RNA interference in the era of nucleic acid therapeutics

Advances in locally administered nucleic acid therapeutics

Nucleic acid drugs represent the latest generation of precision therapeutics, holding significant promise for the treatment of a wide range of intractable diseases. Delivery technology is crucial for the clinical application of nucleic acid drugs. However, extrahepatic delivery of nucleic acid drugs remains a significant challenge. Systemic administration often fails to achieve sufficient drug enrichment in target tissues. Localized administration has emerged as the predominant approach to facilitate extrahepatic delivery. While localized administration can significantly enhance drug accumulation at the injection sites, nucleic acid drugs still face biological barriers in reaching the target lesions. This review focuses on non-viral nucleic acid drug delivery techniques utilized in local administration for the treatment of extrahepatic diseases. First, the classification of nucleic acid drugs is described. Second, the current major non-viral delivery technologies for nucleic acid drugs are discussed. Third, the bio-barriers, administration approaches, and recent research advances in the local delivery of nucleic acid drugs for treating lung, brain, eye, skin, joint, and heart-related diseases are highlighted. Finally, the challenges associated with the localized therapeutic application of nucleic acid drugs are addressed.

Molecular mechanisms of lncRNA NEAT1 in the pathogenesis of liver-related diseases, with special focus on therapeutic approaches

Liver diseases are a major worldwide health concern, with high rates of dysfunction and mortality. In recent years, a variety of lncRNAs have been studied and discovered to be engaged in numerous cellular-level regulatory mechanisms as competing endogenous RNAs (ceRNAs), which play a significant role in the development of liver-related diseases. A class of RNA molecules known as lncRNAs, which are over 200 nucleotides long, do not translate into proteins. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a type of lncRNA that has a critical function in paraspeckles formation and stability. NEAT1 levels are consistently found to be higher than normal in a number of different types of diseases, as well as patients who have high levels of NEAT1 expression often have a poor prognosis. The significance and mode of action of NEAT1 in liver illnesses, such as nonalcoholic fatty liver disease (NAFLD), alcohol-related liver disease (ALD), liver fibrosis/cirrhosis, hepatocellular carcinoma (HCC), viral hepatitis, and liver injury, are becoming more widely known. In this review, we highlighted significant recent studies concerning the various roles of lncRNA NEAT1 in hepatic diseases. As well as, we reviewed novel therapeutic potential of lncRNAs in several liver-related diseases.

Mechanistic insights into RNA cleavage by human Argonaute2-siRNA complex

In animals, AGO-clade Argonaute proteins utilize small interfering RNAs (siRNAs) as guides to recognize target with complete complementarity, resulting in target RNA cleavage that is a critical step for target silencing. These proteins feature a constricted nucleic acid-binding channel that limits base pairing between the guide and target beyond the seed region. How the AGO-siRNA complexes overcome this structural limitation and achieve efficient target cleavage remains unclear. We performed cryo-electron microscopy of human AGO-siRNA complexes bound to target RNAs of increasing lengths to examine the conformational changes associated with target recognition and cleavage. Initially, conformational transition propagates from the opening of the PAZ domain and extends through a repositioning of the PIWI-L1-N domain toward the binding channel, facilitating the capture of siRNA-target duplex. Subsequent extension of base pairing drives the downward movement of the PIWI-L1-N domain to enable catalytic activation. Finally, further base pairing toward the 3' end of siRNA destabilizes the PAZ-N domain, resulting in a "uni-lobed" architecture, which might facilitate the multi-turnover action of the AGO-siRNA enzyme complex. In contrast to PIWI-clade Argonautes, the "uni-lobed" structure of the AGO complex makes multiple contacts with the target in the central region of the siRNA-target duplex, positioning it within the catalytic site. Our findings shed light on the stepwise mechanisms by which the AGO-siRNA complex executes target RNA cleavage and offer insights into the distinct operational modalities of AGO and PIWI proteins in achieving such cleavage.

Targeted Collagen Degradation by an MRI Probe Facilitates siRNA Delivery for Sequential Theranostics in Pulmonary Fibrosis

Pulmonary fibrosis (PF) is characterized by dense collagen and mucus barriers that significantly limit drug delivery to the lungs. Clearing the collagen barrier can enhance drug delivery efficiency. Nevertheless, the heterogeneity of collagen states among patients poses a challenge. Therefore, real-time monitoring of the collagen clearance status is essential for PF personalized therapy. Herein, sequential theranostic platforms are proposed for collagen targeting and magnetic resonance imaging (MRI) monitoring to guide small interfering RNA (siRNA) delivery. First, for collagen barrier targeting-degrading, collagenase is conjugated with a collagen-targeting peptide capable of chelating the MRI contrast agent Gd(III), forming Col I T-D. This allows real-time, noninvasive MRI monitoring of the dynamic collagen clearance process. Second, guided by MRI, the zwitterionic polymer-based siRNA vectors (siTGF-β1@TZ) with mucus-penetrating and fibroblast-targeting capabilities are inhaled under an optimal state of collagen barrier. The sequential application of Col I T-D and siTGF-β1@TZ demonstrates significant lesion enrichment and therapeutic efficacy in PF treatment. Collectively, this study provides a novel perspective on dynamically monitoring collagen clearance status and guiding the sequential delivery of siRNA, offering a promising strategy for personalized PF therapy.

siRNA self-assembled carboxymethyl chitosan and pymetrozine nucleic pesticides for enhanced control of Sogatella furcifera: Bidirectional transduction and detoxification inhibition

Sogatella furcifera (Horváth) is a significant migratory pest in southeast Asia and northern Australia, exhibiting a notable resistance to the conventional insecticides, and RNAi pesticide is a promising approach for managing resistance. However, the poor stability and difficulty in delivery hinders its wide application. Here, we present a self-assembled siRNAs, carboxymethyl chitosan (CMCS) and pymetrozine complex (abbreviated as PM-CMCS/siRNAs micro-complex) to facilitate the control of S. furcifera in rice. When the transcription factors USP and KrH1 were interfered with dsUSP or dsKr-H1, a mortality of 84.4 % ~ 88.9 % was observed at a concentration of 150 μg/mL of pymetrozine, indicating a potential strategy for managing pymetrozine resistance. With the envelope of CMCS, the micro-complex effectively enhances the siRNA stability >96 h, downregulates the expression of USP, KrH1, and CYP6FJ3, leading to a mortality of 100 % at 100 μg/mL pymetrozine. Moreover, the time-dependent disintegration of micro-complex induces the release of lesser PM-CMCS/siRNAs, allowing that more fluorescently labeled complexes were enriched in the phloem of rice via the apoplastic pathway. The integration of PM-CMCS/siRNAs enable precise enrichment in phloem and effective management of pest resistance by silencing their detoxification genes, and promises an environmental-friendly strategy for controlling devastating pest.

Metabolic Stability and Targeted Delivery of Oligonucleotides: Advancing RNA Therapeutics Beyond The Liver

Oligonucleotides have emerged as a formidable new class of nucleic acid therapeutics. Fully modified oligonucleotides exhibit enhanced metabolic stability and display successful clinical applicability for targets formerly considered "undruggable". Accumulating studies show that conjugation to targeting modalities of stabilized oligonucleotides, especially small interfering RNAs (siRNAs), has enabled robust delivery to intended cells/tissues. However, the major challenge in the field has been the stability and targeted delivery of oligonucleotides (siRNAs and antisense oligonucleotides (ASOs)) to extrahepatic tissues. In this Perspective, we review chemistry innovations and emerging delivery approaches that have revolutionized oligonucleotide drug discovery and development. We explore findings from both academia and industry that highlight the potential of oligonucleotides for indications involving different extrahepatic organs─including skeletal muscles, brain, lungs, skin, heart, adipose tissue, and eyes. In all, continued advances in chemistry coupled with conjugation-based approaches or novel administration routes will further advance the delivery of oligonucleotides to extrahepatic tissues.

All-In-One Gadolinium-Doxorubicin Nanoassemblies for Spatial Delivery and Chemoresistance Reversal in Tumor Microenvironments

Efficiently overcoming chemoresistance in tumor microenvironments remains a critical hurdle in cancer therapy due to tumor heterogeneity, limited drug penetration, and adaptive resistance mechanisms. Herein, we report the design and application of all-in-one gadolinium-doxorubicin nanoassemblies (GDNAs) for spatially targeted delivery and chemoresistance reversal. These multifunctional nanoassemblies integrate a lanthanide-based component for real-time imaging and doxorubicin for chemotherapy, coupled with bioinformatics-guided small interfering RNAs (siRNAs) to silence key resistance-associated genes such as BCL2 and BIRC5. The GDNAs demonstrate enhanced tumor penetration and specificity for chemoresistant cells, achieving deep tissue delivery and synergistic effects in human-derived organoids and xenograft breast cancer models. Remarkably, GDNAs significantly reduce tumor viability and growth while attenuating invasive potential, showcasing superior therapeutic efficacy compared to conventional treatments. Comprehensive preclinical evaluations confirm their biocompatibility and low systemic toxicity, underscoring the translational potential of this platform. This work introduces a paradigm-shifting strategy by integrating imaging, targeted therapy, and gene silencing to address chemoresistance, offering a versatile approach for personalized cancer treatment.

Familial chylomicronemia syndrome and treatments to target hepatic APOC3 mRNA

Familial chylomicronemia syndrome (FCS) is a rare, recessive monogenic disorder characterized by severely elevated plasma triglyceride (TG) levels due to absent or markedly impaired lipoprotein lipase activity, leading to a greatly increased risk of acute pancreatitis. Naturally occurring very low levels of apoC-III are associated with low TG levels; thus, apoC-III is a target for TG lowering, and therapies have been developed to reduce apoC-III. Strategies to inhibit hepatic apoC-III synthesis include antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs). In the last decade, technologies have been developed to enhance hepatic delivery of these potential therapeutic agents by conjugation of the ligand triantennary N-acetyl galactosamine to ASO and siRNA for receptor-mediated uptake by hepatocytes, where apoC-III is predominantly expressed. Enhanced delivery of these pharmacological agents to the target tissue has been found to support lower and/or less frequent dosing with consequent lower total systemic exposure. One antisense agent, the ASO olezarsen, is now approved by the US Food and Drug Administration (FDA) as an adjunct to diet to lower triglycerides in adults with FCS, and the other, the siRNA plozasiran, is in late-stage clinical development. Both agents have shown effectiveness in reducing both apoC-III and TG levels across several study populations. Reduced TG, lower rates of acute pancreatitis events, and similar proportions of adverse events in placebo and treated patients were recently demonstrated in placebo-controlled phase 3 trials of patients with FCS treated with olezarsen in Balance and with plozasiran in PALISADE. This review discusses causes and consequences of FCS and the rationale and progress made in developing APOC3 RNA-targeted therapeutics for the treatment of FCS.

Therapeutic potential of synthetic microRNA mimics based on the miR-15/107 consensus sequence

MicroRNA expression is frequently suppressed in cancer, and previously we demonstrated coordinate downregulation of multiple related microRNAs of the miR-15/107 group in malignant pleural mesothelioma (PM). From an alignment of the miR-15 family and the related miR-103/107, we derived a consensus sequence and used this to generate synthetic mimics. The synthetic mimics displayed tumour suppressor activity in PM cells in vitro, which was greater than that of a mimic based on the native miR-16 sequence. These mimics were also growth inhibitory in cells from non-small cell lung (NSCLC), prostate, breast and colorectal cancer, and sensitised all cell lines to the chemotherapeutic drug gemcitabine. The increased activity corresponded to enhanced inhibition of the expression of target genes and was associated with an increase in predicted binding to target sites, and proteomic analysis revealed a strong effect on proteins involved in RNA and DNA processes. Applying the novel consensus mimics to xenograft models of PM and NSCLC in vivo using EGFR-targeted nanocells loaded with mimic led to tumour growth inhibition. These results suggest that mimics based on the consensus sequence of the miR-15/107 group have therapeutic potential in a range of cancer types.

Streamlining Bacterial Gene Regulation via Nucleic Acid Delivery with Gold Nanoclusters

Delivery of exogenous nucleic acids (NAs) for gene regulation in bacteria, bypassing the barrier of the cell wall, is essential for advancing fundamental microbiology and genetic engineering, and the treatment of bacterial diseases. However, current methods that rely on electrical or chemical interventions are limited by their complexity, specialized expertise, and laboratory-specific instrumentation. This study explores the capability of gold nanoclusters (AuNCs) as carriers for delivering small-interfering RNA and antisense oligonucleotides into bacteria for targeted gene regulation while shielding them from degradation during transport. By enhancing the cytoplasmic membrane permeability, the AuNCs enable efficient internalization of NAs into both Gram-positive and Gram-negative bacteria while exerting negligible influence on bacterial activity. It is demonstrated that the rationally designed NAs can be released from the AuNCs within bacteria, enabling ~70% knockdown of mecA in Methicillin-resistant Staphylococcus aureus (MRSA). This significantly reduces MRSA's antibiotic resistance and enhances oxacillin treatment efficacy. Furthermore, the successful silencing of ligA in Escherichia coli and pilQ in Pseudomonas aeruginosa highlights the broad adaptability of the approach across diverse bacterial species. The AuNCs-based next-generation NA delivery system has the potential to transform bacterial gene regulation-previously restricted to laboratory settings-into a versatile and scalable solution for real-world application.

Engineered Bacterial Outer Membrane Vesicles-Based Doxorubicin and CD47-siRNA Co-Delivery Nanoplatform Overcomes Immune Resistance to Potentiate the Immunotherapy of Glioblastoma

Apart from the blood-brain barrier (BBB), the efficacy of immunotherapy for glioblastoma (GBM) is limited by the presence of intrinsic and adaptive immune resistance, implying that co-delivery of various immunotherapeutic agents or simultaneous regulation of different cells is urgently needed. Bacterial outer membrane vesicles (OMVs) offer a unique advantage in the treatment of GBM, owing to their multifunctional properties as carriers and immune adjuvants and their ability to cross the BBB. However, traditional OMVs can lead to toxic side effects and disruption of tight junctions in the BBB. Therefore, to enhance the in vivo safety and targeting capability of OMVs, we introduced engineered OMVs to reduce toxicity and further constructed a modularly assembled nanoplatform by performing simple peptide modifications. This nanoplatform demonstrates satisfactory biosafety and is able to continuously cross the BBB and target GBM with the assistance of Angiopep-2. Subsequently, immunogenic substances on OMVs, along with carried small-interfering RNA (siRNA) and doxorubicin, can promote and enhance the reprogramming and phagocytic abilities of macrophages and microglia, respectively, and increase the immunogenicity of GBM, ultimately overcoming GBM immune resistance to enhance the efficacy of immunotherapy. This OMVs-based nanoplatform provides a new paradigm and insights into the development of immunotherapy for GBM.

Liver-specific inactivation of Cideb improves metabolic profiles and ameliorates steatohepatitis and fibrosis in animal models for MASH

Germline mutations of CIDEB, a lipid droplets (LDs)-associated protein, confer protection against various liver diseases in humans. It remains to be determined whether liver-specific inhibition of CIDEB will bring clinical benefits. We aim to establish pharmacological proof of concept by testing GalNAc-conjugated Cideb surrogate siRNAs in respective animal models of obesity and MASH and to develop siRNA drug candidates for clinical investigations. Surrogate siRNAs targeting mouse Cideb were designed and evaluated via a panel of assays. Concurrently, humanized CIDEB knock-in mice were generated as a research tool to facilitate human therapeutic siRNA discovery. In vivo administration of the surrogate siRNAs was conducted in the diet-induced obesity (DIO) model and CDAA-HFD model of MASH. In the DIO model, Cideb knockdown led to significant reductions of serum total cholesterol (TC) and triglyceride (TG) levels, a significant decrease in hepatic macro-steatosis and notable weight loss. In the CDAA-HFD model, Cideb siRNA treatment significantly reduced liver TC and TG levels. Furthermore, remarkable reductions of hepatic steatosis and the composite NAS score were observed with a concomitant amelioration of liver fibrosis. Transcriptome analyses revealed that integrin pathways may contribute to the major pharmacological activities upon Cideb inactivation beyond lipid metabolism. CIDEB exhibits significant potential as a therapeutic target for the treatment of MASH. Liver-targeting siRNA candidates are under development for therapeutic hypothesis testing in humans.

Lactylation-Driven HECTD2 Limits the Response of Hepatocellular Carcinoma to Lenvatinib

Drug resistance remains a major hurdle for the therapeutic efficacy of lenvatinib in hepatocellular carcinoma (HCC). However, the underlying mechanisms remain largely undetermined. Unbiased proteomic screening is performed to identify the potential regulators of lenvatinib resistance in HCC. Patient-derived organoids, patient-derived xenograft mouse models, and DEN/CCl4 induced HCC models are constructed to evaluate the effects of HECTD2 both in vitro and in vivo. HECTD2 is found to be highly expressed in lenvatinib-resistant HCC cell lines, patient tissues, and patient-derived organoids and xenografts. In vitro and in vivo experiments demonstrated that overexpression of HECTD2 limits the response of HCC to lenvatinib treatment. Mechanistically, HECTD2 functions as an E3 ubiquitin ligase of KEAP1, which contributes to the degradation of KEAP1 protein. Subsequently, the KEAP1/NRF2 signaling pathway initiates the antioxidative response of HCC cells. Lactylation of histone 3 on lysine residue 18 facilitates the transcription of HECTD2. Notably, a PLGA-PEG nanoparticle-based drug delivery system is synthesized, effectively targeting HECTD2 in vivo. The NPs achieved tumor-targeting, controlled-release, and biocompatibility, making them a promising therapeutic strategy for mitigating lenvatinib resistance. This study identifies HECTD2 as a nanotherapeutic target for overcoming lenvatinib resistance, providing a theoretical basis and translational application for HCC treatment.

General Platform for Efficient and Modular Assembly of GalNAc-siRNA Conjugates via Primary Amines and o-Nitrobenzyl Alcohol Cyclization Photoclick Chemistry Enabling Rapid Access to Therapeutic Oligonucleotides

Oligonucleotide-based therapies, especially ligand-conjugated siRNAs, offer significant therapeutic potential for a wide array of diseases. However, conventional solid-phase synthesis and current postsynthetic in-solution conjugation methods face notable challenges related to efficiency, accessibility, and the scalability of diverse ligand-oligonucleotide conjugates. Herein, we introduce a novel strategy for highly efficient, rapid, and modular assembly of GalNAc-siRNA conjugates based on light-induced primary amine and o-nitrobenzyl alcohol cyclization (PANAC) chemistry. Leveraging the advantages of PANAC photoclick chemistry and modular conjugation linkers, our method enables the direct assembly of trivalent GalNAc (tGalNAc) with commercially available primary-amine-modified siRNAs. This approach demonstrates the efficient and rapid assembly of therapeutically relevant oligonucleotides with ligands of interest, offering operational simplicity and practicality; thus, it effectively overcomes the limitations of existing methods. More importantly, the developed siRNA-tGalNAc conjugates showed a robust gene silencing effect superior to the parent siRNA conjugate, highlighting the effectiveness of our method in generating and screening siRNA conjugates to enhance in vivo potency. Overall, our method enables modular and rapid assembly of therapeutically relevant oligonucleotide-tGalNAc conjugates using readily accessible oligonucleotides and commercially available tGalNAc-amine ligands. This approach expands the toolkit for generating ligand-oligonucleotide conjugates, providing a general and efficient platform with broad applicability, thereby advancing the optimization and development of oligonucleotide-based therapeutics.

Natural, modified and conjugated carbohydrates in nucleic acids

Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.

Modulation of TTR Gene Expression in the Eye using Modified Duplex RNAs

Small interfering RNAs (siRNAs) are a proven therapeutic approach for controlling gene expression in the liver. Expanding the clinical potential of RNA interference (RNAi) requires developing strategies to enhance delivery to extra-hepatic tissues. In this study we examine inhibiting transthyretin (TRR) gene expression by short interfering RNAs (siRNAs) in the eye. Anti-TTR siRNAs have been developed as successful drugs to treat TTR amyloidosis. When administered systemically, anti-TTR siRNAs alleviate symptoms by blocking TTR expression in the liver. However, TTR amyloidosis also affects the eye, suggesting a need for reducing ocular TTR gene expression. Here, we demonstrate that C5 and 2'-O-linked lipid-modified siRNAs formulated in saline can inhibit TTR expression in the eye when administered locally by intravitreal (IVT) injection. Modeling suggests that length and accessibility of the lipid chains contributes to in vivo silencing. GalNAc modified anti-dsRNAs also inhibit TTR expression, albeit less potently. These data support lipid modified siRNAs as an approach to treating the ocular consequences of TTR amyloidosis. Inhibition of TTR expression throughout the eye demonstrates that lipid-siRNA conjugates have the potential to be a versatile platform for ocular drug discovery.

Targeted delivery systems of siRNA based on ionizable lipid nanoparticles and cationic polymer vectors

As an emerging therapeutic tool, small interfering RNA (siRNA) had the capability to down-regulate nearly all human mRNAs via sequence-specific gene silencing. Numerous studies have demonstrated the substantial potential of siRNA in the treatment of broad classes of diseases. With the discovery and development of various delivery systems and chemical modifications, six siRNA-based drugs have been approved by 2024. The utilization of siRNA-based therapeutics has significantly propelled efforts to combat a wide array of previously incurable diseases and advanced at a rapid pace, particularly with the help of potent targeted delivery systems. Despite encountering several extracellular and intracellular challenges, the efficiency of siRNA delivery has been gradually enhanced. Currently, targeted strategies aimed at improving potency and reducing toxicity played a crucial role in the druggability of siRNA. This review focused on recent advancements on ionizable lipid nanoparticles (LNPs) and cationic polymer (CP) vectors applied for targeted siRNA delivery. Based on various types of targeted modifications, we primarily described delivery systems modified with receptor ligands, peptides, antibodies, aptamers and amino acids. Finally, we discussed the challenges and opportunities associated with siRNA delivery systems based on ionizable LNPs and CPs vectors.

A circRNA-mRNA pairing mechanism regulates tumor growth and endocrine therapy resistance in ER-positive breast cancer

The molecular mechanisms underlying estrogen receptor (ER)-positive breast carcinogenesis and drug resistance remain incompletely understood. Elevated expression of CCND1 is linked to enhanced invasiveness, poorer prognosis, and resistance to drug therapies in ER-positive breast cancer. In this study, we identify a highly expressed circular RNA (circRNA) derived from FOXK2, called circFOXK2, which plays a key role in stabilizing CCND1 mRNA, thereby promoting cell cycle progression, cell growth, and endocrine therapy resistance in ER-positive breast cancer cells. Mechanistically, circFOXK2 binds directly to CCND1 mRNA via RNA-RNA pairing and recruits the RNA-binding protein ELAVL1/HuR, stabilizing the CCND1 mRNA and enhancing CCND1 protein levels. This results in activation of the CCND1-CDK4/6-p-RB-E2F signaling axis, driving the transcription of downstream E2F target genes and facilitating the G1/S transition during cell cycle progression. Notably, targeting circFOXK2 with antisense oligonucleotide (ASO-circFOXK2) suppresses ER-positive breast cancer cell growth both in vitro and in vivo. Moreover, combination therapy with ASO-circFOXK2 and tamoxifen exhibits synergistic effects and restores tamoxifen sensitivity in tamoxifen-resistant cells. Clinically, high circFOXK2 expression is positively correlated with CCND1 levels in both ER-positive breast cancer cell lines and patient tumor tissues. Overall, our findings reveal the critical role of circFOXK2 in stabilizing the oncogene CCND1 and promoting cancer progression, positioning circFOXK2 as a potential therapeutic target for ER-positive breast cancer in clinical settings.

Preclinical testing of antiviral siRNA therapeutics delivered in lipid nanoparticles in animal models - a comprehensive review

The advent of RNA interference (RNAi) technology through the use of short-interfering RNAs (siRNAs) represents a paradigm shift in the fight against viral infections. siRNAs, with their ability to directly target and silence specific posttranscriptional genes, offer a novel mechanism of action distinct from that of traditional pharmacotherapeutics. This review delves into the growing field of siRNA therapeutics against viral infections, highlighting their critical role in contemporary antiviral strategies. Importantly, this review will solely focus on the use of lipid nanoparticles (LNPs) as the ideal antiviral siRNA delivery agent for use in vivo. We discuss the challenges of siRNA delivery and how LNPs have emerged as a pivotal solution to enhance antiviral efficacy. Specifically, this review focuses on work that have preclinically tested LNP formulated siRNA on virus infection animal models. Since the COVID-19 pandemic, we have witnessed a resurgence in the field of RNA-based therapies, including siRNAs against viruses including, SARS-CoV-2. Notably, the critical importance of LNPs as the ideal carrier for precious 'RNA cargo' can no longer be ignored with the advent of mRNA-LNP based COVID-19 vaccines. siRNA-based therapeutics represents an emerging class of anti-infective drugs with a foreseeable future as suitable antiviral agents.

The structural basis for RNA slicing by human Argonaute2

Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene silencing through RNA interference (RNAi), which is essential for many eukaryotes and the basis for new clinical therapies. Despite this importance, structural information on eukaryotic AGOs in a fully paired, slicing-competent conformation-hypothesized to be intrinsically unstable-has been lacking. Here, we present the cryogenic electron microscopy structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable this conformation. Critically, the N domain of AGO rotates to allow the RNA full access to the central channel and forms contacts that license rapid slicing. Moreover, a conserved loop in the PIWI domain secures the RNA near the active site to enhance slicing rate and specificity. These results explain how AGO accommodates targets possessing pairing specificity typically observed in biological and clinical slicing substrates.

Lipid nanoparticle delivery of siRNA to dorsal root ganglion neurons to treat pain

Sensory neurons within the dorsal root ganglion (DRG) are the primary trigger of pain, relaying activity about noxious stimuli from the periphery to the central nervous system; however, targeting DRG neurons for pain management has remained a clinical challenge. Here, we demonstrate the use of lipid nanoparticles (LNPs) for effective intrathecal delivery of small interfering RNA (siRNA) to DRG neurons, achieving potent silencing of the transient receptor potential vanilloid 1 (TRPV1) ion channel that is predominantly expressed in nociceptor sensory neurons. This leads to a reversible interruption of heat-, capsaicin-, and inflammation-induced nociceptive conduction, as observed by behavioral outputs. Our work provides a proof-of-concept for intrathecal siRNA therapy as a novel and selective analgesic modality.

Application of Strontium Chloride Hexahydrate to Synthesize Strontium-Substituted Carbonate Apatite as a pH-Sensitive, Biologically Safe, and Highly Efficient siRNA Nanocarrier

Naked siRNAs are sensitive to enzymatic degradation, phagocytic entrapment, quick renal excretion, membrane impermeability, endosomal escape, and off-target effects. Designing a safe and efficient nanocarrier for siRNA delivery to the target site without toxicity remains a significant hurdle in gene therapy. CA is a unique derivative of hydroxyapatite and a highly pH-sensitive nanocarrier with strong particle aggregation and a high polydispersity index. Strontium (Sr2+), a group two divalent metal in the periodic table, has been reported for substituting calcium (Ca2+) ions from the apatite lattice and limiting particle growth/aggregation. This study used strontium chloride hexahydrate (SrCl2·6H2O) salt to develop a Sr-substituted CA (Sr-CA) nanocarrier with ∼30 nm size, spherical shape, less aggregation, homodispersity, and a fair anionic charge. Sr-CA demonstrated a large surface area-to-volume ratio, an improved cargo loading efficiency, and enhanced cellular uptake in HEK-293 cells. Moreover, Sr-CA is a pH-responsive nanocarrier responsible for its long physiological stability, efficient endosomal escape, and optimal cargo delivery within cells. These NPs have differential effects on MAPK1, MAP2K4, PIK3Ca, CAMK4, and p53 gene expression in HEK-293 cells without showing any significant cytotoxicity in cell growth properties. Gene silencing by Sr-CA-mediated siRNA delivery against MAPK1, MAP2K4, PIK3Ca, and CAMK4 genes significantly decreased the level of target gene expression and cell survival, demonstrating successful intracellular siRNA delivery in HEK-293 cells. Additionally, biocompatibility testing confirmed the biological safety of the Sr-CA nanocarrier in mice. These findings suggest that Sr-CA nanocarriers are a promising siRNA delivery system, combining high efficiency with pH-sensitive release and excellent biocompatibility, making them a viable option for future therapeutic applications.

Rat Sarcoma Virus Family Genes in Acute Myeloid Leukemia: Pathogenetic and Clinical Implications

Acute myeloid leukemias (AMLs) comprise a group of genetically heterogeneous hematological malignancies that result in the abnormal growth of leukemic cells and halt the maturation process of normal hematopoietic stem cells. Despite using molecular and cytogenetic risk classification to guide treatment decisions, most AML patients survive for less than five years. A deeper comprehension of the disease's biology and the use of new, targeted therapy approaches could potentially increase cure rates. RAS oncogene mutations are common in AML patients, being observed in about 15-20% of AML cases. Despite extensive efforts to find targeted therapy for RAS-mutated AMLs, no effective and tolerable RAS inhibitor has received approval for use against AMLs. The frequency of RAS mutations increases in the context of AMLs' chemoresistance; thus, novel anti-RAS strategies to overcome drug resistance and improve patients' therapy responses and overall survival are the need of the hour. In this article, we aim to update the current knowledge on the role of RAS mutations and anti-RAS strategies in AML treatments.

Stapled Peptides as Inhibitors of mRNA Deadenylation

Therapeutic intervention targeting mRNA typically aims at reducing the levels of disease-causing sequences. Achieving the opposite effect of blocking the destruction of beneficial mRNA remains underexplored. The degradation of mRNA starts with the removal of poly(A) tails, reducing their stability and translational activity, which is mainly regulated by the CCR4-NOT complex. The subunit NOT9 binds various RNA binding proteins, that recruit mRNA in a sequence-specific manner to the CCR4-NOT complex to promote their deadenylation. These RNA binding proteins interact with NOT9 through a helical NOT9 binding motif, which we used as a starting point for development of the hydrocarbon stapled peptide NIP-2. The peptide (KD=60.4 nM) was able to inhibit RNA-binding (IC50=333 nM) as well as the deadenylation activity of the CCR4-NOT complex in vitro while being cell-permeable (cell-permeability EC50=2.44 μM). A co-crystal structure of NIP-2 bound to NOT9 allowed further optimization of the peptide through point mutation leading to NIP-2-H27A-N3 (KD=122 nM) with high cell permeability (cell-permeability EC50=0.34 μM). The optimized peptide was able to inhibit deadenylation of target mRNAs when used in HeLa cells at a concentration of 100 μM, demonstrating the feasibility of increasing mRNA stability.

A dual-locked cyclopeptide-siRNA conjugate for tumor-specific gene silencing

Strategies allowing tumor-selective siRNA delivery while minimizing off-tumor gene silencing effects are highly demanded to advance cancer gene therapy, which however still remain challenging. We herein report a dual-locking bioconjugation approach to address this challenge. A dual-locked cyclopeptide-siRNA conjugate (DPRC) was designed to simultaneously endow siRNA with tumor-targeting properties and tumor-biomarker/visible-light dually controllable action. The DPRC consisted of a programmed death-ligand 1 (PD-L1)-targeting cyclopeptide as a tumor-homing ligand and B-cell lymphoma-2 (Bcl-2)-targeting siRNA as a payload. They were conjugated via a tandem-responsive cleavable linker containing a photocleavable coumarin moiety quenched by naphthylamide through a disulfide linkage. Owing to the interaction between cell-membrane PD-L1 and the cyclopeptide, the DPRC was efficiently taken up by PD-L1-positive cancer cells. Notably, the internalized DPRC could only release and restore the gene silencing activity of siBcl-2 upon GSH-mediated disulfide bond breakage followed by visible light irradiation on the coumarin moiety to induce photo-cleavage. The released siBcl-2 further silenced the expression of anti-apoptotic Bcl-2 to suppress cancer cell growth. We demonstrated the tumor-targeting and dual-locked action of siRNA by the DPRC in both two-dimensional and three-dimensional cancer cell cultures. This study thus presents a novel strategy for precise tumor-specific gene silencing by siRNA.

Noncanonical role of ALAS1 as a heme-independent inhibitor of small RNA-mediated silencing

microRNAs (miRNAs) and small interfering RNAs (siRNAs) are 21- to 22-nucleotide RNAs that guide Argonaute-class effectors to targets for repression. In this work, we uncover 5-aminolevulinic acid synthase 1 (ALAS1), the initiating enzyme for heme biosynthesis, as a general repressor of miRNA accumulation. Although heme is known to be a positive cofactor for the nuclear miRNA processing machinery, ALAS1-but not other heme biosynthesis enzymes-limits the assembly and activity of Argonaute complexes under heme-replete conditions. This involves a cytoplasmic role for ALAS1, previously considered inactive outside of mitochondria. Moreover, conditional depletion of ALAS activity from mouse hepatocytes increases miRNAs and enhances siRNA-mediated knockdown. Notably, because ALAS1 is the target of a Food and Drug Administration-approved siRNA drug, agents that suppress ALAS may serve as adjuvants for siRNA therapies.

Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers

First-line immune checkpoint inhibitor (ICI) combinations show responses in subsets of hepatocellular carcinoma (HCC) patients. Nearly half of HCCs are Wnt-active with mutations in CTNNB1 (encoding for β-catenin), AXIN1/2, or APC, and demonstrate limited benefit to ICI due to an immune excluded tumor microenvironment. We show significant tumor responses in multiple β-catenin-mutated immunocompetent HCC models to a novel siRNA encapsulated in lipid nanoparticle targeting CTNNB1 (LNP-CTNNB1). Both single-cell and spatial transcriptomics revealed cellular and zonal reprogramming of CTNNB1-mutated tumors, along with activation of immune regulatory transcription factors IRF2 and POU2F1, re-engaged type I/II interferon signaling, and alterations in both innate and adaptive immune responses upon β-catenin suppression with LNP-CTNNB1. Moreover, LNP-CTNNB1 synergized with ICI in advanced-stage disease through orchestrating enhanced recruitment of cytotoxic T cell aggregates. Lastly, CTNNB1-mutated patients treated with atezolizumab plus bevacizumab combination had decreased presence of lymphoid aggregates, which were prognostic for response and survival. In conclusion, LNP-CTNNB1 is efficacious as monotherapy and in combination with ICI in CTNNB1-mutated HCCs through impacting tumor cell intrinsic signaling and remodeling global immune surveillance, providing rationale for clinical investigations.

Structural basis for gene silencing by siRNAs in humans

Small interfering RNAs (siRNAs) guide mRNA cleavage by human Argonaute2 (hAgo2), leading to targeted gene silencing. Despite their laboratory and clinical impact, structural insights into human siRNA catalytic activity remain elusive. Here, we show that disrupting siRNA 3'-end binding by hAgo2 accelerates target cleavage and stabilizes its catalytic conformation, enabling detailed structural analysis. A 3.16 Å global resolution cryo-EM reconstruction reveals that distortion of the siRNA-target duplex at position 6 allows target RNA entry into the catalytic cleft and shifts Lysine-709, a previously unrecognized catalytic residue, into the active site. A pyrimidine at target nucleotide t10 positions another unrecognized catalytic residue, Arginine-710, for optimal cleavage. Expansion of the guide-target duplex major groove docks the scissile phosphate for hydrolysis and subsequent groove compression after position 16 permits target RNAs to exit the catalytic cleft. These findings reveal how hAgo2 catalyzes siRNA target hydrolysis, providing a high-resolution model for therapeutic design.

Nanoparticle-Mediated Gene Delivery for Bone Tissue Engineering

Critical-sized bone defects represent an urgent clinical problem, necessitating innovative treatment approaches. Gene-activated grafts for bone tissue engineering have emerged as a promising solution. However, traditional gene delivery methods are constrained by limited osteogenic efficacy and safety concerns. Recently, organic and inorganic nanoparticle (NP) vectors have attracted significant attention in bone tissue engineering for their safe, stable, and controllable gene delivery. Targeted gene delivery guided by insights into bone healing mechanisms, coupled with the multifunctional design of NPs, is crucial for enhancing therapeutic outcomes. Here, the theoretical foundations underlying NP-mediated gene therapy for enhancing bone healing across different histological stages are elucidated. Furthermore, the distinct attributes of functionalized NP vectors are discussed, and cutting-edge strategies aimed at optimizing gene delivery efficiency throughout the therapeutic process are highlighted. Additionally, the review addresses the unresolved challenges and prospects of this technology. This review may contribute to the continued development and clinical application of NP-mediated gene delivery for treating critical-sized bone defects.

Noncoding RNAs in chronic obstructive pulmonary disease: From pathogenesis to therapeutic targets

Chronic obstructive pulmonary disease (COPD) is the most prevalent chronic respiratory disorder that is becoming the leading cause of morbidity and mortality on a global scale. There is an unmet need to investigate the underlying pathophysiological mechanisms and unlock novel therapeutic avenues for COPD. Recent research has shed light on the significant roles played by diverse noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), in orchestrating the development and progression of COPD. This review provides an overview of the regulatory roles of ncRNAs in COPD, elucidating their underlying mechanisms, and illuminating the potential prospects of RNA-based therapeutics in the management of COPD.

Advanced siRNA delivery in combating hepatitis B virus: mechanistic insights and recent updates

Hepatitis B virus (HBV) infection is a major health problem, causing thousands of deaths each year worldwide. Although current medications can often inhibit viral replication and reduce the risk of liver carcinoma, several obstacles still hinder their effectiveness. These include viral resistance, prolonged treatment duration, and low efficacy in clearing viral antigens. To address these challenges in current HBV treatment, numerous approaches have been developed with remarkable success. Among these strategies, small-interfering RNA (siRNA) stands out as one of the most promising therapies for hepatitis B. However, naked siRNAs are vulnerable to enzymatic digestion, easily eliminated by renal filtration, and unable to cross the cell membrane due to their large, anionic structure. Therefore, effective delivery systems are required to protect siRNAs and maintain their functionality. In this review, we have discussed the promises of siRNA therapy in treating HBV, milestones in their delivery systems, and products that have entered clinical trials. Finally, we have outlined the future perspectives of siRNA-based therapy for HBV treatment.

Sele-targeted siRNA liposome nanoparticles inhibit pathological scars formation via blocking the cross-talk between monocyte and endothelial cells: a preclinical study based on a novel mice scar model

BACKGROUND

Pathological scars (PS) are one of the most common complications in patients with trauma and burns, leading to functional impairments and aesthetic concerns. Mechanical tension at injury sites is a crucial factor in PS formation. However, the precise mechanisms remain unclear due to the lack of reliable animal models.

RESULTS

We developed a novel mouse model, the Retroflex Scar Model (RSM), which induces PS by applying controlled tension to wounds in vivo. RNA sequencing identified significant transcriptome changes in RSM-induced scars. Elevated expression of E-Selectin (Sele) was observed in endothelial cells from both the RSM model and human PS (Keloid) samples. In vitro studies demonstrated that cyclic mechanical stretching (CMS) increased Sele expression, promoting monocyte adhesion and the release of pro-inflammatory factors. Single-cell sequencing analysis from the GEO database, complemented by Western blotting, immunofluorescence, and co-immunoprecipitation, confirmed the role of Sele-mediated monocyte adhesion in PS formation. Additionally, we developed Sele-targeted siRNA liposome nanoparticles (LNPs) to inhibit monocyte adhesion. Intradermal administration of these LNPs effectively reduced PS formation in both in vivo and in vitro studies.

CONCLUSIONS

This study successfully established a reliable mouse model for PS, highlighting the significant roles of mechanical tension and chronic inflammation in PS formation. We identified Sele as a key therapeutic target and developed Sele-targeted siRNA LNPs, which demonstrated potential as a preventive strategy for PS. These findings provide valuable insights into PS pathogenesis and open new avenues for developing effective treatments for pathological scars.

Dendritic mesoporous silica-delivered siRNAs nano insecticides to prevent Sogatella furcifera by inhibiting metabolic detoxification and reproduction

BACKGROUND

Migratory insect infestation caused by Sogatella furcifera is a serious threat to rice production. The most effective method available for S. furcifera control is intensive insecticide spraying, which cause widespread resistance. RNA interference (RNAi) insecticides hold enormous potential in managing pest resistance. However, the instability and the poor efficiency of cross-kingdom RNA trafficking are key obstacles for the application in agricultural pest management.

METHODS

We present dendritic mesoporous silica nanoparticles (DMSNs)-based nanocarrier for delivering siRNA and nitenpyram to inhibit the metabolic detoxification and development of S. furcifera, thereby preventing its proliferation.

RESULTS

This nano complex (denoted as N@UK-siRNA/DMSNs) significantly enhanced the stability of siRNA (efficacy lasting 21 days) and released cargos in GSH or planthopper bodily fluid with a maximum release rate of 84.99%. Moreover, the released UK-siRNA targeting two transcription factors (Ultraspiracle and Krüppel-homolog 1) downregulated the developmental genes Ultraspiracle (0.09-fold) and Krüppel-homolog 1 (0.284-fold), and downstream detoxification genes ABC SfABCH4 (0.016-fold) and P450 CYP6FJ3 (0.367-fold).

CONCLUSION

The N@UK-siRNA/DMSNs inhibited pest development and detoxification, significantly enhancing susceptibility to nitenpyram to nanogram level (LC50 is 250-252 ng/mL), resulting in a 5.37-7.13-fold synergistic ratio. This work proposes a comprehensive management strategy for controlling S. furcifera to ensure the green and safe production of rice.

Effect of Lipid Nanoparticle Physico-Chemical Properties and Composition on Their Interaction with the Immune System

Lipid nanoparticles (LNPs) have shown promise as a delivery system for nucleic acid-based therapeutics, including DNA, siRNA, and mRNA vaccines. The immune system plays a critical role in the response to these nanocarriers, with innate immune cells initiating an early response and adaptive immune cells mediating a more specific reaction, sometimes leading to potential adverse effects. Recent studies have shown that the innate immune response to LNPs is mediated by Toll-like receptors (TLRs) and other pattern recognition receptors (PRRs), which recognize the lipid components of the nanoparticles. This recognition can trigger the activation of inflammatory pathways and the production of cytokines and chemokines, leading to potential adverse effects such as fever, inflammation, and pain at the injection site. On the other hand, the adaptive immune response to LNPs appears to be primarily directed against the protein encoded by the mRNA cargo, with little evidence of an ongoing adaptive immune response to the components of the LNP itself. Understanding the relationship between LNPs and the immune system is critical for the development of safe and effective nucleic acid-based delivery systems. In fact, targeting the immune system is essential to develop effective vaccines, as well as therapies against cancer or infections. There is a lack of research in the literature that has systematically studied the factors that influence the interaction between LNPs and the immune system and further research is needed to better elucidate the mechanisms underlying the immune response to LNPs. In this review, we discuss LNPs' composition, physico-chemical properties, such as size, shape, and surface charge, and the protein corona formation which can affect the reactivity of the immune system, thus providing a guide for the research on new formulations that could gain a favorable efficacy/safety profile.

Epigenetics-targeted drugs: current paradigms and future challenges

Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.

Bioinspired and biomimetic nucleobase-containing polymers: the effect of selective multiple hydrogen bonds

Bioinspired and biomimetic nucleobase-containing polymers are a series of polydisperse nucleic acid analogs, mainly obtaining through highly efficient and scalable step-growth or chain polymerizations. The combination of pendant nucleobase groups and various backbones endows the polymers/materials with selective multiple H-bonds under distinct conditions, demonstrating the broad applicability of this new family of polymeric materials. In this perspective, we critically summarize recent advances of bioinspired and biomimetic nucleobase-containing polymers and materials in both solution and the bulk. Then, we discuss the effect of multiple H-bonds between complementary nucleobases on the structures and properties of the nucleobase-containing polymers and materials. Selective multiple H-bonds between complementary nucleobases are feasible to modulate the polymer sequence and self-assembly behaviour, achieve templated polymerization, tune nanostructure morphologies and functions, and selectively bind with nucleic acids in various solutions. Meanwhile, bioinspired and biomimetic nucleobase-containing polymers are capable of forming robust polymeric materials such as hydrogels, bioplastics, elastomers, adhesives, and coatings by optimizing the inter- and intramolecular multiple H-bonding interactions. Further, the conclusions and outlook for future development and challenges of bioinspired and biomimetic nucleobase-containing polymers are also presented. This perspective presents useful guidelines for fabricating novel bioinspired and biomimetic polymers and materials through rational design of multiple H-bonds nucleobase interactions.

Functions and applications of RNA interference and small regulatory RNAs

Small regulatory RNAs play a variety of crucial roles in eukaryotes, influencing gene regulation, developmental timing, antiviral defense, and genome integrity via a process termed RNA interference (RNAi). This process involves Argonaute/small RNA (AGO/sRNA) complexes that target transcripts via sequence complementarity and modulate gene expression and epigenetic modifications. RNAi is a highly conserved gene regulatory phenomenon that recognizes self- and non-self nucleic acids, thereby defending against invasive sequences. Since its discovery, RNAi has been widely applied in functional genomic studies and a range of practical applications. In this review, we focus on the current understanding of the biological roles of the RNAi pathway in transposon silencing, fertility, developmental regulation, immunity, stress responses, and acquired transgenerational inheritance. Additionally, we provide an overview of the applications of RNAi technology in biomedical research, agriculture, and therapeutics.

Analyte and probe melting temperature guided method development strategy for hybridization LC-MS/MS quantification of siRNAs

Small interfering RNA (siRNA) is a novel class of double-stranded oligonucleotide therapeutics rapidly growing in drug research and development. Accurate, sensitive, and reliable quantification of siRNA analytes in biological samples is required to study their pharmacokinetics, toxicokinetics, and biodistribution. Hybridization LC-MS/MS can achieve highly sensitive and specific bioanalysis of single-stranded oligonucleotides, e.g., antisense oligonucleotides (ASOs); however, its application for bioanalysis of siRNA or other double-stranded oligonucleotides is limited. The detailed rationale and principles for assay development are still not well understood. In this work, we systematically evaluated key steps and parameters of hybridization LC-MS/MS assays, including probes (five different types compared), hybridization procedure and temperature, elution temperature, and column temperature using patisiran, an approved siRNA drug, as the test siRNA. Based on the evaluation, a practical and efficient melting temperature (Tm) guided strategy was developed for fast and reliable method development of hybridization LC-MS/MS assays for siRNA bioanalysis. The strategy was successfully applied to siRNA-A, a test siRNA, in mouse plasma over the range of 1.00-1000 ng/mL and the resulting method has been used to support multiple mouse studies. This method-development strategy showed great value as a general approach for other siRNAs or double-stranded oligonucleotides.

Circular RNA circWBSCR22 facilitates colorectal cancer metastasis by enhancing CHD4's protein stability

Widespread metastases continue to be a massive challenge for colorectal cancer (CRC) therapy and contribute to the high mortality rate in patients with CRC. Circular RNAs (circRNAs) are a novel group of endogenous RNAs identified as agents modulating tumorigenesis and aggressiveness with tissue heterogeneity. However, the biological functions of circRNAs in CRC metastasis remain largely unknown. Here, we identified that circWBSCR22, a novel circRNA back-spliced from the WBSCR22 pre-mRNA, was significantly elevated in CRC tissue compared with adjacent normal tissue. Further gain- and loss-of-function assays manifested that circWBSCR22 promotes epithelial-mesenchymal transition (EMT) and metastasis in vitro and in vivo, which are mediated by the chromodomain helicase-DNA-binding protein 4 (CHD4) protein. Mechanically, circWBSCR22 binds directly to up-frameshift protein 1 (UPF1), an RNA binding protein recognized for its function in RNA surveillance, and hinders its role in directing CHD4 protein ubiquitination for degradation. Consequently, by stabilizing the CHD4 protein, circWBSCR22 hastens the development and metastasis of CRC. Therefore, our findings first delineate the oncogenic role and mechanism of circWBSCR22 in CRC growth and metastasis and its potential to serve as a therapeutic target for CRC.

Emerging Roles of ncRNAs in Type 2 Diabetes Mellitus: From Mechanisms to Drug Discovery

Type 2 diabetes mellitus (T2DM), a high-incidence chronic metabolic disorder, has emerged as a global health issue, where most patients need lifelong medication. Gaining insights into molecular mechanisms involved in T2DM development is expected to provide novel strategies for clinical prevention and treatment. Growing evidence validates that non-coding RNAs (ncRNAs) including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as crucial regulators in multiple biological processes of T2DM, inspiring various potential targets and drug candidates. In this review, we summarize the current understanding of ncRNA roles in T2DM and discuss the potential use of ncRNAs as targets and active molecules for drug discovery.

Advanced Nanotechnology-Based Nucleic Acid Medicines

Nucleic acid medicines are a highly attractive modality that act in a sequence-specific manner on target molecules. To date, 21 such products have been approved by the Food and Drug Administration. However, the development of nucleic acid medicines continues to face various challenges, including tissue and cell targeting as well as intracellular delivery. Numerous research groups are addressing these issues by advancing the development of nucleic acid medicines through nanotechnology. In countries other than Japan (including Europe and the USA), >40 nanotechnology-based nucleic acid medicines have been tested in clinical trials, and 15 clinical trials are ongoing. In Japan, three phase I trials are ongoing, and future results are awaited. The review summarizes the latest research in the nanotechnology of nucleic acid medicines and statuses of clinical trials in Japan, with expectations of further evolutions.

Inhibition of NLRP3 inflammasome contributes to paclitaxel efficacy in triple negative breast cancer treatment

Chronic inflammation and NLRP3 inflammasome activation are among the determining factors of breast malignancies. Paclitaxel (PTX) is a drug used in breast cancer treatment which sustains prolonged inflammation, reducing the effectiveness of chemotherapy. Considering the impact of inflammatory processes in cancer progression, there is a strong concern to develop therapeutic strategy targeting NLRP3 inflammasome for triple-negative breast cancer (TNBC) treatment. Therefore, the aim of this study was to evaluate the potential of PTX and NLRP3 inflammasome modulation to counterbalance TNBC by inducing programmed cell death and inhibiting the activity of pro-inflammatory cytokines. The obtained results suggested the strong interaction between NLRP3 inflammasome and TNBC and revealed that pharmacological inhibition, using NLRP3-specific inhibitor MCC950, and genetic silencing of NLRP3 inflammasome using specific small interfering RNA, reduced inflammatory responses and facilitated PTX-determined tumor cell death. Thus, NLRP3 inflammasome manipulation in combination with anti-tumor drugs opens up new therapeutic perspectives for TNBC therapy.

Evolving understanding of autoimmune mechanisms and new therapeutic strategies of autoimmune disorders

Autoimmune disorders are characterized by aberrant T cell and B cell reactivity to the body's own components, resulting in tissue destruction and organ dysfunction. Autoimmune diseases affect a wide range of people in many parts of the world and have become one of the major concerns in public health. In recent years, there have been substantial progress in our understanding of the epidemiology, risk factors, pathogenesis and mechanisms of autoimmune diseases. Current approved therapeutic interventions for autoimmune diseases are mainly non-specific immunomodulators and may cause broad immunosuppression that leads to serious adverse effects. To overcome the limitations of immunosuppressive drugs in treating autoimmune diseases, precise and target-specific strategies are urgently needed. To date, significant advances have been made in our understanding of the mechanisms of immune tolerance, offering a new avenue for developing antigen-specific immunotherapies for autoimmune diseases. These antigen-specific approaches have shown great potential in various preclinical animal models and recently been evaluated in clinical trials. This review describes the common epidemiology, clinical manifestation and mechanisms of autoimmune diseases, with a focus on typical autoimmune diseases including multiple sclerosis, type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosus, and sjögren's syndrome. We discuss the current therapeutics developed in this field, highlight the recent advances in the use of nanomaterials and mRNA vaccine techniques to induce antigen-specific immune tolerance.

Combinatorial Synthesis of Alkyl Chain-Capped Poly(β-Amino Ester)s for Effective siRNA Delivery

Poly (β-amino ester) (PBAE) is a class of biodegradable polymers containing ester bonds in their main chain, extensively investigated as cationic polymer carriers for siRNA. Most current PBAE carriers rely on termination with hydrophilic or charged amines. In this study, a polymer platform consisting of 168 PBAE polymers with hydrophobic alkyl chain terminals is constructed through sequential aza-Michael addition. A large number of effective carriers are identified through in vitro screening of the PBAE platform for siLuc delivery to HeLa-Luc cells. Specifically, PA8-C6 and PA8-C8 achieve remarkable gene knockdown efficacies of up to 80% with low cytotoxicity. Certain materials from the PA2 and PA5 series demonstrate potent siRNA delivery capabilities associated with elevated cytotoxicity. The pKa value of PBAE is predominantly determined by the hydrophilic amine side chains rather than the end-capping groups. A pKa range of ≈6.2-6.5 may contribute to the excellent delivery capability for PA8 series carriers. The co-formulation of PBAE carriers with helper lipids leads to the reduced size and surface charges of the polyplex NPs with siRNA, consequently decreasing the cytotoxicity and enhancing siRNA delivery efficacy. These findings hold significant implications for the development of novel degradable polymer carriers for siRNA delivery.

Lipopolymer/siRNA Nanoparticles Targeting the Signal Transducer and Activator of Transcription 5A Disrupts Proliferation of Acute Lymphoblastic Leukemia

The therapeutic potential of small interfering RNAs (siRNAs) in gene-targeted treatments is substantial, but their suboptimal delivery impedes widespread clinical applications. Critical among these is the inability of siRNAs to traverse the cell membranes due to their anionic nature and high molecular weight. This limitation is particularly pronounced in lymphocytes, which pose additional barriers due to their smaller size and scant cytoplasm. Addressing this, we introduce an innovative lipid-conjugated polyethylenimine lipopolymer platform, engineered for delivery of therapeutic siRNAs into lymphocytes. This system utilizes the cationic nature of the polyethylenimine for forming stable complexes with anionic siRNAs, while the lipid component facilitates cellular entry of siRNA. The resulting lipopolymer/siRNA complexes are termed lipopolymer nanoparticles (LPNPs). We comprehensively profiled the efficacy of this platform in human peripheral blood mononuclear cells (PBMCs) as well as in vitro and in vivo models of acute lymphoblastic leukemia (ALL), emphasizing the inhibition of the oncogenic signal transducer and activator of transcription 5A (STAT5A) gene. The lipopolymers demonstrated high efficiency in delivering siRNA to ALL cell lines (RS4;11 and SUP-B15) and primary patient cells, effectively silencing the STAT5A gene. The resultant gene silencing induced apoptosis and significantly reduced colony formation in vitro. Furthermore, in vivo studies showed a significant decrease in tumor volumes without causing substantial toxicity. The lipopolymers did not induce the secretion of proinflammatory cytokines (IL-6, TNF-α, and INF-γ) in PBMCs from healthy volunteers, underscoring their immune safety profile. Our observations indicate that LPNP-based siRNA delivery systems offer a promising therapeutic approach for ALL in terms of both safety and therapeutic efficacy.

Systematic Review of Genetic Substrate Reduction Therapy in Lysosomal Storage Diseases: Opportunities, Challenges and Delivery Systems

BACKGROUND

Genetic substrate reduction therapy (gSRT), which involves the use of nucleic acids to downregulate the genes involved in the biosynthesis of storage substances, has been investigated in the treatment of lysosomal storage diseases (LSDs).

OBJECTIVE

To analyze the application of gSRT to the treatment of LSDs, identifying the silencing tools and delivery systems used, and the main challenges for its development and clinical translation, highlighting the contribution of nanotechnology to overcome them.

METHODS

A systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guidelines was performed. PubMed, Scopus, and Web of Science databases were used for searching terms related to LSDs and gene-silencing strategies and tools.

RESULTS

Fabry, Gaucher, and Pompe diseases and mucopolysaccharidoses I and III are the only LSDs for which gSRT has been studied, siRNA and lipid nanoparticles being the silencing strategy and the delivery system most frequently employed, respectively. Only in one recently published study was CRISPR/Cas9 applied to treat Fabry disease. Specific tissue targeting, availability of relevant cell and animal LSD models, and the rare disease condition are the main challenges with gSRT for the treatment of these diseases. Out of the 11 studies identified, only two gSRT studies were evaluated in animal models.

CONCLUSIONS

Nucleic acid therapies are expanding the clinical tools and therapies currently available for LSDs. Recent advances in CRISPR/Cas9 technology and the growing impact of nanotechnology are expected to boost the clinical translation of gSRT in the near future, and not only for LSDs.

The structural basis for RNA slicing by human Argonaute2

Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene-silencing pathways that are essential for many eukaryotes and the basis for new clinical therapies. Despite this importance, structural information on eukaryotic AGOs in a fully paired, slicing-competent conformation-hypothesized to be intrinsically unstable-has been lacking. Here we present the cryogenic-electron microscopy structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable this conformation. Critically, the N domain of AGO rotates to allow the RNA full access to the central channel and forms contacts that license rapid slicing. Moreover, a conserved loop in the PIWI domain secures the RNA near the active site to enhance slicing rate and specificity. These results explain how AGO accommodates targets possessing the pairing specificity typically observed in biological and clinical slicing substrates.

Synthesis of Natural and Sugar-Modified Nucleosides Using the Iodine/Triethylsilane System as N-Glycosidation Promoter

The reagent system based on the combined use of Et3SiH/I2 acts as an efficient N-glycosidation promoter for the synthesis of natural and sugar-modified nucleosides. An analysis of reaction stereoselectivity in the absence of C2-positioned stereodirecting groups revealed high selectivity with six-membered substrates, depending on the nucleophilic character of the nucleobase or based on anomerization reactions. The synthetic utility of the Et3SiH/I2-mediated N-glycosidation reaction was highlighted by its use in the synthesis of the investigational drug apricitabine.

Synthesis and Properties of RNA Modified with Thioamide Internucleoside Linkage

Recent success of RNA therapeutics has reinvigorated interest in chemical modifications of RNA. As exemplified by the phosphorothioates, modifications of sugar-phosphate backbone have been remarkably impactful but relatively underexplored in therapeutic RNAs. The present study reports synthesis, thermal stability, and RNA interference activity of RNAs modified with thioamide linkages. Compared to the previously studied amide-modified RNA, thioamide linkages strongly destabilized a short self-complementary RNA model duplex. However, in short interfering RNAs amides and thioamides had a similar effect on duplex stability and target RNA cleavage activity and specificity. Hence, the thioamide may be added to the toolbox of chemical biologist as a useful backbone modification well tolerated by the RNA interference machinery.

The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex

The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that, for different guide-RNA sequences, slicing rates of perfectly complementary bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.