Search Results (781)

Therapeutics based on RNA are commonly produced via biocatalytic approaches using RNA polymerases. The most frequently applied enzyme is the RNA polymerase of Enterobacteria phage T7. However, this enzyme has unfavorable properties, like the formation of double-stranded RNA (dsRNA). This undesired by-product can activate the innate immune system via pattern recognition receptors and cause inflammation. Removal of the contaminant is time-consuming and expensive. In this work, we applied a genome mining approach to identify unidentified single-subunit RNA polymerases with minimal dsRNA generation. A large meta database was screened, and 74 sequences were selected. Two RNA polymerases generating barely detectable amounts of dsRNA were identified from the initial sequence portfolio. Their promoters were detected via a fluorescent RNA aptamer screening, and slightly acidic transcription conditions were established. Further activity characterization showed a significant reduction of dsRNA to 0.001% and 0.02%. Due to these beneficial attributes, these RNA polymerases generate mRNA with enhanced stability, which most likely lowers the immune response towards the desired mRNA. This could be especially useful for producing long RNAs, such as self-amplifying RNA, as these typically require improved stability and low dsRNA content. Full article

Human rhinovirus (HRV) is one of the common respiratory viral infection agents that triggers airway obstruction and asthma exacerbations, especially during childhood. This project aimed at evaluating the mechanism of ultraviolet (UV) and infrared (IR) radiations to inactivate HRV infection and replication inside and outside infected airway epithelial cells and the resulting impact on interferon responses and epithelial barrier integrity. Hereby, airway epithelial cells were infected with different RV concentrations. Later these cells are exposed to UV and IR light to analyze their impact on the viral immune response of the host by real-time PCR. It was found that RV1B disrupted cell junctions of airway epithelial cell barriers. Moreover, high doses of RV1B activated pattern recognition receptor (TLR3), induced interferon (IFN-β) response and reduced SOCS1, which is a negative regulator of IFN-β. Further, IR lights inhibited rhinovirus post infection in primary nasal epithelial cells (NECs). Finally, UVC exposure significantly inhibited the antiviral effects of the host via SOCS1 inhibition and decreased RV1B within 72 h. Collectively, these findings support the role of UV light as an effective therapeutic approach for acutely eliminating RV but resulting in barrier and antiviral damage, which can have a drawback effect for asthma. Full article

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that were integrated into the human genome millions of years ago. They constitute approximately 8% of the human genome. Once considered “Junk DNA” it is now clear that ERVs are dynamic elements engaged in a continuous dialogue with the host innate immune system. This review further advances our current understanding of how ERV expression interfaces with innate immune signalling by providing insights into the dual nature of this interaction: (i) how the accidental detection of ERV-derived nucleic acids and proteins by pattern recognition receptors (PRRs), such as cGAS, RIG-I, and TLRs, can trigger protective interferon responses and inflammation, and (ii) the key innate immune regulatory mechanisms that suppress or control ERV activity, maintaining genomic stability. Furthermore, the study also sheds light on this balance for maintaining cellular homeostasis, providing the idea of how the disruption of this balance leads to the pathogenesis of autoimmune diseases, cancer, and neurological disorders, consequently unlocking therapeutic innovations. Full article

For decades, immunology has followed a clear paradigm: immunological memory resides only within the adaptive immunity, as a unique property of lymphocytes giving the host the ability to recognize specific antigens and offer long-term protection. However, this raises an important question: how valid is this belief in light of new evidence? The discovery of trained immunity shows that innate immune cells can also develop lasting functional changes. This finding prompts a profound reconsideration of the traditional framework. Trained immunity is a functional reprogramming of the innate immune cells driven by long-term epigenetic and metabolic reprogramming, resulting in enhanced responses upon subsequent exposure to the same pathogen or even to unrelated stimuli. The presence of pattern recognition receptors (PRRs) on innate immune cells already suggested a certain level of specificity in this compartment thanks to the engagement of a PRR by a pathogen-associated molecular pattern (PAMP) inducing memory-like properties in the responding cell. While such partial specificity can enhance protection, it may also amplify aberrant inflammatory circuits, thereby contributing to the initiation or worsening of autoimmune and chronic inflammatory diseases. This dual nature of trained immunity raises important questions for the field: is trained immunity ultimately harmful or beneficial in autoimmunity, and can its mechanisms be harnessed therapeutically rather than pathologically? The present Perspective will address these issues by examining recent findings that reveal the specificity, pathogenic potential, and translational opportunities in given examples of autoimmune diseases (ADs). Full article

Plant pathogens are a major cause of crop yield loss, making disease resistance breeding crucial for crop improvement. Plants have evolved innate immune systems, mediated by immune-related genes such as nucleotide-binding site leucine-rich repeat (NLR), pattern-recognition receptors (PRR) and susceptibility genes, which are essential resources for breeding disease-resistant plants. To identify immunity genes, extensive genetic approaches that examine the association between resistance phenotypes and genomic regions have been applied with great success. While genetic methods remain important for identifying immunity genes, novel strategies that rely on functional rather than genetic association with disease resistance offer unique advantages. For example, mutagenesis with R gene enrichment sequencing (MutRenSeq) enabled the identification of wheat resistance genes Sr22 and Sr45 by comparing the NLRomes of resistant and susceptible lines while single-cell RNA sequencing resolved cell-type-specific responses to pathogen infection and revealed ZmChit7, especially in maize epidermal and guard cells. These approaches reach beyond existing natural variation, can accelerate experimental timelines, reduce the experimental scale, and provide mechanistic insights into pathogen resistance. This review discusses emerging techniques that generate focused candidate immunity gene lists or accelerate their validation, as both are required to identify causal variants for resistance breeding. We consider advances in RenSeq-derived methods, spatial omics, proximity labelling, computational prediction, Clustered regularly interspaced short palindromic repeats (CRISPR) screens, and cell death assays. These approaches are reshaping resistance breeding pipelines beyond association-based discovery. By discussing the strengths and limitations of these emerging methods and their combinations, we outline current opportunities and future directions to help plant pathologists to more effectively identify and validate plant immunity genes. Full article

Retinoic acid-inducible gene I (RIG-I) is a crucial pattern recognition receptor for detecting viral RNA and initiating an immune response against influenza A viruses (IAVs). The activation of RIG-I in mammalian cells requires ubiquitination by two E3 ubiquitin ligases: TRIM25 and RIPLET. Using dual luciferase assays, we demonstrate that duck RIPLET enhances the activation of RIG-I, driving the IFN-β promoter activity in chicken DF-1 fibroblasts. qPCR analyses show that the co-expression of duck RIG-I and RIPLET significantly upregulates key immune genes and reduces viral RNA transcripts in DF-1 cells challenged with low pathogenic avian influenza (LPAI) H6N2. Co-immunoprecipitation and confocal microscopy studies suggest the interaction and confirm the colocalization of duck RIG-I and RIPLET in the cytoplasm. Further, we show that the non-structural protein 1 (NS1) of IAV, known for its role in immune evasion, suppression, and pathogenicity, from five different strains of IAV (PR8, BC500, CA431, D4AT, and VN1203) can all inhibit duck RIPLET activation of RIG-I, with NS1 from avian strains showing the greatest decrease in IFN-β promoter activity in chicken DF-1 cells. Overall, our research provides valuable insight into the E3 ubiquitin ligases required for RIG-I activation and susceptibility of this pathway to IAV interference across species. Full article

The highly pathogenic avian influenza virus HPAI A(H5N1) genotype AF was detected in southern Europe during the 2021/2022 season and spread widely. It emerged in Bulgaria in 2022/2023, mainly affecting mallard ducks. The DA genotype of the virus was detected in a diverse group of birds, including wild birds, zoo birds, and domestic poultry, across a wide area of eastern and southern Europe in 2023. In Bulgaria, following its introduction in 2023, the DA genotype became the predominant virus in laying hens. During 2024–2025, DA spread throughout the country, displacing AF from mallard flocks. The predominant subtype in Europe in 2025 was H5N1 genotype DI.2. This genotype became dominant after December 2024, accounting for over 90% of viruses within the EA-2024-DI genotype lineage, and has been detected in a wide range of bird species. In Bulgaria, DI.2 was identified in only one outbreak in a flock of laying hens in autumn 2024 and in a single case involving a western marsh harrier (Circus aeruginosus) in early 2025. These observations are consistent with a pattern of putative hidden circulation of avian influenza virus in duck farms in Bulgaria, potentially establishing a cycle of continuous circulation of the same viral subtype. In this study, we analysed viruses originating from Bulgaria, with a particular focus on EA-2024-DI genotype DI.2, and examined mutations related to host cell receptor binding, host specificity shifts, ligand binding, antibody recognition sites, viral oligomerization interfaces, and other functional regions. Some of these mutations have been associated with antigenic drift, immune escape, and virulence. Importantly, several are linked to changes in host specificity, a critical step in the potential transition of avian influenza viruses to humans. Consequently, such mutations represent key factors in the spread of highly pathogenic avian influenza and may pose a pandemic risk. Full article

Toll-like receptors (TLRs) are essential pattern recognition receptors of the innate immune system and play critical roles in pathogen invasion in teleosts. In this study, we identified and characterized full-length open reading frames of three TLRs belonging to the TLR11 subfamily from Schizothorax prenanti, termed spTLR19 (2868 bp), spTLR20 (2835 bp), and spTLR21 (2946 bp), encoding 955, 944, and 981 amino acids, respectively. All three proteins exhibited the conserved domain architecture typical of TLRs, comprising a leucine-rich repeat (LRR) domain, a transmembrane region, and a Toll/IL-1 receptor (TIR) domain. Phylogenetic and homology analyses revealed that spTLR19 and spTLR20 clustered most closely with their homologues from Cyprinus carpio, while spTLR21 showed the highest similarity to Onychostoma macrolepis TLR21. Expression profiling showed that these TLRs were ubiquitously expressed across examined tissues, with relatively higher expression in immune-related tissues such as spleen and gills. Furthermore, challenge with Streptococcus agalactiae and Aeromonas veronii significantly up-regulated the expression of spTLR19, spTLR20, and spTLR21 in spleen, liver, and gills, suggesting their involvement in antibacterial immune responses. These findings enhance the functional understanding of the teleost TLR11 subfamily and provide a foundation for elucidating disease resistance and immune regulation in S. prenanti. Full article

Colorectal cancer (CRC) cachexia is a multifactorial, treatment-limiting syndrome characterized by progressive loss of skeletal muscle with or without loss of fat mass, accompanied by systemic inflammation, anorexia, metabolic dysregulation, and impaired treatment tolerance. Despite decades of work, cachexia remains clinically underdiagnosed and therapeutically underserved, in part because canonical models treat tumor-derived factors and host inflammatory mediators as a largely ‘host-only’ network. In parallel, CRC is strongly linked to intestinal dysbiosis, barrier disruption, and microbial translocation. Extracellular vesicles (EVs)—host small EVs, tumor-derived EVs, and bacterial extracellular vesicles (including outer membrane vesicles)—may provide a mechanistically plausible, information-dense route by which these domains could be coupled. Here, we synthesize emerging evidence suggesting that cross-kingdom EV signaling may operate as a vesicular ecosystem spanning gut lumen, mucosa, circulation, and peripheral organs. We propose the “vesicular intersection layer” as a unifying framework for how heterogeneous EV cargos converge on shared host decoding hubs (e.g., pattern-recognition receptors and stress-response pathways) to potentially contribute to muscle catabolism. We critically evaluate what is known—and what remains unproven—about EV biogenesis, trafficking, and causal mechanisms in CRC cachexia, highlight methodological constraints in microbial EV isolation and attribution, and outline minimum evidentiary standards for cross-kingdom claims. Finally, we translate the framework into actionable hypotheses for EV-informed endotyping, biomarker development (including stool EV assays), and therapeutic strategies targeting shared signaling nodes (e.g., TLR4–p38) and endocrine mediators that are predominantly soluble but may be fractionally vesicle-associated (e.g., GDF15). By reframing CRC cachexia as an emergent property of tumor–host–microbiota vesicular communication, this review provides a roadmap for mechanistic studies and clinically tractable interventions. Full article

Background: Acquired cholesteatoma is a chronic inflammatory middle ear disease characterized by keratinizing squamous epithelium overgrowth and bone erosion. While the upregulation of pattern-recognition receptor (PRR) signaling has been consistently observed, it remains unclear whether this reflects a secondary response to microbial infection or a primary dysfunction driven by genetic predisposition. Methods: Using the UK Biobank, we analyzed 678 individuals with cholesteatoma (ICD-10: H71) among 502,164 participants. Candidate genes implicated in cholesteatoma-related inflammatory pathways (n = 17) were selected, and 147 polymorphisms were studied. Gene-specific genetic risk scores (GRSs) were calculated for cholesteatoma patients (GRSchol) and the general UK Biobank population (GRSpop). The difference (ΔGRSchol-GRSpop) was used to assess the relative contribution of each gene. Results: Genes with the highest ΔGRS were IL6, TREM1, IL1R1, IL1A, HIF1A, ID1, RAGE, and TNFA. These genes represent key downstream mediators and amplifiers of PRR signaling rather than the receptors themselves. Variants in cytokine genes (IL6, IL1R1, IL1A, and TNFA) may enhance inflammatory signaling and bone resorption; Trem1 amplifies TLR responses; RAGE sustains sterile DAMP-driven inflammation, while HIF1A and ID1 implicate hypoxia, tissue remodeling, and keratinocyte proliferation in disease persistence. Conclusions: Our findings suggest that cholesteatoma pathogenesis may not be driven solely by microbial activation of PRRs but rather by genetic variants that amplify and sustain downstream inflammatory responses. This supports a model of cholesteatoma as a disease of self-perpetuating inflammation triggered by diverse stressors, including microbial and non-microbial insults. These insights may inform preventive strategies targeting environmental stressors, as well as therapeutic approaches using biologics to interrupt chronic inflammatory amplification in cholesteatoma. Full article

Background: Salt-sensitive blood pressure (SSBP) represents a prevalent yet underrecognized hypertensive phenotype, in which blood pressure (BP) and volume status are disproportionately influenced by dietary sodium intake. Beyond BP elevation alone, salt sensitivity reflects a convergence of renal sodium handling abnormalities, neurohormonal activation, vascular dysfunction, and inflammatory pathways that link excessive sodium exposure to progressive kidney injury and adverse cardiac remodeling. Given its association with chronic kidney disease (CKD) and the association of heart failure with preserved ejection fraction (HFpEF), improved recognition of SSBP has direct clinical relevance. Objective: This narrative review aims to synthesize current mechanistic and clinical evidence on SSBP, focusing on pathophysiology, cardiorenal interactions, diagnostic challenges, and phenotype-guided therapeutic strategies with practical applicability. Methods: A narrative literature review was conducted using PubMed, Scopus, and Web of Science from inception through January 2026. Experimental, translational, and clinical studies, along with relevant guideline documents, were integrated to provide conceptual and clinical interpretation rather than quantitative analysis. Key Findings: Impaired renal sodium excretion, intrarenal RAAS activation, sympathetic overactivity, endothelial dysfunction, and immune-mediated inflammation contribute to sodium retention, microvascular dysfunction, and fibrotic remodeling across the kidney–heart axis. These pathways are strongly supported by experimental and translational data, but direct interventional clinical validation remains limited for several mechanisms. Clinically, salt-sensitive individuals often exhibit non-dipping BP patterns, albuminuria, salt-induced edema, and a predisposition to HFpEF. Dynamic BP monitoring combined with targeted laboratory assessment improves identification of this phenotype and supports individualized management. Conclusions: Early recognition of SSBP enables targeted interventions beyond uniform sodium restriction. Phenotype-guided strategies integrating lifestyle modification, RAAS blockade, thiazide-like diuretics, mineralocorticoid receptor antagonists, and sodium-glucose co-transporters 2 inhibitors (SGLT2i) may improve cardiorenal outcomes. Emerging precision tools (e.g., wearable blood-pressure sensors, digital sodium tracking technologies, etc.) remain exploratory but may further refine individualized management. Full article

This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine. Full article

Helicobacter pylori is a prevalent gastric pathogen that establishes chronic infection and contributes to gastritis, peptic ulcer disease, and gastric cancer. Its persistence depends on immune evasion strategies that promote sustained low-grade inflammation in the gastric mucosa. Nucleotide-binding oligomerization domain-like receptors (NLRs) are cytosolic pattern recognition receptors that play key roles in innate immune responses against H. pylori. Nod1 and Nod2 detect bacterial peptidoglycan delivered via the type IV secretion system or outer membrane vesicles, activating NF-κB, MAPK, and interferon signaling pathways that regulate inflammatory cytokine production, epithelial barrier function, autophagy, and antimicrobial defense. The NLRP3 inflammasome mediates the maturation of IL-1β and IL-18 primarily in myeloid cells, thereby shaping inflammatory and immunoregulatory responses during infection. In contrast, NLRC4 functions in a context-dependent manner in epithelial cells and is largely dispensable for myeloid IL-1β production. Emerging evidence also implicates noncanonical NLRs, including NLRP6, NLRP9, NLRP12, NLRX1, and NLRC5, in regulating inflammation, epithelial homeostasis, and gastric tumorigenesis. In addition, genetic polymorphisms in NLR genes influence host susceptibility to H. pylori-associated diseases. This review highlights the interplay between NLR signaling, bacterial virulence, and host immunity and identifies potential therapeutic targets. Full article

Viral RNA structure plays a critical regulatory role in viral replication, serving as a dual-purpose mechanism for encoding genetic information and controlling biological processes. However, these structural elements also serve as pathogen-associated molecular patterns (PAMPs), which are recognized by pattern recognition receptors (PRRs) of the host innate immune system. This review discusses the complex and poorly understood relationship between viral RNA structure and recognition of RNA by PRRs, specifically focusing on Toll-like receptor 3 (TLR3) and Retinoic acid-inducible gene I (RIG-I). While current interaction models rely upon data generated from use of synthetic ligands such as poly(I:C) or perfectly base-paired double-stranded RNA stems, this review highlights significant gaps in our understanding of how PRRs recognize naturally occurring viral RNAs that fold into highly complex three-dimensional structures. Furthermore, we explore how viral evolution and nucleotide variations, such as those observed in influenza viruses, can drastically alter local and distal RNA structure, potentially impacting immune detection. We conclude that moving beyond synthetic models to understand natural RNA structural dynamics is essential for elucidating the mechanisms of viral immune evasion and pathogenesis. Full article

Background/Objectives: This review integrates evolutionary, metabolic, genetic, and nutritional perspectives to explain how sterol-derived vitamin D pathways shape human physiology and inter-individual variability in vitamin D status. Methods: The literature on sterol and vitamin D metabolism across animals, plants, fungi, and algae was synthesized with data from metabolomics databases, genome-wide association studies, RNA-seq resources (including GTEx), structural biology, and functional genomics. Results: Vitamin D₂ and vitamin D₃ likely emerged early in evolution as non-enzymatic photochemical sterol derivatives and were later co-opted into a tightly regulated endocrine system in vertebrates. In humans, cytochrome P450 enzymes coordinate vitamin D activation and degradation and intersect with oxysterol production, thereby linking vitamin D signaling to cholesterol and bile acid metabolism. Tissue-specific gene expression and regulatory genetic variants, particularly in the genes DHCR7, CYP2R1, CYP27B1, and CYP27A1, contribute to population-level differences in vitamin D status and metabolic outcomes. Structural analyses reveal selective, high-affinity binding of 1,25-dihydroxyvitamin D₃ to VDR, contrasted with broader, lower-affinity ligand recognition by LXRs. Dietary patterns modulate nuclear receptor signaling through distinct yet convergent ligand sources, including cholesterol-derived oxysterols, oxidized phytosterols, and vitamin D₂ versus vitamin D₃. Conclusions: Sterol and vitamin D metabolism constitute an evolutionarily conserved, adaptable network shaped by UV exposure, enzymatic control, genetic variation, and diet. This framework explains inter-individual variability in vitamin D biology and illustrates how evolutionary and dietary modulation of sterol-derived ligands confers functional flexibility to nuclear receptor signaling in human health. Full article