The circRNA circVAMP3 restricts influenza A virus replication by interfering with NP and NS1 proteins

CircMYO9A inhibits influenza A virus replication by dampening haemagglutinin cleavage via increasing SERPINE1/PAI-1 expression

Circular RNAs (circRNAs) represent a class of widespread and diverse covalently closed circular endogenous RNAs that play critical roles in regulating gene expression in mammals. However, the roles and regulatory mechanisms of circRNAs during influenza A virus (IAV) infection remain largely unexplored. In this study, we screened the circRNA transcription profiles of WSN-infected cells to identify circRNAs involved in viral replication and identified a novel differentially expressed circular RNA, circMYO9A. Mechanistically, circMYO9A acts as a competing endogenous RNA (ceRNA) for SERPINE1/PAI-1 by sponging miR-6059-3p, thereby increasing SERPINE1/PAI-1 expression, which restricts IAV haemagglutinin cleavage and subsequently reduces the infectivity of progeny viruses. Importantly, our findings demonstrate that circMYO9A significantly inhibits viral replication in the lungs of infected mice, potentially increasing their survival during IAV infection. These results demonstrate that circRNAs play crucial roles in inhibiting IAV replication and provide novel insights into potential therapeutic strategies involving circRNAs.

Functional characterization of a novel protein-coding circular RNA, circRNA_1193, from the mAAP gene in silkworm and its role in antiviral defense against BmCPV

A novel circular RNA, circRNA_1193, which originates from the membrane alanyl aminopeptidase-like gene in silkworms, was explored for its potential function and regulatory mechanism. We validated the presence of circRNA_1193 in Bombyx mori cytoplasmic polyhedrosis virus (BmCPV)-infected silkworm ovary cell line (BmN) cells through a combination of reverse transcription polymerase chain reaction, Northern blotting, and in situ hybridization. CircRNA_1193 exhibited tissue-specific expression, being highly enriched in the midgut and Malpighian tubules, and displayed a specific response to BmCPV infection, but not to Bombyx mori nucleopolyhedrovirus or lipopolysaccharide. Functional analyses revealed that the overexpression of circRNA_1193 suppressed BmCPV replication, whereas its knockdown increased viral replication. Bioinformatic analyses revealed potential internal ribosome entry sites, m6A methylation sites, and open reading frames (ORFs) within circRNA_1193, suggesting its potential coding capacity. We confirmed the translation of the ORF by constructing a DsRed reporter vector and demonstrating DsRed expression in transfected cells. Furthermore, a mutation of the start codon within circRNA_1193 abolished its antiviral activity, highlighting the crucial role of the translated protein, which is 35 kDa and is designated as VSP35. Furthermore, our data suggest that the formation of circRNA_1193 relies on reverse complementary flanking sequences. These findings unveil a novel protein-coding circular RNA in silkworms that plays a critical role in antiviral defense.

IMPORTANCE

This study identified a novel circular RNA, circRNA_1193, in the silkworm Bombyx mori, and revealed its critical role in antiviral defense against Bombyx mori cytoplasmic polyhedrosis virus (BmCPV). We demonstrated that circRNA_1193 exhibits tissue-specific expression, is upregulated in response to BmCPV infection, and possesses antiviral activity. Importantly, we show that circRNA_1193 encodes the viral protein VSP35, which is essential for its antiviral function. These findings provide new insights into the complex regulatory mechanisms of circular RNAs in antiviral immunity and underscore the potential of circular RNAs as therapeutic targets in viral diseases. The identification of a protein-coding circular RNA with antiviral activity in B. mori has broader implications for understanding the evolution and diversity of host defense mechanisms against viruses.

Clade 2.3.4.4b Highly pathogenic H5N1 influenza viruses from birds in China replicate effectively in bovine cells and pose potential public health risk

In February 2024, H5N1 highly pathogenic avian influenza viruses (HPAIVs) of clade 2.3.4.4b were first reported in dairy cows in the USA. Subsequent multiple outbreaks on dairy farms and sporadic human infections have raised substantial public health concerns. In the same year, four H5N1 HPAIVs of clade 2.3.4.4b were isolated from ducks and geese in live poultry markets (LPMs) spanning seven provinces in China. Evolutionary analysis demonstrated that these viruses had undergone two genetic reassortments with H5 influenza viruses from wild birds in different countries. Except for 565/H5N1, the other three viruses exhibited over 99% genetic homology with avian-origin H5N1 HPAIVs from South Korea and Japan. Notably, 571/H5N1 demonstrated high replication efficiency in bovine-derived cells, particularly in bovine mammary epithelial (MAC-T) cells, and caused 16.7% (1/6) mortality in mice at a dose of 10⁵ EID₅₀/50 μL, indicating its zoonotic potential. Given the potential cross-species transmission risk of H5N1 HPAIVs to cattle herds, we collected 228 serum samples from 12 cattle farms across five provinces and conducted serological testing to investigate seroprevalence of H5N1 HPAIVs in Chinese cattle herds. All tested samples were negative, indicating no widespread infection in the sampled cattle populations. However, infections in cattle from other regions cannot be ruled out. Nevertheless, due to the high mutability of H5N1 HPAIVs, enhanced surveillance of avian influenza viruses is critical to ensure timely responses to potential outbreaks.

Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities

Circular RNAs (circRNAs) are emerging as important regulatory molecules in both host and viral systems, acting as microRNA sponges, protein decoys or scaffolds, and templates for protein translation. Host-derived circRNAs are increasingly recognized for their roles in immune responses, while virus-encoded circRNAs, especially those from DNA viruses, have been shown to modulate host cellular machinery to favor viral replication and immune evasion. Recently, RNA virus-encoded circRNAs were also discovered, but evidence suggests that they might be generated using a different mechanism compared to the circRNAs produced from the host and DNA viruses. This review highlights recent advances in our understanding of both host and virus-derived circRNAs, with a focus on their biological roles and contributions to pathogenesis. Furthermore, we discuss the potential of circRNAs as biomarkers and their application as therapeutic targets or scaffolds for RNA-based therapies. Understanding the roles of circRNAs in host-virus interactions offers novel insights into RNA biology and opens new avenues for therapeutic strategies against viral diseases and associated cancers.

The identification of a blood circular RNA signature that differentiates Chikungunya virus infection

Objective

Chikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen, which poses critical threats to the public health. However, an effective diagnostic method for early CHIKV infection remains scarce. Circular RNAs (CircRNAs) are a novel class of RNAs with important biological functions. They have been shown to be promising biomarkers for many human diseases. In this study, we sought to identify circRNA biomarkers in human peripheral whole blood for the early diagnosis of CHIKV infection.

Design

Candidate circRNA biomarkers were identified by group comparison using a case-control study, which was further validated using an independent cohort. The performance of this signature and its correlation with clinical factors were estimated in both cohorts.

Results

Using two public RNA-seq datasets of CHIKV infection, we developed and validated a 13-circRNA based blood signature that can discriminate CHIKV infectious patients from healthy controls. Furthermore, this blood circRNA signature was correlated with viral load in patients with CHIKV infection. Functional analysis implicated that these biomarker circRNAs were involved in the activation and regulation of immune processes against CHIKV infection.

Conclusion

Collectively, our findings indicated that peripheral blood circRNAs were potential biomarkers for the early diagnosis of CHIKV infection.

Quaking RNA-Binding protein (QKI) mediates circular RNA biogenesis in Litopenaeus vannamei during WSSV infection

The Quaking RNA-binding protein (QKI), a member of the STAR family, is considered critical in the formation of circular RNAs (circRNAs), as it aids in catalyzing a back-splicing phenomenon by interacting with RNA precursors. CircRNAs have progressively been revealed to play central roles in the regulation of various biological processes, such as antiviral defense mechanisms. This study identifies a QKI in L. vannamei, referred to as LvQKI, comprised of conserved STAR and KH RNA-binding domains. Analysis through tissue-specific expression using qRT-PCR has revealed a high expression level of LvQKI in the gill - one of the primary regions heavily populated by the white spot syndrome virus (WSSV) - and its activation was triggered during WSSV infection. From an RNA interference-mediated suppression targeting LvQKI, a decrease and increase in survival rates and WSSV copy number were observed, respectively. Notably, circRNA levels were significantly lowered in LvQKI-silenced shrimp, whereas linear RNAs remained stable. Conversely, administration of recombinant LvQKI (rLvQKI) protein before a WSSV challenge not only enhanced survival rates but also reduced viral load, wherein both circRNAs and linear RNAs underwent up-regulation in rLvQKI-treated shrimp. Our results introduce LvQKI as a crucial factor in circRNA biogenesis and immune defense in shrimp, emphasizing the interplay between LvQKI's and circRNAs' roles in fighting viral invasion.

circEgg inhibits BmCPV infection by regulating the transition between H3K9me3 and H3K9ac

Our previous study demonstrated that the expression level of circRNA circEgg, which is encoded by histone-lysine N-methyltransferase eggless (BmEgg), is responsive to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection in the silkworm. However, the precise relationship between BmCPV infection and circEgg remains unclear. In this study, we observed that the expression level of circEgg in both the midguts and cultured BmN cells significantly increased after BmCPV infection, while the expression of its host gene, BmEgg, exhibited an opposite trend. Transient expression experiments revealed that circEgg acts to inhibit BmCPV infection. Additionally, Western blot analyses indicated that BmCPV infection leads to a downregulation of histone 3 lysine 9 trimethylation (H3K9me3) and an upregulation of histone 3 lysine 9 acetylation (H3K9ac). Notably, the levels of H3K9ac and H3K9me3 were found to be positively and negatively correlated with circEgg expression, respectively, suggesting that circEgg may regulate the transition between H3K9me3 and H3K9ac. Mechanistically, we discovered that circEgg inhibits BmCPV infection by enhancing the H3K9ac level through the circEgg-bmo-miR-3391-5p-histone deacetylase Rpd3 network, while simultaneously reducing the H3K9me3 level via the circEgg-encoded protein circEgg-P122. Collectively, these findings indicate that circEgg plays a crucial role in inhibiting BmCPV infection by modulating the balance between H3K9me3 and H3K9ac.

Emerging role and clinical applications of circular RNAs in human diseases

Circular RNAs (circRNAs) are a large family of non-coding RNAs characterized by a single-stranded, covalently closed structure, predominantly synthesized through a back-splicing mechanism. While thousands of circRNAs have been identified, only a few have been functionally characterized. Although circRNAs are less abundant than other RNA types, they exhibit exceptional stability due to their covalently closed structure and demonstrate high cell and tissue specificity. CircRNAs play a critical role in maintaining cellular homeostasis by influencing gene transcription, translation, and post-translation processes, modulating the immune system, and interacting with mRNA, miRNA, and proteins. Abnormal circRNA expression has been associated with a wide range of human diseases and various infections. Due to their remarkable stability in body fluids and tissues, emerging research suggests that circRNAs could serve as diagnostic and therapeutic biomarkers for these diseases. This review focuses on the emerging role of circRNAs in various human diseases, exploring their biogenesis, molecular functions, and potential clinical applications as diagnostic and therapeutic biomarkers with current evidence, challenges, and future perspectives. The key theme highlights the significance of circRNAs in regulating gene expression, their involvement in diseases like cancer, neurodegenerative disorders, cardiovascular diseases, and diabetes, and their potential use in translational medicine for developing novel therapeutic strategies. We also discuss recent clinical trials involving circRNAs. Thus, this review is important for both basic researchers and clinical scientists, as it provides updated insights into the role of circRNAs in human diseases, aiding further exploration and advancements in the field.

Roles of circRNAs in viral pathogenesis

Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed circular structure, lacking 5'-caps or 3'-poly(A) tails. They are relatively conserved, highly stable, and often exhibit tissue- or cell-specific production in eukaryotic cells. Based on the advances in sequencing technologies and bioinformatics, multiple reports have suggested that viruses and other microorganisms may encode circRNA-like molecules, providing new insights into the physiological and pathological roles of circRNAs. The innate immune system functions as the body's primary defense mechanism against viral infections. It detects pathogen-associated molecular patterns (PAMPs) and activates signaling pathways to suppress viral replication and limit their spread. CircRNAs are involved in regulation of the host innate immune signaling pathways and play essential roles in viral pathogenesis. It has been shown that circRNAs can regulate gene expression by acting as miRNA sponges or protein sponges, or encoding small proteins in specific cases. For example, previous studies have revealed that circRNAs participate in the host antiviral immune response through the competitive endogenous RNA (ceRNA) network by acting as miRNA sponges. This review highlights research progress in the regulation and functions of host- and virus-encoded circRNAs in host-virus interactions, as well as their potential as diagnostic biomarkers and therapeutic targets in clinical applications.

Circular RNAs in Viral Infection and Antiviral Treatment

Circular RNAs (circRNAs) are a class of noncoding RNAs that lack the 5'-cap structure and the 3' poly(A) tail. Their distinguishing feature is that the 3' and 5' ends are covalently linked to form a closed circular structure. CircRNAs have a longer half-life and stronger ribonuclease resistance compared with linear RNA. Viral infections lead to the production of circRNA molecules through the transcription and splicing mechanisms of host cells. circRNAs are produced from the transcription and splicing of the viral genome or from the splicing reactions of the host cell gene. They participate in regulating the replication of many viruses, including coronaviruses, human herpesviruses, human immunodeficiency virus, and cytomegalovirus. CircRNAs regulate the infection process by modulating circRNA expression in host cells and affect cellular biological processes. Some circRNAs have been proposed as diagnostic markers for viral infections. In this review, we discussed the properties of virus-derived circRNAs, the biological functions of diverse viruses-derived and host circRNAs during viral infections, and the critical role of circRNAs in the host's antiviral immune defense. Extensive research on the applications of circRNAs can help us better understand gene regulatory networks and disease mechanisms.

A previously unidentified circRNA inhibits virus replication by regulating the miR-24-3p/KEAP1 axis

Circular RNAs (circRNAs) exert diverse biological functions in different processes. However, the role of circRNAs during virus infection is mostly unknown. Herein, we explored the characteristics of host circRNAs using alphaherpesvirus pseudorabies virus (PRV) as a model. PRV infection upregulated the expression of circRNA circ29164, which does not encode a protein. RNA pulldown assays identified that circ29164 interacts with the microRNA ssc-miRNA-24-3p. Further analysis indicated that ssc-miR-24-3p targets the mRNA encoding kelch-like ECH-associated protein 1 (KEAP1), and circ29164 competitively binds to ssc-miR-24-3p to prevent it binding to Keap1. Apoptosis detection demonstrated that circ29164 or Keap1 overexpression, but not knockdown, induced caspase 3 activity and the release of cytochrome C from mitochondria, and inhibited PRV replication. Taken together, these data identified a previously undiscovered circRNA, circ29164, which inhibits PRV replication by competitively binding to ssc-24-3p to maintain KEAP1 levels.

Lnc-RPS6P3 Inhibits Influenza A Virus Replication and Attenuates the Inhibitory Effect of NS1 on Innate Immune Response

Host factors play important roles in influenza A virus (IAV) replication. In order to identify novel host factors involved in IAV replication, we compared the differentially expressed genes in A549 cells after IAV infection. We found that lncRNA lnc-RPS6P3 was up-regulated upon viral infection and poly(I:C) and IFN-β treatment, indicating it was an interferon-stimulated gene. Functional analysis demonstrated that overexpression of lnc-RPS6P3 inhibited IAV replication while knockdown of lnc-RPS6P3 promoted viral infection in A549 cells. Lnc-RPS6P3 inhibited both transcription and replication of IAV. Further study showed that lnc-RPS6P3 interacted with viral NP and interfered with NP self-oligomerization and, consequently, inhibited vRNP activity. In addition, lnc-RPS6P3 interacted with viral NS1 and reduced the interaction of NS1 and RIG-I; it also attenuated the inhibitory effect of NS1 on IFN-β stimulation. In conclusion, we revealed that lnc-RPS6P3 is an interferon-stimulated gene that inhibits IAV replication and attenuates the inhibitory effect of NS1 on innate immune response.

Influenza Virus Host Restriction Factors: The ISGs and Non-ISGs

Influenza virus has been one of the most prevalent and researched viruses globally. Consequently, there is ample information available about influenza virus lifecycle and pathogenesis. However, there is plenty yet to be known about the determinants of influenza virus pathogenesis and disease severity. Influenza virus exploits host factors to promote each step of its lifecycle. In turn, the host deploys antiviral or restriction factors that inhibit or restrict the influenza virus lifecycle at each of those steps. Two broad categories of host restriction factors can exist in virus-infected cells: (1) encoded by the interferon-stimulated genes (ISGs) and (2) encoded by the constitutively expressed genes that are not stimulated by interferons (non-ISGs). There are hundreds of ISGs known, and many, e.g., Mx, IFITMs, and TRIMs, have been characterized to restrict influenza virus infection at different stages of its lifecycle by (1) blocking viral entry or progeny release, (2) sequestering or degrading viral components and interfering with viral synthesis and assembly, or (3) bolstering host innate defenses. Also, many non-ISGs, e.g., cyclophilins, ncRNAs, and HDACs, have been identified and characterized to restrict influenza virus infection at different lifecycle stages by similar mechanisms. This review provides an overview of those ISGs and non-ISGs and how the influenza virus escapes the restriction imposed by them and aims to improve our understanding of the host restriction mechanisms of the influenza virus.