receptors. These responses involve the upregulation of antiviral genes aimed at countering viral infections. In this review, we delve into recent advances in understanding the diversification of innate antiviral immunity in animals. An evolutionary perspective on the gains and losses of mechanisms in diverse animals coupled to mechanistic studies in model organisms such as the fruit fly Drosophila melanogaster is essential to provide deep understanding of antiviral immunity that can be translated to new strategies in the treatment of viral diseases.

The role of 2'-5'-oligoadenylate synthase-like protein (OASL1) in biliary and hepatotoxin-induced liver injury in mice

Following an injury, the liver embarks on a process that drives the accumulation and reformation of the extracellular matrix, leading to hepatic fibrosis. Type I interferons (IFNs), including IFN-α and IFN-β, play a crucial role in averting chronic liver injury through the activation of IFN-stimulated genes (ISGs), which are instrumental in sculpting adaptive immunity. The role of 2'-5'-oligoadenylate synthase-like protein 1 (OASL1), an antiviral ISG, in the context of liver fibrosis remains to be elucidated. To elicit liver fibrosis, a diet containing 0.1% diethoxycarbonyl-1,4-dihydrocollidine (DDC) and carbon tetrachloride (CCl4) were employed to induce cholestatic- and hepatotoxin-mediated liver fibrosis, respectively. Histological analyses of both models revealed that OASL1-/- mice exhibited reduced liver damage and, consequently, expressed lower levels of fibrotic mediators, notably α-smooth muscle actin. OASL1-/- mice demonstrated significantly elevated IFN-α and IFN-β mRNA levels, regulated by the IFN regulatory factor 7 (IRF7). Additionally, OASL1-/- ameliorated chronic liver fibrosis through the modulation of nuclear factor-κB (NF-κB) signaling. The effect of OASL1 on type I IFN production in acute liver damage was further explored and OASL1-/- mice consistently showed lower alanine transaminase levels and pro-inflammatory cytokines, but IFN-α and IFN-β mRNA levels were upregulated, leading to amelioration of acute liver injury. Additionally, the study discovered that F4/80-positive cells were observed more frequently in OASL1-/- CCl4 acutely treated mice. This implies that there is a significant synergy in the function of macrophages and OASL1 deficiency. These results demonstrate that in instances of liver injury, OASL1 inhibits the production of type I IFN by modulating the NF-κB signaling pathway, thereby worsening disease.

p-STAT3-elevated E3 ubiquitin ligase DTX4 confers the stability of HBV cccDNA by ubiquitinating APOBEC3B in liver

Background: Clinically, the persistence of HBV cccDNA is the major obstacle in anti-HBV therapy. However, the underlying mechanism of HBV cccDNA is poorly understood. The transcriptional factor STAT3 is able to activate HBV replication in liver. Approach & Results: RNA-Seq analysis demonstrated that cucurbitacin I targeting STAT3 was associated with virus replication in liver. HBV-infected human liver chimeric mouse model and HBV hydrodynamic injection mouse model were established. Then, we validated that cucurbitacin I effectively limited the stability of HBV cccDNA and HBV replication in cells, in which cucurbitacin I enhanced the sensitivity of pegylated interferon α (PEG-IFN α) against HBV via combination in vitro and in vivo. Mechanistically, we identified that cucurbitacin I increased the levels of APOBEC3B to control HBV cccDNA by inhibiting p-STAT3 in cells, resulting in the inhibition of HBV replication. Moreover, RNA-Seq data showed that E3 ubiquitin ligase DTX4 might be involved in the events. Then, we observed that HBV particles could upregulate DTX4 by increasing the levels of p-STAT3 in vitro and in vivo. The p-STAT3-elevated DTX4/male-specific lethal 2 (MSL2) independently and synergistically enhanced the stability of HBV cccDNA by facilitating the ubiquitination degradation of APOBEC3B in cells, leading to the HBV replication. Conclusions: p-STAT3-elevated DTX4 confers the stability of HBV cccDNA and HBV replication by facilitating the ubiquitination degradation of APOBEC3B. Cucurbitacin Ⅰ effectively enhances the sensitivity of PEG-IFN α in anti-HBV therapy by inhibiting the p-STAT3/DTX4/MSL2/APOBEC3B signalling. Our finding provides new insights into the mechanism of HBV cccDNA. The p-STAT3 and DTX4/MSL2 might serve as the therapeutical targets of HBV cccDNA.

Protein kinase R is highly expressed in dermatomyositis and promotes interferon-beta-induced muscle damage

OBJECTIVES

Dermatomyositis (DM) has been consistently linked to the type I interferon (IFN-I) pathway. However, the precise pathogenesis remains incompletely elucidated. We aimed to explore potential molecular mechanisms and identify promising therapeutic targets in DM.

METHODS

We employed bioinformatics analysis to investigate molecular signatures, aiming to shed light on the pathogenesis of DM. The expression of protein kinase R (PKR) in DM muscle tissues was determined by real-time quantitative PCR, western blot and immunohistochemistry (IHC) analysis. We then assessed the sensitivity and specificity of sarcoplasmic PKR expression by IHC in a consecutive DM cohort and other diseases in this retrospective study. Furthermore, IFN-β was used to stimulate myoblasts and myotubes, and the relationship between PKR and IFN-β-induced pathogenic molecules was investigated in vitro.

RESULTS

Bioinformatics analysis indicated two primary pathological processes: viral infection and the IFN-I signalling pathway. We subsequently verified that PKR was notably expressed in the cytoplasm of myofibers in DM patients. The sensitivity and specificity of sarcoplasmic PKR expression in DM were 84.6% and 97.6%, respectively. In vitro studies revealed that IFN-β upregulates the expression of PKR, along with several molecules associated with DM muscle damage. Conversely, inhibiting PKR has been shown to downregulate IFN-β-induced pathogenic molecules in both myoblasts and myotubes.

CONCLUSIONS

We observed that PKR exhibits specific expression in the cytoplasm of DM muscle and inhibiting PKR ameliorates IFN-β-induced muscle damage in vitro. These findings provide insights into the diagnostic and therapeutic roles of PKR in DM.

Genomic insight into COVID-19 severity in MAFLD patients: a single-center prospective cohort study

This study investigated the influence of single nucleotide polymorphisms (SNPs) in genes associated with the interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) on COVID-19 severity and their association with nonalcoholic fatty liver disease (MAFLD). We did not observe a significant association between the investigated SNPs and COVID-19 severity. While the IFNAR2 rs2236757 A allele was correlated with higher creatinine levels upon admission and the G allele was correlated with lower band neutrophils upon discharge, these findings require further investigation. The distribution of OAS gene polymorphisms (rs10774671 and rs10735079) did not differ between MAFLD patients and non-MAFLD patients. Our study population's distribution of ACE2 rs2074192 genotypes and alleles differed from that of the European reference population. Overall, our findings suggest that these specific SNPs may not be major contributors to COVID-19 severity in our patient population, highlighting the potential role of other genetic factors and environmental influences.