Search Results (624)

Background/Objectives: Single-stranded oligonucleotides (ssODNs) are used as donor templates for therapeutic gene editing by CRISPR-Cas9 cleavage and homology-directed repair (HDR). Although ssODN sequence fidelity is critical to the safety and efficacy of editing, standard quality control methods cannot resolve individual nucleotide errors. Methods: We performed deep sequencing of ssODNs from three manufacturers and amplicons from edited hematopoietic stem/progenitor cells. Results: We find that synthesis errors are present in all ssODNs tested at rates that vary more than two-fold among manufacturers, at positions that are dependent on sequence context. These synthesis errors are propagated into the genome by HDR at frequencies proportional to their abundance in the ssODN. In our sickle cell mutation correction protocol, the most prevalent SNEs are predicted to produce benign β-globin variants, while the less frequent frameshift deletions are predicted to generate β-thalassemia-like alleles. Conclusions: Current quality control standards are insufficient to detect these errors, and deep sequencing of ssODNs should be incorporated into regulatory submissions for clinical gene editing programs. Full article

Antisense oligonucleotides (ASOs) are a class of nucleic acid therapeutics that modulate gene expression through diverse mechanisms. Since their initial demonstration in inhibiting viral genes, advances in medicinal chemistry, pharmacology, and delivery have enabled robust and durable target engagement across multiple tissues. Chemical modifications to the backbone, ribose, and nucleobases have improved nuclease resistance, binding affinity, and pharmacokinetics, while conjugation and delivery technologies have expanded tissue accessibility. Beyond classical RNase H–mediated RNA degradation, ASOs regulate gene expression via splicing modulation, microRNA inhibition, transcriptional activation, and translation modulation, supporting both gene silencing and upregulation strategies. Multiple ASO drugs are now approved, particularly for genetic diseases, with many more in clinical development. This review outlines the evolution of antisense technology, key chemical and delivery innovations, ASO pharmacokinetics and intracellular trafficking, the mechanisms underlying gene regulation, and current clinical applications and future opportunities. Full article

Molecular heterogeneity of malignant tumours remains a central challenge in oncology. Although neoplasms of distinct histogenesis share core oncogenic properties, the signalling networks sustaining these phenotypes are tumour-specific, highlighting the need for regulatory-level therapeutics adaptable to distinct molecular contexts. Oncogenic microRNAs (miRNAs), among which miR-21, miR-17, and miR-155 are broadly overexpressed in epithelial, lymphoid, and glial-neuronal neoplasms, represent attractive targets for therapeutic intervention. MiRNA inhibition by antisense oligonucleotides has emerged as a promising therapeutic strategy, and mesyl (methanesulfonyl) phosphoramidate oligonucleotides (µ-AMOs) represent a next-generation class of anti-miRNA agents with superior nuclease resistance and biological activity. Here, we report a systematic screening of 23 tumour cell lines of diverse histogenesis for sensitivity to paired combinations of µ-AMOs targeting miR-21, miR-17, and miR-155. Epithelial-derived lines exhibited the highest responsiveness, while lymphoid cell lines demonstrated the lowest sensitivity. The efficacy of specific µ-AMO pairs was found to be cell type-specific: combinations containing miR-21-targeting µ-AMO were most effective in epithelial lines, whereas the miR-17/miR-155-targeting pair showed superior activity in neuroglial models. Cellular responsiveness was driven by the extent of miRNA suppression, with no correlation detected for delivery efficiency or basal miRNA levels. The obtained results provide a basis for tumour-type-specific selection of µ-AMO combinations for clinical translation. Full article

TIDEs (therapeutic peptides, oligonucleotides, and related molecules) represent a rapidly expanding market that has gained significant momentum due to the recent success of Glucagon-like peptide-1 (GLP-1) receptor agonists for the treatment of obesity, diabetes and as cardiovascular and kidney diseases. Chemical synthesis remains the dominant manufacturing route for candidates containing approximately 10–40 amino acids and includes non-proteinogenic amino acids. Consequently, various combinations of solid-phase peptide synthesis (SPPS), liquid-phase peptide synthesis (LPPS), hybrid approaches, or tag-assisted peptide synthesis (TAPS) can be applied to achieve full-sequence assembly. However, identifying the most eco-efficient pathway through experimental trials alone is impractical because of the vast number of possible process combinations and the growing variety of green solvent alternatives. Therefore, process simulation studies—widely established in chemical engineering—must be adapted to the specific physicochemical characteristics of these large, multi-component molecules. This paper provides an overview of the current state of research and illustrates potential process improvements enabled by digital twin technologies as exemplified for the first manufacturing steps of tirzepatide. Full article

RNA-based therapeutics are reshaping the treatment landscape for skeletal muscle disorders by enabling modulation of RNA processing or direct correction of disease-causing alleles. In Duchenne muscular dystrophy (DMD), four antisense oligonucleotides—eteplirsen, golodirsen, viltolarsen, and casimersen—have received FDA approval; these phosphorodiamidate morpholino oligomers (PMOs) induce exon skipping to restore the reading frame and enable expression of internally truncated dystrophin. Beyond splice switching, RNA therapeutics include RNase H-active gapmers and steric-blocking antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs) that mediate post-transcriptional gene silencing, and RNA-guided gene-modifying technologies such as CRISPR systems that can reframe or repair endogenous alleles. Despite major progress in DMD, broader clinical impact remains constrained by inefficient delivery to skeletal and especially cardiac muscle, the need for repeat administration for most modalities, and safety considerations that limit dose escalation and durability. Next-generation approaches aim to overcome these barriers through peptide- or antibody-conjugated oligonucleotides that enhance cellular uptake and tissue distribution, alternative chemistries with improved stability and potency, and viral or non-viral platforms for durable splice modulation. In parallel, CRISPR-based strategies—including base and prime editing—offer the prospect of one-time correction, while raising important questions regarding delivery, immunogenicity, editing specificity, and long-term safety. This review synthesizes recent advances in antisense and gene-modifying strategies for skeletal muscle and highlights practical priorities for translation, including improved muscle/heart delivery, controllable safety mechanisms, scalable manufacturing, and standardized biomarker-to-clinical outcome relationships. Full article

Since the discovery of RNA interference (RNAi), small interfering RNA (siRNA) has emerged as a transformative therapeutic modality, shifting the paradigm from permanent genomic modification to the flexible interception of genetic information. Despite the delivery gap caused by biological barriers, innovations in chemical stabilization and delivery platforms have propelled siRNA from niche applications to the mainstream management of chronic conditions. This review provides a comprehensive analysis of the distinct mechanistic advantages of siRNA over antisense oligonucleotides, with particular emphasis on its catalytic turnover via the RISC and high target specificity. We further evaluate the critical transition from first-generation lipid nanoparticles to ligand-conjugated systems, specifically trivalent N-acetylgalactosamine (GalNAc). Through an examination of the clinical success of Inclisiran and the recent approval of Plozasiran, we discuss how these advances have improved patient compliance and extended dosing intervals. Furthermore, this article explores the emerging frontier of extra-hepatic delivery and the expansion toward metabolic and oncological targets. Ultimately, this review highlights the potential of siRNA to become a programmable standard of care for a broad spectrum of previously intractable diseases. Full article

RNA viruses encode multiple layers of regulatory information within their genomes, extending beyond their protein-coding sequences. Through local secondary structures and long-range RNA–RNA interactions, viral RNAs control essential steps of the viral life cycle, including translation, replication, genome cyclization, packaging, and evasion of host defenses. Over the last two decades, chemical probing approaches—particularly Selective 2′-Hydroxyl Acylation analyzed by a primer extension (SHAPE) and its high-throughput derivatives—have transformed our ability to investigate these structures at a single nucleotide resolution and on a genome-wide scale. These technologies have revealed that viral genomes are highly structured and contain numerous functional RNA elements within untranslated regions as well as coding sequences. In this review, we summarize the main experimental strategies used to profile viral RNA architecture, with a focus on SHAPE-based methodologies and complementary approaches. We then discuss the major classes of functional RNA structures identified across diverse viral families, focusing on elements involved in translation and replication, such as internal ribosome entry sites (IRES) and cyclization elements, as well as other functional structures, including XRN1-resistant and frameshifting elements. Finally, we examine how structure-guided analyses are opening new avenues for antiviral intervention, including antisense oligonucleotides, small molecules, and RNA-degrading chimeras. Together, these advances highlight the viral RNA structure as both a key determinant of virus biology and a promising target for therapeutic innovation. Full article

Hypertriglyceridemia is a well-recognized contributor to residual atherosclerotic cardiovascular disease risk and a predisposing factor for acute pancreatitis. Despite the availability of pharmacologic agents and lifestyle interventions, patients with severe and refractory hypertriglyceridemia often fail to achieve adequate control. Recent advances in the molecular understanding of triglyceride metabolism have driven the development of targeted therapies that selectively modulate key regulatory pathways. This study sought to provide an overview of triglyceride regulation, the atherogenic role of remnant lipoproteins, and clinical evidence of emerging triglyceride-lowering therapies. Lipoprotein metabolism is regulated by a complex network of regulatory proteins that include lipoprotein lipase (LPL), apolipoproteins such as apolipoprotein C-III (ApoC-III), and angiopoietin-like proteins (ANGPTLs). Targeting these proteins in the metabolic cascade has shown promising results in reducing triglyceride levels. Emerging therapies such as antisense oligonucleotides (ASOs) and small interfering RNA (siRNA) directed against ApoC-III (volanesorsen, olezarsen, and plozasiran), inhibitors of ANGPTL3 (evinacumab and zodasiran), and fibroblast growth factor 21 (FGF-21) analogs (pegozafermin) have demonstrated substantial triglyceride-lowering efficacy. These agents have achieved reductions in triglyceride levels of up to 80% in clinical trials. Additionally, preliminary evidence suggests that these agents may also reduce the incidence of acute pancreatitis and improve cardiometabolic risk profiles, although dedicated trials are still needed to confirm these outcomes. The therapeutic landscape for hypertriglyceridemia is rapidly evolving. Integrating these novel agents into clinical practice will require individualized treatment plans, sustained lifestyle modification, and careful safety monitoring. Full article

While the Blood–Brain Barrier (BBB) is essential for the protection and function of the Central Nervous System (CNS), it also represents a challenge for drug delivery in the treatment of CNS disorders due to its limited permeability and high expression of efflux transporters. Crossing the BBB becomes even more difficult when dealing with biomolecular therapeutics (e.g., monoclonal antibodies and Antisense Oligonucleotides) due to their hydrophilic nature and high molecular weight. Over the years, different strategies have been developed in order to maximize the ability of biopharmaceuticals to cross the BBB and be delivered to the CNS. Both non-invasive techniques, mainly consisting of developing innovative vectors or using non-conventional routes of administration (e.g., intranasal delivery), and invasive methods, such as intracerebroventricular/intrathecal administration, have been tested individually and in combination. Given the improvements achieved nowadays with both approaches, here, we plan to compare the advances in invasive techniques, such as those based on the use of device-assisted strategies, and the employment of the intranasal route of administration. We are also interested in reporting the applicability of both strategies in the treatment of aggressive forms of cancer, such as glioblastoma, as well as neurodegenerative diseases, in order to determine which technique can be considered a better choice in each specific case. Full article

Glioblastomas represent the most aggressive and lethal form of primary brain cancer and continue to pose a major challenge to global health. MicroRNAs (miRNAs), as central regulators of gene expression, are intimately involved in the initiation, progression, and therapeutic resistance of numerous malignancies, including glioblastoma. Therefore, this class of non-coding RNAs are considered to be valuable candidates for innovative therapeutic strategies. However, despite many promising preclinical studies, miRNA-based therapies have yet to be translated into routine clinical practice. In the context of glioblastoma, one of the principal obstacles to the effective delivery of synthetic miRNA therapy is their limited ability to cross the blood–brain barrier (BBB). To address this challenge, a variety of locoregional delivery strategies have been developed in recent years. In this review, we provide a detailed discussion and a state-of-the-art overview of these local delivery methods in the context of glioblastoma treatment, with a specific emphasis on their application for delivering miRNA-based therapeutic oligonucleotides, formulated either with or without synthetic nanoparticles. Full article

Background/Objectives: Sporotrichosis is an emerging zoonotic subcutaneous fungal infection with limited therapeutic options, highlighting the need for improved immunomodulatory strategies. CTLA-4 is an inhibitory immune checkpoint that negatively regulates T-cell activation. In this study, we evaluated whether a CTLA-4 antisense oligonucleotide (CTLA-4 ASO) is associated with enhanced immune responses to an adjuvanted recombinant Sporothrix sp. enolase antigen (rSsEno) formulation. Methods: CTLA-4 ASO uptake, cytotoxicity, and gene-silencing activity were assessed in murine splenocytes in vitro. BALB/c mice were immunized with rSsEno formulated with Montanide Gel 01, either alone or in combination with 5 µg CTLA-4 ASO. Antigen-specific serum antibody responses were quantified by ELISA. Splenocytes from immunized mice were restimulated with enolase, and cytokine production (IFN-γ, IL-2, IL-17, and TNF-α) was measured using Cytometric Bead Array (CBA). Results: CTLA-4 ASO was efficiently internalized by splenocytes and was associated with reduced expression of CTLA-4 without detectable cytotoxicity in vitro. Mice receiving the ASO-supplemented formulation developed significantly higher anti-enolase antibody titers compared to those immunized with adjuvant alone. Upon antigen restimulation, splenocytes from ASO-treated mice produced higher levels of IFN-γ, IL-2, TNF-α, and IL-17, consistent with an enhanced recall response characterized by a mixed Th1/Th17 cytokine profile. Conclusions: CTLA-4 ASO was associated with an enhanced recall response characterized by a mixed Th1/Th17 cytokine profile. These findings suggest a potential immunomodulatory effect of CTLA-4 targeting. Further studies incorporating dose optimization, infection challenge models, and appropriate sequence controls are required to determine the specificity and relevance of these effects for protective immunity against sporotrichosis. Full article

Extensive evidence now confirms Lipoprotein(a) [Lp(a)] as a causal, independent risk factor for atherosclerotic cardiovascular disease. Elevated Lp(a) levels are detected in approximately 20% of the global population, positioning it as a major contributor to residual cardiovascular risk. Circulating Lp(a) levels are determined predominantly by genetic factors, so they are largely unresponsive to lifestyle modifications or conventional lipid-lowering therapies. Therefore, multiple international guidelines now endorse a one-time, lifetime measurement of Lp(a), as lowering Lp(a) concentrations is expected to have a positive impact on the reduction of cardiovascular risk. Currently, the therapeutic landscape of Lp(a) lowering drugs is rapidly evolving. Some RNA-based therapies (antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs)) have been demonstrated to reduce plasma Lp(a) concentrations by up to 98% in early-phase clinical trials. The efficacy and safety of these compounds are currently being evaluated in large-scale cardiovascular outcome trials. The results of these studies will be critical in validating the “Lp(a) hypothesis”: specific reduction of Lp(a) levels can lead to a measurable decrease in cardiovascular events. The purpose of this narrative review is to examine and discuss the available evidence on the role of Lp(a) as a risk factor and pharmacological target to provide a practical tool for decision-making in clinical practice. Full article

In this study, an ion-pair reverse-phase high-performance liquid chromatography–electrospray ionization mass spectrometry (RP-HPLC-ESI-MS) method was optimized and validated for purity determination for the quality control of the proposed generic nusinersen oligonucleotide drug substance and drug product. The optimization and considerations of sample preparation, chromatographic and mass spectrometry conditions are discussed. The limit of detection was 2.5 × 10⁻⁵ mg/mL and the limit of quantitation was 4.9 × 10⁻⁵ mg/mL. The linearity of the signal (XIC) for all impurities was linear with correlation coefficients of R² ≥ 0.9669. This study, associated with the development of therapeutic oligonucleotides, examines the subject of product-related impurities. The authors consider an ion-pair reverse-phase high-performance liquid chromatography in combination with mass spectrometry for impurity quantitative control. This study contributes to the field by elucidating several critical aspects that, while previously unaddressed in the existing literature, are essential for developing effective analytical methods. Full article

Antisense oligonucleotides (ASOs) are emerging therapeutic agents that modulate gene expression at the RNA level, offering distinct therapeutic advantages over conventional small-molecule drugs and biologics. By directly targeting RNA, ASOs expand the spectrum of druggable targets to include those previously considered “undruggable”, and enable shorter development timelines with improved research and development efficiency. These attributes position ASOs as a highly promising platform for precision and personalized medicine. Recent advances in chemical modification strategies and delivery technologies have markedly accelerated their clinical translation. This review systematically examines the technological evolution of ASO therapeutics, detailing their mechanisms of action, key chemical modification strategies, and advanced delivery systems. It also provides a comprehensive overview of the current global clinical landscape, including approved drugs, discontinued candidates, and ongoing clinical trials. Finally, this review discusses the major challenges facing the field and outlines future directions, with the aim of informing subsequent basic research and clinical development efforts. Full article

Graphene oxide (GO) is a promising nanocarrier for the delivery of oligonucleotides. It offers a high loading capacity, efficient cellular uptake, and surface functionalization. MicroRNA-21 (miR-21) is a well-characterized oncomiR commonly overexpressed in hepatocellular carcinoma (HCC). In HCC, miR-21 contributes to tumor progression, inflammation, and angiogenesis. In a previous in vitro study, we showed that GO alone induces the upregulation of pro-inflammatory and tumor-related genes in HepG2 cells. However, conjugation with an antisense miR-21 (GO-antisense miRNA 21) reverses this effect, suggesting a potential therapeutic application. This study aims to evaluate the antitumor and anti-angiogenic efficacy of the GO-antisense miR-21 nanosystem in ovo using the chick embryo chorioallantoic membrane (CAM) model. Fertilized chicken eggs (n = 4 per group) were randomized into untreated, GO-treated, and GO–antisense miR-21-treated cohorts. A dose of 200 μL (GO 10.0 µg/mL: antisense miR-21 5.0 pmol/mL) was administered intratumorally. Tumor size, volume, and vascularization were monitored through stereomicroscopy and histological analysis. The expression of inflammatory and tumor-associated genes (IL-8, MCP-1, TIMP-2, ICAM-1 and NF-kB) was assessed by quantitative PCR. Given its prominent response, IL-8 protein expression was further analyzed via immunofluorescence. To evaluate tumor-specific delivery, FITC-labeled GO was tracked by confocal microscopy. Our data revealed that treatment with unfunctionalized graphene oxide (GO) unexpectedly promoted tumor vascularization and led to a significant increase in tumor weight. This was accompanied by upregulation of inflammatory markers. In contrast, GO-antisense miR-21 significantly reduced the tumor volume and vessel density. It also successfully downregulated all target genes. Confocal imaging demonstrated preferential accumulation of the nanosystem within the tumor mass. Our results highlight the dual anti-inflammatory and anti-angiogenic effects of GO-antisense miRNA 21 in ovo and support its potential as a targeted nanoplatform for HCC treatment. Full article