Structured elements drive extensive circular RNA translation

Unlock the sustained therapeutic efficacy of mRNA

mRNA therapies have emerged as a transformative class of medicines, offering immense potential across a diverse array of applications. This progress has been particularly evident in the wake of the success of lipid nanoparticle (LNP)-based mRNA vaccines during the COVID-19 pandemic. As these applications expand, the demand for sustained protein production has become increasingly critical. However, conventional mRNA therapies face significant challenges, including inherent RNA instability and suboptimal expression efficiency, often requiring repeated dosing to maintain therapeutic efficacy over time. This review highlights recent advances in strategies to prolong the therapeutic efficacy of LNP-mRNA systems. We focus on preclinical and emerging approaches aimed at extending the period of protein translation by engineering both the mRNA molecule and the LNP delivery system. Sustained protein expression is a cornerstone of mRNA-based therapeutics, and addressing this challenge is vital for unlocking their therapeutic potential. We hope this review provides valuable insights to guide the development of optimized delivery platforms for LNP-mRNA therapeutics.

Nuclear circGUSBP1 promotes cancer stemness via transcriptional coordination with OCT4

AIMS

Endometrial cancer (ECa) is a prevalent gynecological malignancy, with treatment often hindered by metastasis and recurrence driven by cancer stem-like cells. While circular RNAs (circRNAs) are well known for their cytoplasmic roles as microRNA sponges, their nuclear functions remain largely unexplored. This study investigates nuclear circRNAs and their roles in regulating cancer stem-like properties in ECa.

MATERIALS AND METHODS

Nuclear RNA sequencing data were analyzed to identify nuclear-enriched circRNAs. The subcellular localization of circGUSBP1 and circZNF680 was assessed via nuclear-cytoplasmic fractionation and RT-qPCR. The functional impact of circGUSBP1 was evaluated using tumorsphere formation, migration, and cisplatin sensitivity assays. Transcriptomic profiling and survival analysis were conducted using circGUSBP1-knockdown ECa cells and The Cancer Genome Atlas (TCGA) dataset.

KEY FINDINGS

CircGUSBP1 exhibited a high circular-to-linear transcript ratio and was preferentially nuclear, independent of intron retention. Its expression correlated with NANOG and OCT4 upregulation. Overexpression of circGUSBP1 enhanced tumorsphere formation, whereas circGUSBP1-knockdown (KD) reduced tumorsphere formation, impaired migration, and increased cisplatin sensitivity. Transcriptomic analysis revealed downregulation of stemness-related genes, supporting its role as a transcriptional co-activator. Notably, 230 circGUSBP1-regulated genes were co-targeted by OCT4, including SUPT16H and SUV39H2, chromatin remodelers linked to poor prognosis in ECa patients. Higher GUSBP1 expression, but not GUSB, correlated with worse survival outcomes in TCGA data.

SIGNIFICANCE

These findings identify circGUSBP1 as a nuclear regulator of cancer stemness. Through circGUSBP1/OCT4 co-regulation of chromatin modulators, circGUSBP1 promotes aggressive tumor behavior, highlighting its potential as a therapeutic target.

Novel Truncated Peptide Derived From circCDYL Exacerbates Cardiac Hypertrophy

BACKGROUND

Circular RNAs (circRNAs) have been gradually revealed to regulate the progression of heart disease in depth, showing their clinical significance. However, a mass of cardiac circRNAs still has not been functionally characterized. We aimed to explore the potential candidates that are involved in pathological cardiac hypertrophy.

METHODS

Public substantial RNA-sequencing data of cardiac circRNAs were utilized to search the cardiac hypertrophy-related circRNAs. Cardiomyocyte hypertrophy in vitro was induced by Ang II (angiotensin II) treatment. Mice were subjected to Ang II infusion to induce cardiac hypertrophy in vivo. Gain-of-function and loss-of-function assays were conducted to detect the effect of RNAs or proteins in cardiac hypertrophy.

RESULTS

A circRNA derived from the cdyl (chromodomain Y-like) gene was screened out and named circCDYL. Our results showed that the expression of circCDYL in primary rat cardiomyocytes was significantly induced by Ang II. Gain-of-function and loss-of-function assays demonstrated that circCDYL effectively promoted cardiomyocyte hypertrophy in vitro. CircCDYL could encode a ≈100-aa truncated CDYL peptide (tCDYL-100), whose sequence highly overlaps that of full-length CDYL. The translation of tCDYL-100 was activated by N6-methylation of circCDYL under prohypertrophic stimulation. tCDYL-100 fulfilled the prohypertrophic function of circCDYL. Mechanistically, tCDYL-100 competed with CDYL for binding REST (RE1-silencing transcription factor) and further disrupted the formation of REST-CDYL-EHMT2 (euchromatic histone-lysine N-methyltransferase 2) transcriptional repression complex, resulting in transcriptional activation of rhoa and nppb. Silence of circCDYL in mouse hearts could inhibit Ang II-induced cardiac hypertrophy, while forced expression of tCDYL-100 could cause cardiac hypertrophy.

CONCLUSIONS

In summary, our study uncovered an important circRNA-derived peptide and a regulatory mechanism on transcription mediated by N6-methyladenosine-circRNA-histone methylation in pathological cardiac hypertrophy.

TransRM: Weakly supervised learning of translation-enhancing N6-methyladenosine (m6A) in circular RNAs

As our understanding of Circular RNAs (circRNAs) continues to expand, accumulating evidence has demonstrated that circRNAs can interact with microRNAs and RNA-binding proteins to modulate gene expression. More importantly, a subset of circRNAs has been reported to possess coding potential, enabling them to translate into functional proteins. Recent studies also indicate that the N6-methyladenosine (m6A)-modified start codon may function as an Internal Ribosome Entry Site (IRES), influencing the translation of circRNAs. Therefore, elucidating how m6A regulates circRNA translation potential could significantly advance circRNA research, including the development of circRNA-based vaccines. However, to our knowledge, there are currently no computational tools specifically designed for this purpose. To bridge this gap, we have developed the first computational model, termed TransRM, to predict the impact of base-resolution m6A sites on circRNA translation. Our model employs weakly supervised learning with two convolution layers. These layers extract RNA modification features, and a bidirectional gated recurrent unit predicts the contribution of each RNA modification to circRNA translation. Subsequently, the RNA modification features are then integrated with their contribution to assess the probability of circRNA translation using a random forest algorithm. TransRM has demonstrated efficiency in identifying translation-enhancing m6A sites, with an AUROC of 0.9188 and an AUPRC of 0.9371, respectively. We hope that our newly proposed model could help to broaden our understanding of circRNA regulation at the epitranscriptome layer, particularly in identifying translated circRNAs, thereby contributing to the development of more effective circular RNA-based therapeutics.

Epigenetics of nonobstructive azoospermia

ABSTRACT

Nonobstructive azoospermia (NOA) is a severe and heterogeneous form of male factor infertility caused by dysfunction of spermatogenesis. Although various factors are well defined in the disruption of spermatogenesis, not all aspects due to the heterogeneity of the disorder have been determined yet. In this review, we focus on the recent findings and summarize the current data on epigenetic mechanisms such as DNA methylation and different metabolites produced during methylation and demethylation and various types of small noncoding RNAs involved in the pathogenesis of different groups of NOA.

Complete substitution with modified nucleotides in self-amplifying RNA suppresses the interferon response and increases potency

The use of modified nucleotides to suppress the interferon response and maintain translation of self-amplifying RNA (saRNA), which has been achieved for mRNA, has not yet succeeded. We identify modified nucleotides that, when substituted at 100% in saRNA, confer innate immune evasion and robust long-term protein expression, and when formulated as a vaccine, protect against lethal SARS-CoV-2 challenge in mice. This discovery advances saRNA therapeutics by enabling prolonged protein expression at low doses.

A versatile toolbox for determining IRES activity in cells and embryonic tissues

Widespread control of gene expression through translation has emerged as a key level of spatiotemporal regulation of protein expression. A prominent mechanism by which ribosomes can confer gene regulation is via internal ribosomal entry sites (IRESes), whose functions have however, remained difficult to rigorously characterize. Here we present a set of technologies in embryos and cells, including IRES-mediated translation of circular RNA (circRNA) reporters, single-molecule messenger (m)RNA isoform imaging, PacBio long-read sequencing, and isoform-sensitive mRNA quantification along polysome profiles as a new toolbox for understanding IRES regulation. Using these techniques, we investigate a broad range of cellular IRES RNA elements including Hox IRESes. We show IRES-dependent translation in circRNAs, as well as the relative expression, localization, and translation of an IRES-containing mRNA isoform in specific embryonic tissues. We thereby provide a new resource of technologies to elucidate the roles of versatile IRES elements in gene regulation and embryonic development.

The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

Acute myeloid leukaemia (AML) is a prevalent haematologic malignancy characterized by significant heterogeneity. Despite the application of aggressive therapeutic approaches, AML remains associated with poor prognosis. Circular RNAs (circRNAs) constitute a unique class of single-stranded RNAs featuring covalently closed loop structures that are ubiquitous across species. These molecules perform crucial regulatory functions in the pathogenesis of various diseases through diverse mechanisms, including acting as miRNA sponges, interacting with DNA or proteins, and encoding functional proteins/polypeptides. Recently, numerous circRNAs have been confirmed to have aberrant expression patterns in AML patients. In particular, certain circRNAs are closely associated with specific clinicopathological characteristics and thus have great potential as diagnostic/prognostic biomarkers and therapeutic targets in AML. Herein, we systematically summarize the biogenesis, degradation, and functional mechanisms of circRNAs while highlighting their clinical relevance. We also outline a series of online databases and analytical tools available to facilitate circRNA research. Finally, we discuss the current challenges and future research priorities in this evolving field.

Plasmodium Infection Modulates Host Inflammatory Response through circRNAs during the Intracellular Stage in Red Blood Cells

The integration of RNA- and DNA-based assays enables the investigation of disease dynamics, specifically assessing the role of asymptomatic or subclinical infections in malaria transmission. Circular RNAs (circRNAs), a distinct category of noncoding RNAs, are implicated in numerous pathogenic mechanisms. As of now, research has yet to explore circRNAs' function in malaria infection. The findings revealed that Plasmodium infection upregulated 60 circRNAs and downregulated 71 in BALB/c mice. We selected 11 differentially expressed (DE) circRNAs according to function prediction of target miRNA-mRNA and coding protein, and these were further confirmed by validation experiments. IRESfinder, GO, and KEGG evaluations indicated that 7 DE circRNAs possess protein-coding potential and are enriched in the MAPK signaling cascade. In P.y17XL-infected BALB/c mouse models, the findings substantiated that the dynamic characteristics of DE circRNAs correlated with inflammation, and the MAPK and NF-κB signaling cascades were activated, also contributing to the inflammatory reaction during malaria infection. This study establishes Plasmodium-induced circRNA expression as a novel mechanism by which the parasite modulates host immune signaling, advancing the understanding of Plasmodium-host cell interactions. In addition, 42 circRNAs were found in normal BALB/c mice, and 25 circRNAs were discovered in P.y17XL-infected BALB/c mice, excluding 1238 circRNAs shared by normal and P.y17XL-infected BALB/c mice. Plasmodium infection changes the expression profile of circRNAs in the host, and these altered circRNAs are involved in the inflammatory response during malaria infection. In addition, Plasmodium possibly regulates the reverse splicing of pre-mRNA or m6A modification of RNA, inducing the production of novel circRNAs in the host.

Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials

Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.

Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications

Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

Decoding the regulatory roles of circular RNAs in cardiac fibrosis

Cardiovascular diseases (CVDs) are the primary cause of death globally. The evolution of nearly all types of CVDs is characterized by a common theme: the emergence of cardiac fibrosis. The precise mechanisms that trigger cardiac fibrosis are still not completely understood. In recent years, a type of non-coding regulatory RNA molecule known as circular RNAs (circRNAs) has been reported. These molecules are produced during back splicing and possess significant biological capabilities, such as regulating microRNA activity, serving as protein scaffolds and recruiters, competing with mRNA, forming circR-loop structures to modulate transcription, and translating polypeptides. Furthermore, circRNAs exhibit a substantial abundance, notable stability, and specificity of tissues, cells, and time, endowing them with the potential as biomarkers, therapeutic targets, and therapeutic agents. CircRNAs have garnered growing interest in the field of CVDs. Recent investigations into the involvement of circRNAs in cardiac fibrosis have yielded encouraging findings. This study aims to provide a concise overview of the existing knowledge about the regulatory roles of circRNAs in cardiac fibrosis.

CircRNAs in Colorectal Cancer: Unveiling Their Roles and Exploring Therapeutic Potential

Colorectal cancer (CRC) is the most common malignancy of the digestive system. Although research into the causes of CRC's origin and progression has advanced over the past few decades, many details are still not fully understood. Circular RNAs (circRNAs), as a novel regulatory molecule, have been found to be closely involved in various key biological processes in CRC. CircRNAs also have been shown to encode proteins, which could offer new possibilities for therapeutic applications. This ability to produce tumor-specific proteins makes circRNA-based vaccines a potentially valuable approach for targeted cancer treatment. In this review, we summarize recent findings on the various roles of circRNAs in CRC and explore their potential in the development of protein-encoding circRNA vaccines for CRC therapy.

Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective

Bioinformatics has significantly advanced RNA-based therapeutics, particularly circular RNAs (circRNAs), which outperform mRNA vaccines, by offering superior stability, sustained expression, and enhanced immunogenicity due to their covalently closed structure. This review highlights how bioinformatics and computational biology optimise circRNA vaccine design, elucidates internal ribosome entry sites (IRES) selection, open reading frame (ORF) optimisation, codon usage, RNA secondary structure prediction, and delivery system development. While circRNA vaccines may not always surpass traditional vaccines in stability, their production efficiency and therapeutic efficacy can be enhanced through computational strategies. The discussion also addresses challenges and future prospects, emphasizing the need for innovative solutions to overcome current limitations and advance circRNA vaccine applications.

The circular RNA circbabo(5,6,7,8S) regulates lipid metabolism and neuronal integrity via TGF-β/ROS/JNK/SREBP signaling axis in Drosophila

BACKGROUND

Lipid droplets (LDs) are dynamic cytoplasmic lipid-storing organelles that play a pivotal role in maintaining cellular energy balance, lipid homeostasis, and metabolic signaling. Dysregulation of lipid metabolism, particularly excessive lipogenesis, contributes to the abnormal accumulation of LDs in the nervous system, which is associated with several neurodegenerative diseases. Circular RNAs (circRNAs) are a new class of non-coding and regulatory RNAs that are widely expressed in eukaryotes. However, only a subset has been functionally characterized. Here, we identified and functionally characterized a new circular RNA circbabo(5,6,7,8S) that regulates lipogenesis and neuronal integrity in Drosophila melanogaster.

RESULTS

circbabo(5,6,7,8S) is derived from the babo locus which encodes the type I receptor for transforming growth factor β (TGF-β). Depletion of circbabo(5,6,7,8S) in flies causes elevated lipid droplet accumulation, progressive photoreceptor cell loss and shortened lifespan, phenotypes that are rescued by restoring circbabo(5,6,7,8S) expression. In addition, RNA-seq and epistasis analyses reveal that these abnormalities are caused by aberrant activation of the SREBP signaling pathway. Furthermore, circbabo(5,6,7,8S)-depleted tissues display enhanced activation of the TGF-β signaling pathway and compromised mitochondrial function, resulting in upregulation of reactive oxygen species (ROS). Moreover, we provide evidence that circbabo(5,6,7,8S) encodes the protein circbabo(5,6,7,8S)-p, which inhibits TGF-β signaling by interfering with the assembly of babo/put receptor heterodimer complex. Lastly, we show that dysregulation of the ROS/JNK/SREBP signaling cascade is responsible for the LD accumulation, neurodegeneration, and shortened lifespan phenotypes elicited by circbabo(5,6,7,8S) depletion.

CONCLUSIONS

Our study demonstrates the physiological role of the protein-coding circRNA circbabo(5,6,7,8S) in regulating lipid metabolism and neuronal integrity.

Recent advances and perspectives on the development of circular RNA cancer vaccines

Engineered circular RNAs (circRNAs) are emerging as promising platforms for RNA-based vaccines in cancer treatment. We summarize the recent advances of design, synthesis, and delivery of circRNA-based cancer vaccines, and highlight the applications and challenges of circRNA vaccines in cancer therapy. Further enhancements are required in areas such as antigen selection, targeted delivery, multidimensional crosstalks, and clinical trial assessments to advance the efficacy and safety of circRNA vaccines in cancer.

Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)

Dual reporters encoding two distinct proteins within the same mRNA have had a crucial role in identifying and characterizing unconventional mechanisms of eukaryotic translation. These mechanisms include initiation via internal ribosomal entry sites (IRESs), ribosomal frameshifting, stop codon readthrough and reinitiation. This design enables the expression of one reporter to be influenced by the specific mechanism under investigation, while the other reporter serves as an internal control. However, challenges arise when intervening test sequences are placed between these two reporters. Such sequences can inadvertently impact the expression or function of either reporter, independent of translation-related changes, potentially biasing the results. These effects may occur due to cryptic regulatory elements inducing or affecting transcription initiation, splicing, polyadenylation and antisense transcription as well as unpredictable effects of the translated test sequences on the stability and activity of the reporters. Unfortunately, these unintended effects may lead to misinterpretation of data and the publication of incorrect conclusions in the scientific literature. To address this issue and to assist the scientific community in accurately interpreting dual-reporter experiments, we have developed comprehensive guidelines. These guidelines cover experimental design, interpretation and the minimal requirements for reporting results. They are designed to aid researchers conducting these experiments as well as reviewers, editors and other investigators who seek to evaluate published data.

Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition

Thermal adaptability is a crucial characteristic for mammalian pathogenic fungi that originally inhabit natural ecosystems. Thermally dimorphic fungi have evolved a unique ability to respond to host body temperature by shifting from mycelia to yeast. The high similarity of protein-coding genes between these fungi and their relatives suggests the indispensable but often overlooked roles of non-coding elements in fungal thermal adaptation. Here, we systematically delineated the landscape of full-length circRNAs in both mycelial and yeast conditions of Talaromyces marneffei, a typical thermally dimorphic fungus causing fatal Talaromycosis, by optimizing an integrative pipeline for circRNA detection utilizing next- and third-generation sequencing. We found T. marneffei circRNA demonstrated features such as shorter length, lower abundance, and circularization-biased splicing. We then identified and validated that circDS-1, independent of its parental gene, promotes the hyphae-to-yeast transition, maintains yeast morphology, and is involved in virulence regulation. Further analysis and experiments among Talaromyces confirmed that the generation of circDS-1 is driven by a T. marneffei-specific region in the flanking intron of circDS-1. Together, our findings not only provide fresh insights into the role of circRNA in fungal thermal adaptation but also reveal a novel molecular mechanism for the adaptive evolution of functional circRNAs derived from intronic mutations.

Microglial circDlg1 modulates neuroinflammation by blocking PDE4B ubiquitination-dependent degradation associated with Alzheimer's disease

Background: Abnormal activation of microglia occurs in the early stage of Alzheimer's disease (AD) and leads to subsequent neuroinflammation and major AD pathologies. Circular RNAs (circRNAs) are emerging as great potential therapeutic targets in AD. However, the extent of circRNAs entwined and the underlying mechanism in microglia-driven neuroinflammation in AD remain elusive. Methods: The circular RNA Dlg1 (circDlg1) was identified using circRNA microarray screening in magnetic-isolated microglia of APP/PS1 mice. CircDlg1 expression in microglia of APP/PS1 mice and AD patients was validated by FISH. Flow cytometry and immunostaining were conducted to explore the roles of circDlg1 in microglia. Adeno-associated virus 9 preparations for interfering with microglial circDlg1 were microinjected into mouse lateral ventricle to explore influences on microglial response, neuroinflammation and AD pathologies. Y-maze, novel object recognition and Morris water maze tasks were performed to assess cognitive performance. RNA pulldown assays, mass spectrometry analysis, RNA immunoprecipitation, and co-immunoprecipitation were performed to validate the underlying regulatory mechanisms of circDlg1. Results: A novel circular RNA circDlg1 was observed elevated using circRNA microarray screening in microglia isolated from APP/PS1 mice and validated increased in intracerebral microglia of AD patients. Microglia-specific knockdown of circDlg1 remarkably ameliorated microglial recruitment and envelopment of amyloid-β (Aβ), mitigated neuroinflammation, and prevented cognitive decline in APP/PS1 mice. Mechanistically, circDlg1 interfered with the interaction between phosphodiesterase 4b (PDE4B) and Smurf2, an E3 ubiquitin ligase of PDE4B. The formed ternary complex protected PDE4B from ubiquitination-dependent degradation via unique N-terminal targeting domain, thus consequently decreasing cAMP levels. We further confirmed that microglial circDlg1 downregulation significantly activated PKA/CREB anti-inflammatory pathway by decreasing PDE4B protein levels in APP/PS1 mice. Conclusion: The novel microglia-upregulated circDlg1 tightly involves in neuroinflammation in APP/PS1 mice via determining the protein fate of PDE4B. Microglial loss of circDlg1 promotes microglial protective response to Aβ deposition and relieves neuroinflammation, thus suggesting a potential therapeutic strategy that specifically targets the microglial response in AD.

Characterization of group I introns in generating circular RNAs as vaccines

Circular RNAs are an increasingly important class of RNA molecules that can be engineered as RNA vaccines and therapeutics. Here, we screened eight different group I introns for their ability to circularize and delineated different features that are important for their function. First, we identified the Scytalidium dimidiatum group I intron as causing minimal innate immune activation inside cells, underscoring its potential to serve as an effective RNA vaccine without triggering unwanted reactogenicity. Additionally, mechanistic RNA structure analysis was used to identify the P9 domain as important for circularization, showing that swapping sequences can restore pairing to improve the circularization of poor circularizers. We also determined the diversity of sequence requirements for the exon 1 and exon 2 (E1 and E2) domains of different group I introns and engineered a S1 tag within the domains for positive purification of circular RNAs. In addition, this flexibility in E1 and E2 enables substitution with less immunostimulatory sequences to enhance protein production. Our work deepens the understanding of the properties of group I introns, expands the panel of introns that can be used, and improves the manufacturing process to generate circular RNAs for vaccines and therapeutics.

Microproteins in cancer: identification, biological functions, and clinical implications

Cancer continues to be a major global health challenge, accounting for 10 million deaths annually worldwide. Since the inception of genome-wide cancer sequencing studies 20 years ago, a core set of ~700 oncogenes and tumor suppressor genes has become the basis for cancer research. However, this research has been based largely on an understanding that the human genome encodes ~19 500 protein-coding genes. Complementing this genomic landscape, recent advances have described numerous microproteins which are now poised to redefine our understanding of oncogenic processes and open new avenues for therapeutic intervention. This review explores the emerging evidence for microprotein involvement in cancer mechanisms and discusses potential therapeutic applications, with an emphasis on highlighting recent advances in the field.

Structural basis of circularly permuted group II intron self-splicing

Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. Structural and mechanistic understanding of circular RNA (circRNA) generation by CP introns remains elusive. We resolve cryo-electron microscopy structures of a natural CP intron in different states during back-splicing at a resolution of 2.5-2.9 Å. Domain 6 (D6) undergoes a conformational change of 65° after branching, to facilitate 3'-exon recognition and circularization. Previously unseen tertiary interactions compact the catalytic triad and D6 for splicing without protein, whereas a metal ion, M35, is observed to stabilize the 5'-exon during splicing. While these unique features were not observed in canonical group II introns and spliceosomes, they are common in CP introns, as demonstrated by the cryo-EM structure of another CP intron discovered by comparative genomics analysis. Our results elucidate the mechanism of CP intron back-splicing dynamics, with potential applications in circRNA research and therapeutics.

The Role of the Dysregulation of circRNAs Expression in Glioblastoma Multiforme

Primary brain tumors that were the most severe and aggressive were called glioblastoma multiforme (GBM). Cancers are caused in part by aberrant expression of circular RNA. Often referred to as competitive endogenous RNA (ceRNA), circRNA molecules act as "miRNA sponges" in cells by decreasing the inhibitory impact of miRNA on their target genes and hence raising the expression levels of those genes. circRNA molecules are rich in miRNA binding sites. The discovery of more structurally diverse and GBM-related circRNAs has great promise for the use of GMB prognostic biomarkers and therapeutic targets, as well as for comprehending the molecular regulatory mechanisms of GBM. In this work, we present an overview of the circRNA expression patterns associated with GBM and offer a potential integrated electrochemical strategy for detecting circRNA with extreme sensitivity in the diagnosis of glioblastoma.

Translation of circular RNAs

Circular RNAs (circRNAs) are covalently closed RNAs that are present in all eukaryotes tested. Recent RNA sequencing (RNA-seq) analyses indicate that although generally less abundant than messenger RNAs (mRNAs), over 1.8 million circRNA isoforms exist in humans, much more than the number of currently known mRNA isoforms. Most circRNAs are generated through backsplicing that depends on pre-mRNA structures, which are influenced by intronic elements, for example, primate-specific Alu elements, leading to species-specific circRNAs. CircRNAs are mostly cytosolic, stable and some were shown to influence cells by sequestering miRNAs and RNA-binding proteins. We review the increasing evidence that circRNAs are translated into proteins using several cap-independent translational mechanisms, that include internal ribosomal entry sites, N6-methyladenosine RNA modification, adenosine to inosine RNA editing and interaction with the eIF4A3 component of the exon junction complex. CircRNAs are translated under conditions that favor cap-independent translation, notably in cancer and generate proteins that are shorter than mRNA-encoded proteins, which can acquire new functions relevant in diseases.

CircSugp1 interacts with CPSF6 to modulate intestinal mucosa repair by regulating alternative polyadenylation-mediated shortening of the Wdr89 3'UTR

Circular RNAs are a single-stranded non-coding RNAs and play an important role in the development of many diseases. Alternative polyadenylation (APA) regulates the gene 3'UTR length for controlling gene expressions. Although the APA mechanism has been widely studied in the development of diseases, there is no data on its role in the burned intestinal mucosa. We thus herein assessed the role of the circSugp1-initiating APA mechanism in the burned intestinal mucosa. CircSugp1 was downregulated in the intestinal mucosa of burned mice. CircSugp1 promoted proliferation and migration in vitro and in vivo. CircSugp1 promotes the expression of CPSF6; the overexpression of CPSF6 can shorten the gene 3'UTR within the transcript APA range. The promoting effect of circSugp1 on value-added migration was mediated by the APA regulation of the Wdr89 short 3'UTR isoform. CircSugp1 targeted the upregulation of the expression of CPSF6, followed by upregulation of the expression of Wdr89 through APA, promoting the repair of intestinal mucosal damage in burned mice.

Robust genome and cell engineering via in vitro and in situ circularized RNAs

Circularization can improve RNA persistence, yet simple and scalable approaches to achieve this are lacking. Here we report two methods that facilitate the pursuit of circular RNAs (cRNAs): cRNAs developed via in vitro circularization using group II introns, and cRNAs developed via in-cell circularization by the ubiquitously expressed RtcB protein. We also report simple purification protocols that enable high cRNA yields (40-75%) while maintaining low immune responses. These methods and protocols facilitate a broad range of applications in stem cell engineering as well as robust genome and epigenome targeting via zinc finger proteins and CRISPR-Cas9. Notably, cRNAs bearing the encephalomyocarditis internal ribosome entry enabled robust expression and persistence compared with linear capped RNAs in cardiomyocytes and neurons, which highlights the utility of cRNAs in these non-dividing cells. We also describe genome targeting via deimmunized Cas9 delivered as cRNA and a long-range multiplexed protein engineering methodology for the combinatorial screening of deimmunized protein variants that enables compatibility between persistence of expression and immunogenicity in cRNA-delivered proteins. The cRNA toolset will aid research and the development of therapeutics.

The Role of circRNAs in the Pathological Mechanisms of Alzheimer's Disease: Potential Biomarkers for Diagnosis

Alzheimer's disease (AD) is the most common neurodegenerative disease leading to dementia in the elderly, and the mechanisms of AD have not been fully defined. Circular RNAs (circRNAs), covalently closed RNAs produced by reverse splicing, have critical effects in the pathogenesis of AD. CircRNAs participate in production and clearance of Aβ and tau, regulate neuroinflammation, synaptic plasticity and the process of apoptosis and autophagy, indicating that circRNAs may be alternative biomarkers and therapeutic targets. Our review summarizes the functions of circRNAs in the progression and development of AD, which provide insights into the prospect of circRNAs in the diagnosis and treatment of AD.

A Review on Circular RNA Translation and Its Implications in Disease

The mRNA vaccine has emerged as a powerful tool against viral infection during the coronavirus disease 2019 (COVID-19) pandemic. In the post-COVID-19 era, the applications of mRNA-based therapy continue to expand and evolve. Circular RNA (circRNA), long assumed to be a noncoding RNA, has been proven to be translatable and subsequently developed as a next-generation mRNA modality due to its higher stability and wider therapeutic window. Nonetheless, the studies of circRNA translation and its application in diseases still present numerous technical features and challenges. In this chapter, we provide a summary and discussion on the mechanisms of circRNA translation and its applications in medicine development, aiming to serve as a reference and inspiration for readers interested in circRNA-based therapy.

Circular RNAs in coronary heart disease: From molecular mechanism to promising clinical application (Review)

Coronary heart disease (CHD) remains a leading cause of morbidity and mortality worldwide, posing a substantial public health burden. Despite advancements in treatment, the complex etiology of CHD necessitates ongoing exploration of novel diagnostic markers and therapeutic targets. Circular RNAs (circRNAs), a distinct class of non‑coding RNAs with a covalently closed loop structure, have emerged as significant regulators in various diseases, including CHD. Their high stability, tissue‑specific expression and evolutionary conservation underscore their potential as biomarkers and therapeutic agents in CHD. This review discusses the current knowledge on circRNAs in the context of CHD and explores the molecular mechanisms by which circRNAs influence the pathophysiology of CHD, including cardiomyocyte death, endothelial injury, vascular dysfunction and inflammation. It also summarizes the emerging evidence highlighting the differential expression of circRNAs in patients with CHD and their potential utilities as non‑invasive diagnostic and prognostic biomarkers and therapeutic targets for this disease.

Cellular functions and biomedical applications of circular RNAs

Circular RNAs (circRNAs) have emerged as a large class of stable and conserved RNAs that are derived primarily from back-splicing of pre-mRNAs and expressed in a cell- and tissue-specific fashion. Recent studies have indicated that a subset of circRNAs may undergo translation through cap-independent pathways mediated by internal ribosome entry sites (IRESs), m6A modifications, or IRES-like short elements. Considering the stability and low immunogenicity of circRNAs, in vitro transcribed circRNAs hold great promise in biomedical applications. In this review, we briefly discuss the noncoding and coding functions of circRNAs in cells, as well as the methods for the in vitro synthesis of circRNAs and current advances in the applications of circRNAs in biomedicine.

Exosomal circular RNAs in tumor microenvironment: An emphasis on signaling pathways and clinical opportunities

Exosomes can regulate the malignant progression of tumors by carrying a variety of genetic information and transmitting it to target cells. Recent studies indicate that exosomal circular RNAs (circRNAs) regulate multiple biological processes in carcinogenesis, such as tumor growth, metastasis, epithelial-mesenchymal transition, drug resistance, autophagy, metabolism, angiogenesis, and immune escape. In the tumor microenvironment (TME), exosomal circRNAs can be transferred among tumor cells, endothelial cells, cancer-associated fibroblasts, immune cells, and microbiota, affecting tumor initiation and progression. Due to the high stability and widespread presence of exosomal circRNAs, they hold promise as biomarkers for tumor diagnosis and prognosis prediction in blood and urine. In addition, designing nanoparticles targeting exosomal circRNAs and utilizing exosomal circRNAs derived from immune cells or stem cells provide new strategies for cancer therapy. In this review, we examined the crucial role of exosomal circRNAs in regulating tumor-related signaling pathways and summarized the transmission of exosomal circRNAs between various types of cells and their impact on the TME. Finally, our review highlights the potential of exosomal circRNAs as diagnostic and prognostic prediction biomarkers, as well as suggesting new strategies for clinical therapy.

RNA technology and nanocarriers empowering in vivo chimeric antigen receptor therapy

The remarkable success of mRNA-based coronavirus 2019 (COVID-19) vaccines has propelled the advancement of nanomedicine, specifically in the realm of RNA technology and nanomaterial delivery systems. Notably, significant strides have been made in the development of RNA-based in vivo chimeric antigen receptor (CAR) therapy. In comparison to the conventional ex vivo CAR therapy, in vivo CAR therapy offers several benefits including simplified preparation, reduced costs, broad applicability and decreased potential for carcinogenic effects. This review summarises the RNA-based CAR constructs in in vivo CAR therapy, discusses the current applications of in vivo delivery vectors and outlines the immune cells edited with CAR molecules. We aim for the conveyed messages to contribute towards the advancement of in vivo CAR application.

The role of polypeptides encoded by ncRNAs in cancer

It was previously thought that ncRNA could not encode polypeptides, but recent reports have challenged this notion. As research into ncRNA progresses, it is increasingly clear that it serves roles beyond traditional mechanisms, playing significant regulatory roles in various diseases, notably cancer, which is responsible for 70% of human deaths. Numerous studies have highlighted the diverse regulatory mechanisms of ncRNA that are pivotal in cancer initiation and progression. The role of ncRNA-encoded polypeptides in cancer regulation has gained prominence. This article explores the newly identified regulatory functions of these polypeptides in three types of ncRNA-lncRNA, pri-miRNA, and circRNA. These polypeptides can interact with proteins, influence signaling pathways, enhance miRNA stability, and regulate cancer progression, malignancy, resistance, and other clinical challenges. Furthermore, we discuss the evolutionary significance of these polypeptides in the transition from RNA to protein, examining their emergence and conservation throughout evolution.

The potential of circular RNAs as biomarkers and therapeutic targets for gastric cancer: A comprehensive review

BACKGROUND

Gastric cancer (GC) is a global health concern, contributing significantly to cancer-related mortality rates. Early detection is vital for improving patient outcomes. Recently, circular RNAs (circRNAs) have emerged as crucial players in the development and progression of various cancers, including GC.

AIM

This comprehensive review underscores the promising potential of circRNAs as innovative biomarkers for the early diagnosis of GC, as well as their possible utility as therapeutic targets for this life-threatening disease. Specifically, the review focuses on recent findings, mechanistic insights, and clinical applications of circRNAs in GC.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Dysregulation of circRNAs has been consistently observed in GC tissues, offering potential diagnostic value due to their stability in bodily fluids such as blood and urine. For instance, circPTPN22 and hsa_circ_000200. Furthermore, the expression levels of circRNAs such as circCUL2, hsa_circ_0000705 and circSHKBP1 have shown strong associations with critical clinical features of GC, including diagnosis, prognosis, tumor size, lymph node metastasis, tumor-node-metastasis (TNM) stage, and treatment response. Additionally, circRNAs such as circBGN, circLMO7, and circMAP7D1 have shown interactions with specific microRNAs (miRNAs), proteins, and other molecules that play key roles in development and progression of GC. This further highlighting their potential as therapeutic targets. Despite their potential, several challenges need to be addressed to effectively apply circRNAs as GC biomarkers. These include standardizing detection methods, establishing cutoff values for diagnostic accuracy, and validating findings in larger patient cohorts. Moreover, the functional mechanisms by which circRNAs contribute to GC pathogenesis and therapeutic resistance warrant further investigation. Advances in circRNAs research could provide valuable insights into the early detection and targeted treatment of GC, ultimately improving patient outcomes.

The crosstalk between alternative splicing and circular RNA in cancer: pathogenic insights and therapeutic implications

RNA splicing is a fundamental step of gene expression. While constitutive splicing removes introns and joins exons unbiasedly, alternative splicing (AS) selectively determines the assembly of exons and introns to generate RNA variants corresponding to the same transcript. The biogenesis of circular RNAs (circRNAs) is inextricably associated with AS. Back-splicing, the biogenic process of circRNA, is a special form of AS. In cancer, both AS and circRNA deviate from the original track. In the present review, we delve into the intricate interplay between AS and circRNAs in the context of cancer. The relationship between AS and circRNAs is intricate, where AS modulates the biogenesis of circRNAs and circRNAs in return regulate AS events. Beyond that, epigenetic and posttranscriptional modifications concurrently regulate AS and circRNAs. On the basis of this modality, we summarize current knowledge on how splicing factors and other RNA binding proteins regulate circRNA biogenesis, and how circRNAs interact with splicing factors to influence AS events. Specifically, the feedback loop regulation between circRNAs and AS events contributes greatly to oncogenesis and cancer progression. In summary, resolving the crosstalk between AS and circRNA will not only provide better insight into cancer biology but also provoke novel strategies to combat cancer.

Development of hydrophobic tag purifying monophosphorylated RNA for chemical synthesis of capped mRNA and enzymatic synthesis of circular mRNA

We developed phosphorylation reagents with a nitrobenzyl hydrophobic tag and used them for 5'-phosphorylation of chemically or transcriptionally synthesized RNA. The capability of hydrophobic tags to synthesize 5'-monophosphorylated RNA was evaluated based on the yield of the desired oligonucleotides, stability of protecting groups during cleavage/deprotection, separation ability in reverse-phase HPLC (RP-HPLC), and deprotection efficiency after RP-HPLC purification. The results showed that a nitrobenzyl derivative with a tert-butyl group at the benzyl position was most suitable for RNA 5'-phosphorylation. Using the developed phosphorylation reagent, we chemically synthesized 5'-phosphorylated RNA and confirmed that it could be purified by RP-HPLC and the following deprotection. In addition, we demonstrated complete chemical synthesis of minimal mRNA by chemical capping of 5'-monophosphorylated RNA. Ribonucleoside 5'-monophosphates with hydrophobic protecting groups have also been developed and used as substrates to transcriptionally synthesize 5'-phosphorylated RNA with >1000 bases. From the mixture of the by-products and the desired RNA, only 5'-monophosphorylated RNA could be effectively isolated by RP-HPLC. Furthermore, monophosphorylated RNA can be converted into circular mRNA via RNA ligase-mediated cyclization. Circular mRNA expression of nanoluciferase in cultured cells and mice. These techniques are important for the production of chemically synthesized mRNA and circular mRNA.

Synthetic circRNA therapeutics: innovations, strategies, and future horizons

Small molecule drugs are increasingly emerging as innovative and effective treatments for various diseases, with mRNA therapeutics being a notable representative. The success of COVID-19 vaccines has underscored the transformative potential of mRNA in RNA therapeutics. Within the RNA family, there is another unique type known as circRNA. This single-stranded closed-loop RNA molecule offers notable advantages over mRNA, including enhanced stability and prolonged protein expression, which may significantly impact therapeutic strategies. Furthermore, circRNA plays a pivotal role in the pathogenesis of various diseases, such as cancers, autoimmune disorders, and cardiovascular diseases, making it a promising clinical intervention target. Despite these benefits, the application of circRNA in clinical settings remains underexplored. This review provides a comprehensive overview of the current state of synthetic circRNA therapeutics, focusing on its synthesis, optimization, delivery, and diverse applications. It also addresses the challenges impeding the advancement of circRNA therapeutics from bench to bedside. By summarizing these aspects, the review aims to equip researchers with insights into the ongoing developments and future directions in circRNA therapeutics. Highlighting both the progress and the existing gaps in circRNA research, this review offers valuable perspectives for advancing the field and guiding future investigations.

Metabolomics combined with proteomics reveals phytotoxic effects of norfloxacin under drought stress on Oryza sativa

In recent decades, plants enduring abiotic stresses such as drought and chemical stresses. Currently, the mechanism of combined antibiotic and drought stress response and its impact on crop growth and food security remains poorly understood. Here, the mechanism of stress responses under the exposure of norfloxacin (NF) and drought (D) individually and in combination (DNF) were explored on rice (Oryza sativa) cultivar Hanyou73 through proteomics and metabolomic analysis. All treatments adversely affected chlorophyll fluorescence kinetics, antioxidant enzyme activities, rice grain composition and yield. The results showed that in DNF the antibiotic was accumulated 627% more than NF treatment in rice grains while in leaves there was no significant difference under both treatments. The proteomic revealed that differentially expressed identified proteins were involved in carbohydrate metabolism, amino acid metabolism, photosynthesis and mRNA binding. However, the metabolomics results showed that the abundance of metabolites related to RNA biosynthesis and amino acid metabolism were more affected. The disruptions caused in rice plant under DNF treatment become more severe, this makes it more susceptible than individual D and NF treatment. These findings improve our knowledge about the response of rice plant to cope with antibiotic contamination alone and in combination with drought.

A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements

Internal ribosomal entry sites (IRESs) recruit the ribosome to promote translation, typically in an m7G cap-independent manner. Although IRESs are well-documented in viral genomes, they have also been reported in mammalian transcriptomes, where they have been proposed to mediate cap-independent translation of mRNAs. However, subsequent studies have challenged the idea of these "cellular" IRESs. Current methods for screening and discovering IRES activity rely on a bicistronic reporter assay, which is prone to producing false positive signals if the putative IRES sequence has a cryptic promoter or cryptic splicing sites. Here, we report an assay for screening IRES activity using a genetically encoded circular RNA comprising a split nanoluciferase (nLuc) reporter. The circular split nLuc reporter is less susceptible to the various sources of false positives that adversely affect the bicistronic IRES reporter assay and provides a streamlined method for screening IRES activity. Using the circular split nLuc reporter, we find that nine reported cellular IRESs have minimal IRES activity. Overall, the circular split nLuc reporter offers a simplified approach for identifying and validating IRESs and exhibits reduced propensity for producing the types of false positives that can occur with the bicistronic reporter assay.

Dynamic conformation: Marching toward circular RNA function and application

Circular RNA is a group of covalently closed, single-stranded transcripts with unique biogenesis, stability, and conformation that play distinct roles in modulating cellular functions and also possess a great potential for developing circular RNA-based therapies. Importantly, due to its circular conformation, circular RNA generates distinct intramolecular base pairing that is different from the linear transcript. In this perspective, we review how circular RNA conformation can affect its turnover and modes of action, as well as what factors can modulate circular RNA conformation. We also discuss how understanding circular RNA conformation can facilitate learning about their functions as well as the remaining technological issues to further address their conformation. These efforts will ultimately inform the design of circular RNA-based platforms for biomedical applications.

Role of circular RNAs in preeclampsia (Review)

Preeclampsia (PE) is a hypertensive disorder of pregnancy characterized by new-onset hypertension and proteinuria after 20 weeks of gestation, which affects 3-8% of pregnant individuals worldwide each year. Prevention, diagnosis and treatment of PE are some of the most important problems faced by obstetrics. There is growing evidence that circular RNAs (circRNAs) are involved in the pathogenesis of PE. The present review summarizes the research progress of circRNAs and then describes the expression patterns of circRNAs in PE and their functional mechanisms affecting PE development. The role of circRNAs as biomarkers for the diagnosis of PE, and the research status of circRNAs in PE are summarized in the hope of finding novel strategies for the prevention and treatment of PE.

The role of non-coding RNAs in fibroblast-like synoviocytes in rheumatoid arthritis

Rheumatoid arthritis (RA) is an inflammatory autoimmune disease characterized by synovial hyperplasia, and fibroblast-like synoviocytes (FLSs) constitute the majority of cells in the synovial tissue, playing a crucial role in the onset of RA. Dysregulation of FLSs function is a critical strategy in treating joint damage associated with RA. Non-coding RNAs, a class of RNA molecules that do not encode proteins, participate in the development of various diseases. This article aims to review the progress in the study of long non-coding RNAs, microRNAs, and circular RNAs in FLSs. Non-coding RNAs are involved in the pathogenesis of RA, directly or indirectly regulating FLSs' proliferation, migration, invasion, apoptosis, and inflammatory responses. Furthermore, non-coding RNAs also influence DNA methylation and osteogenic differentiation in FLSs. Therefore, non-coding RNAs hold promise as biomarkers for diagnosing RA. Targeting non-coding RNAs in FLSs locally represents a potential strategy for future therapies in RA.

Non-canonical translation in cancer: significance and therapeutic potential of non-canonical ORFs, m6A-modification, and circular RNAs

Translation is a decoding process that synthesizes proteins from RNA, typically mRNA. The conventional translation process consists of four stages: initiation, elongation, termination, and ribosome recycling. Precise control over the translation mechanism is crucial, as dysregulation in this process is often linked to human diseases such as cancer. Recent discoveries have unveiled translation mechanisms that extend beyond typical well-characterized components like the m7G cap, poly(A)-tail, or translation factors like eIFs. These mechanisms instead utilize atypical elements, such as non-canonical ORF, m6A-modification, and circular RNA, as key components for protein synthesis. Collectively, these mechanisms are classified as non-canonical translations. It is increasingly clear that non-canonical translation mechanisms significantly impact the various regulatory pathways of cancer, including proliferation, tumorigenicity, and the behavior of cancer stem cells. This review explores the involvement of a variety of non-canonical translation mechanisms in cancer biology and provides insights into potential therapeutic strategies for cancer treatment.

Efficient circularization of protein-encoding RNAs via a novel cis-splicing system

Circular RNAs (circRNAs) have emerged as a promising alternative to linear mRNA, owing to their unique properties and potential therapeutic applications, driving the development of novel approaches for their production. This study introduces a cis-splicing system that efficiently produces circRNAs by incorporating a ribozyme core at one end of the precursor, thereby eliminating the need for additional spacer elements between the ribozyme and the gene of interest (GOI). In this cis-splicing system, sequences resembling homologous arms at both ends of the precursor are crucial for forming the P9.0 duplex, which in turn facilitates effective self-splicing and circularization. We demonstrate that the precise recognition of the second transesterification site depends more on the structural characteristics of P9.0 adjacent to the ωG position than on the nucleotide composition of the P9.0-ωG itself. Further optimization of structural elements, like P10 and P1-ex, significantly improves circularization efficiency. The circRNAs generated through the cis-splicing system exhibit prolonged protein expression and minimal activation of the innate immune response. This study provides a comprehensive exploration of circRNA generation via a novel strategy and offers valuable insights into the structural engineering of RNA, paving the way for future advancements in circRNA-based applications.

Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have emerged as pivotal players in gene regulation. Our understanding of circRNAs has greatly expanded over the last decade, with studies elucidating their biology and exploring their therapeutic applications. In this review, we provide an overview of the current understanding of circRNA biogenesis, outline their mechanisms of action in cancer, and assess their clinical potential as biomarkers. Furthermore, we discuss circRNAs as a potential therapeutic strategy, including recent advances in circRNA production and translation, along with proof-of-concept preclinical studies of cancer vaccines.

CircHTT(2,3,4,5,6) - co-evolving with the HTT CAG-repeat tract - modulates Huntington's disease phenotypes

Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.

Circular RNA-based therapy provides sustained and robust neuroprotection for retinal ganglion cells

Ocular neurodegenerative diseases like glaucoma lead to progressive retinal ganglion cell (RGC) loss, causing irreversible vision impairment. Neuroprotection is needed to preserve RGCs across debilitating conditions. Nerve growth factor (NGF) protein therapy shows efficacy, but struggles with limited bioavailability and a short half-life. Here we explore a novel approach to address this deficiency by utilizing circular RNA (circRNA)-based therapy. We show that circRNAs exhibit an exceptional capacity for prolonged protein expression and circRNA-expressed NGF protects cells from glucose deprivation. In a mouse optic nerve crush model, lipid nanoparticle (LNP)-formulated circNGF administered intravitreally protects RGCs and axons from injury-induced degeneration. It also significantly outperforms NGF protein therapy without detectable retinal toxicity. Furthermore, single-cell transcriptomics revealed LNP-circNGF's multifaceted therapeutic effects, enhancing genes related to visual perception while reducing trauma-associated changes. This study signifies the promise of circRNA-based therapies for treating ocular neurodegenerative diseases and provides an innovative intervention platform for other ocular diseases.

Developing an enhanced chimeric permuted intron-exon system for circular RNA therapeutics

Rationale: Circular RNA (circRNA) therapeutics hold great promise as an iteration strategy in messenger RNA (mRNA) therapeutics due to their inherent stability and durable protein translation capability. Nevertheless, the efficiency of RNA circularization remains a significant constraint, particularly in establishing large-scale manufacturing processes for producing highly purified circRNAs. Hence, it is imperative to develop a universal and more efficient RNA circularization system when considering synthetic circRNAs as therapeutic agents with prospective clinical applications. Methods: We initially developed a chimeric RNA circularization system based on the original permuted intron-exon (PIE) and subsequently established a high-performance liquid chromatography (HPLC) method to obtain highly purified circRNAs. We then evaluated their translational ability and immunogenicity. The circRNAs expressing human papillomavirus (HPV) E7 peptide (43-62aa) and dimerized receptor binding domain (dRBD) from SARS-CoV-2 were encapsulated within lipid nanoparticles (LNPs) as vaccines, followed by an assessment of the in vivo efficacy through determination of antigen-specific T and B cell responses, respectively. Results: We have successfully developed a universal chimeric permuted intron-exon system (CPIE) through engineering of group I self-splicing introns derived from Anabaena pre-tRNALeu or T4 phage thymidylate (Td) synthase gene. Within CPIE, we have effectively enhanced RNA circularization efficiency. By utilizing size exclusion chromatography, circRNAs were effectively separated, which exhibit low immunogenicity and sustained potent protein expression property. In vivo data demonstrate that the constructed circRNA vaccines can elicit robust immune activation (B cell and/or T cell responses) against tumor or SARS-CoV-2 and its variants in mouse models. Conclusions: Overall, we provide an efficient and universal system to synthesize circRNA in vitro, which has extensive application prospect for circRNA therapeutics.

Noncanonical microprotein regulation of immunity

The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.