mRNA-based therapeutics--developing a new class of drugs

Development and application of an uncapped mRNA platform

BACKGROUND

A novel uncapped mRNA platform was developed.

METHODS

Five lipid nanoparticle (LNP)-encapsulated mRNA constructs were made to evaluate several aspects of our platform, including transfection efficiency and durability in vitro and in vivo and the activation of humoral and cellular immunity in several animal models. The constructs were eGFP-mRNA-LNP (for enhanced green fluorescence mRNA), Fluc-mRNA-LNP (for firefly luciferase mRNA), SδT-mRNA-LNP (for Delta strain SARS-CoV-2 spike protein trimer mRNA), gDED-mRNA-LNP (for truncated glycoprotein D mRNA coding ectodomain from herpes simplex virus type 2 (HSV2)) and gDFR-mRNA-LNP (for truncated HSV2 glycoprotein D mRNA coding amino acids 1-400).

RESULTS

Quantifiable target protein expression was achieved in vitro and in vivo with eGFP- and Fluc-mRNA-LNP. SδT-mRNA-LNP, gDED-mRNA-LNP and gDFR-mRNA-LNP induced both humoral and cellular immune responses comparable to those obtained by previously reported capped mRNA-LNP constructs. Notably, SδT-mRNA-LNP elicited neutralizing antibodies in hamsters against the Omicron and Delta strains. Additionally, gDED-mRNA-LNP and gDFR-mRNA-LNP induced potent neutralizing antibodies in rabbits and mice. The mRNA constructs with uridine triphosphate (UTP) outperformed those with N1-methylpseudouridine triphosphate (N1mψTP) in the induction of antibodies via SδT-mRNA-LNP.

CONCLUSIONS

Our uncapped, process-simplified and economical mRNA platform may have broad utility in vaccines and protein replacement drugs.KEY MESSAGESThe mRNA platform described in our paper uses internal ribosome entry site (IRES) (Rapid, Amplified, Capless and Economical, RACE; Register as BH-RACE platform) instead of caps and uridine triphosphate (UTP) instead of N1-methylpseudouridine triphosphate (N1mψTP) to synthesize mRNA.Through the self-developed packaging instrument and lipid nanoparticle (LNP) delivery system, mRNA can be expressed in cells more efficiently, quickly and economically.Particularly exciting is that potent neutralizing antibodies against Delta and Omicron real viruses were induced with the new coronavirus S protein mRNA vaccine from the BH-RACE platform.

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.

Reverse-phase chromatography removes double-stranded RNA, fragments, and residual template to decrease immunogenicity and increase cell potency of mRNA and saRNA

mRNA is produced by in vitro transcription reaction, which also leads to formation of immuno-stimulatory impurities, such as double-stranded RNA (dsRNA). dsRNA leads to activation of innate immune response linked to inhibition of protein synthesis. Its removal from mRNA preparations increases efficiency of protein translation. Previous studies identified ion-pair reverse-phase high-performance liquid chromatography as a highly efficient approach for dsRNA removal. Here, we present a comprehensive study of IP-RP LC purification on monolith chromatographic supports for mRNA polishing, demonstrating its ability to remove dsRNA, as well as hybridized RNA fragments and residual DNA template, which are not fully removed by mRNA capture methods. We develop step elution methodology, including at microgram scale with novel spin columns operated by centrifugation. We demonstrate SDVB efficiency across a range of molecular sizes and explore the necessity for temperature control for effective dsRNA removal from self-amplifying RNA. SDVB-purified mRNA and saRNA showed significantly increased transgene expression in cell-based assays and reduced the activation of cell autonomous innate immunity in A549 at early time points. Our findings highlight the importance of IP-RP purification for high-quality mRNA production, while simplifying the technological requirements for its adoption in clinical mRNA and saRNA manufacturing processes.

DNAzyme approach for simultaneous mRNA cap and poly(A) tail length analysis: A one-step method to multiple quality attributes

The dynamic landscape of mRNA technology highlights the need for innovative quality control (QC) strategies. In this study, we described an efficient one-step digestion approach for concurrent generation of 5'- and 3'-end fragments, enabling simultaneous mRNA capping and poly(A) tail analysis. Tailored 10-23-type DNAzymes, designed from 5'- and 3'-Untranslated Regions (UTRs), selectively cleaved mRNA to release both the 5'-Capped or uncapped short fragments and 3'-Poly(A) tail cleavage products. Polyacrylamide gel electrophoresis (PAGE) and ion pair reversed-phase liquid chromatography (IP-RP LC) analyses confirmed the production of 5'- and 3'-cleavage fragments in a single-step reaction, and LC-mass spectrometry (LC MS) validated these findings. The DNAzyme-mediated cleavage offers notable advantages over other assays for mRNA cap and tail characterization. Direct and simultaneous analysis of both capping efficiency and poly(A) tail length post-cleavage by DNAzymes, without additional purification steps and costly MS analysis, markedly streamlines the sample preparation and analysis process, making it highly suitable for QC testing.

RNA research for drug discovery: Recent advances and critical insight

The field of RNA research has experienced significant changes and is now at the forefront of contemporary drug development. This narrative overview explores the scientific developments and historical turning points in RNA research, emphasising the field's critical significance in the development of novel therapeutics. Important discoveries like antisense oligonucleotides (ASOs), mRNA therapies, and RNA interference (RNAi) have created novel treatment options that can be targeted, such as the ground-breaking mRNA vaccinations against COVID-19. Advances in high-throughput sequencing, single-cell RNA sequencing, and epitranscriptomics have further unravelled the complexity of RNA biology, shedding light on the intricacies of gene regulation and cellular diversity. The integration of computational tools and bioinformatics has propelled the identification of RNA-based biomarkers and the development of RNA therapeutics. Despite significant progress, challenges such as RNA stability, delivery, and off-target effects persist, necessitating continuous innovation and ethical considerations. This review provides a critical insight into the current state and prospects of RNA research, emphasising its transformative potential in drug discovery. By examining the interplay between technological advancements and therapeutic applications, we underscore the promising horizon for RNA-based interventions in treating a myriad of diseases, marking a new era in precision medicine.

Evaluation of mRNA Transfection Reagents for mRNA Delivery and Vaccine Efficacy via Intramuscular Injection in Mice

The selection of an effective delivery carrier is crucial to assessing mRNA-based vaccines and therapeutics in vivo. Although lipid nanoparticles (LNPs) are commonly used for mRNA delivery, the LNP-mRNA formulation process is laborious and time-consuming and requires a high-cost microfluidic device. Instead, mixing with commercial reagents may simplify mRNA transfection into cells. However, their potential as in vivo carriers in intramuscular vaccination in mouse models remains unclear. In this study, we used three types of commercial RNA transfection reagents, MessengerMAX (MAX; liposome), TransIT-mRNA (IT; cationic polymer), and Invivofectamine (IVF; LNP), to produce nanoparticles directly by pipetting. The particle characteristics and mRNA delivery efficacy of the mRNA-transfection reagent mixtures were analyzed. Additionally, immune responses to vaccine efficacy and protective immunity of the mRNA mixtures as vaccine antigens were evaluated in a mouse model. Although MAX and IT showed high in vitro transfection efficiencies, their in vivo performances were limited. In contrast, IVF exhibited notable particle stability and homogeneity, making it a promising delivery carrier. Intramuscular IVF injection significantly enhanced both innate and adaptive immune responses with a robust systemic protein expression. Notably, when using SARS-CoV-2 Spike mRNA, IVF showed robust humoral immune responses, including production of IgG and neutralizing antibodies, thereby resulting in complete protection against SARS-CoV-2 infection. Therefore, these findings position IVF as an accessible and efficient mRNA carrier for evaluating mRNA vaccines and therapeutic efficacy in basic research.

Graphene Oxide-Modified Resin for Selective dsRNA Removal from In Vitro-Transcribed mRNA

Messenger RNA (mRNA) has proven to be an effective vaccine agent against unexpected pandemics, offering the advantage of rapidly producing customized therapeutics targeting specific pathogens. However, undesired byproducts, such as double-stranded RNA (dsRNA), generated during in vitro transcription (IVT) reactions may impede translation efficiency and trigger inflammatory cytokines in cells after mRNA uptake. In this study, we developed a facile method using PEGylated polystyrene resins that were further surface-modified with graphene oxide (GO@PEG-PS) for the removal of dsRNA from IVT mRNA. The GO@PEG-PS resin adsorbed mRNA due to the property of graphene oxide (GO), which preferentially adsorbs single-stranded nucleic acids over double-stranded nucleic acids in the presence of Mg2+. The resin-bound single-stranded (ss) RNA was readily desorbed with a mixture of EDTA and urea, possibly by chelating Mg2+ and disrupting hydrogen bonding, respectively. Spin-column chromatography with GO@PEG-PS for IVT mRNA eliminated at least 80% of dsRNA, recovering approximately 85% of mRNA. Furthermore, this procedure precluded the salt precipitation step after the IVT reaction, which fractionates mRNAs from the IVT components, including nucleotides and enzymes. The purified mRNA exhibited enhanced protein translation with reduced secretion of interferon (IFN)-β upon mRNA transfection. We anticipate that the mRNA purification chromatography system employing GO@PEG-PS resin will facilitate the removal of dsRNA contamination during mRNA production.

An LNP-mRNA vaccine protects fish against rhabdovirus infection

mRNA vaccines are poised to revolutionize disease prevention, following the approval of their administration to humans against SARS-CoV-2. Although they have been extensively studied for human applications, their potential in the veterinary field has not been explored yet. No mRNA vaccines have yet been reported for fish, despite the urgent need for new vaccines against emerging pathogens in aquaculture. As fish are ectotherms, temperature has an impact on their immune response and on many other biological parameters, including the composition of membrane lipids. It is therefore crucial to identify whether mRNA delivery systems are suitable for in vivo expression in fish for vaccine purposes. In the present study, we developed a proof of concept for mRNA vaccination in rainbow trout, a salmonid, demonstrating the efficacy of current vaccine delivery systems in fish. We used lipid nanoparticles (LNPs), which represent the most advanced delivery technology for mRNA. LNPs use a combination of lipid components that form an encapsulating structure offering protection and promote endosome escape of the mRNA to allow its expression. In vitro assays showed that LNPs are a powerful vehicle for mRNA delivery in fish cells without substantial toxicity. In vivo imaging in adult zebrafish (Danio rerio) demonstrated that intramuscular injection of LNP-formulated egfp mRNA resulted in local expression of eGFP for up to 7 days. An LNP-based mRNA vaccine candidate encoding the viral haemorrhagic septicaemia virus (VHSV) glycoprotein induced neutralizing antibodies in rainbow trout (Oncorhynchus mykiss) and offers almost complete protection against a lethal viral challenge. Our data constitute a first proof of concept of mRNA vaccination in fish, paving the way for new developments in veterinary vaccines for aquaculture.

Spike protein-related proteinopathies: A focus on the neurological side of spikeopathies

BACKGROUND

The spike protein (SP) is an outward-projecting transmembrane glycoprotein on viral surfaces. SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), responsible for COVID-19 (Coronavirus Disease 2019), uses SP to infect cells that express angiotensin converting enzyme 2 (ACE2) on their membrane. Remarkably, SP has the ability to cross the blood-brain barrier (BBB) into the brain and cause cerebral damage through various pathomechanisms. To combat the COVID-19 pandemic, novel gene-based products have been used worldwide to induce human body cells to produce SP to stimulate the immune system. This artificial SP also has a harmful effect on the human nervous system.

STUDY DESIGN

Narrative review.

OBJECTIVE

This narrative review presents the crucial role of SP in neurological complaints after SARS-CoV-2 infection, but also of SP derived from novel gene-based anti-SARS-CoV-2 products (ASP).

METHODS

Literature searches using broad terms such as "SARS-CoV-2", "spike protein", "COVID-19", "COVID-19 pandemic", "vaccines", "COVID-19 vaccines", "post-vaccination syndrome", "post-COVID-19 vaccination syndrome" and "proteinopathy" were performed using PubMed. Google Scholar was used to search for topic-specific full-text keywords.

CONCLUSIONS

The toxic properties of SP presented in this review provide a good explanation for many of the neurological symptoms following SARS-CoV-2 infection and after injection of SP-producing ASP. Both SP entities (from infection and injection) interfere, among others, with ACE2 and act on different cells, tissues and organs. Both SPs are able to cross the BBB and can trigger acute and chronic neurological complaints. Such SP-associated pathologies (spikeopathies) are further neurological proteinopathies with thrombogenic, neurotoxic, neuroinflammatory and neurodegenerative potential for the human nervous system, particularly the central nervous system. The potential neurotoxicity of SP from ASP needs to be critically examined, as ASPs have been administered to millions of people worldwide.

Highly immunogenic DNA/LION nanocarrier vaccine potently activates lymph nodes inducing long-lasting immunity in macaques

A SARS-CoV-2 spike DNA vaccine formulated with a cationic nanoparticle emulsion (LION) was tested in Rhesus macaques. It induced robust, long-lasting (>2 years) cellular and humoral immunity, including increased neutralization breadth. T cell responses were predominantly CD8+, in contrast to other DNA vaccines. A rapid transient cytokine/chemokine response was associated with expansion and trafficking of myeloid cells and lymphocytes. Increased proliferation and dynamic changes between blood and lymph node (LN) were found for monocyte-derived cells, dendritic cells, and B and T cells, resulting in activation of LN and expansion of germinal centers (GCs), likely critical in shaping long-lasting adaptive immunity. Significant GC expansion of B, CD4-, and CD8- cells, including the Tfc3 subset, reflects a balanced immune response, including antibody (Ab) development. DNA/LION vaccination activates myeloid and lymphoid cells in blood and LN and promotes effective antigen presentation, resulting in sustained antigen-specific cellular and humoral responses, emerging as an effective DNA vaccine delivery platform.

Optimizing Peptide-Conjugated Lipid Nanoparticles for Efficient siRNA Delivery across the Blood-Brain Barrier and Treatment of Glioblastoma Multiforme

Glioblastoma multiforme (GBM) is a WHO grade 4 glioma and the most common malignant primary brain tumor. Addressing the clinical management of GBM presents an exceptionally daunting and intricate challenge, particularly in overcoming the blood-brain barrier (BBB) to deliver effective therapies to the brain. Nanotechnology-based drug delivery systems have exhibited considerable promise in tackling this aggressive brain cancer. However, the BBB remains a key challenge in achieving effective brain delivery of nanocarriers. Here, we have optimized a lipid nanoparticle (LNP) formulation (C2) and modified the LNP with Angiopep-2 peptide, which exhibits the most significant improvements in blood-brain barrier penetration and brain accumulation (about 2.23% injection dose). Using the Ang-2-coupled C2 LNP formulation, we researched the therapeutic effect of Polo-like Kinase 1(PLK1)-targeted siRNA delivery to treat a mouse model of GBM. The optimized LNP formulation was demonstrated to significantly inhibit mouse GBM growth and extend the median survival of mice (2.18-fold). This work demonstrates the efficacy of a brain-targeted siRNA delivery system in GBM treatment. As the understanding of the role of RNAs in GBM deepens and innovative delivery methods are continually developed and refined, RNA-based therapies could emerge as a crucial breakthrough in the advancement of brain tumor treatment.

Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines

Despite the widespread use of mRNA vaccines against COVID-19, little is known about the metabolism of therapeutic RNAs. Here we use nanopore sequencing1-3 to analyse individual therapeutic mRNA molecules, focusing on their poly(A) tails. We show that the Moderna mRNA-1273 vaccine4 has a poly(A) tail of around 100 nucleotides, followed by an mΨCmΨAG sequence. In cell lines, mRNA-1273 undergoes rapid degradation initiated by mΨCmΨAG removal, followed by CCR4-NOT-mediated deadenylation. However, in medically relevant preclinical models, particularly in macrophages, mRNA-1273 poly(A) tails are extended to up to 200 nucleotides by the TENT5A poly(A) polymerase5-7, which is induced by the vaccine. Re-adenylation, which stabilizes target mRNAs, is consistently observed in synthetic mRNAs that encode proteins targeted to the endoplasmic reticulum, such as ovalbumin or antigens from Zika virus8 or the malaria parasite9. The extent of re-adenylation varies: the BioNTech-Pfizer BNT162b2 vaccine10 shows less potent re-adenylation than mRNA-1273, which correlates with a smaller proportion of membrane-associated BNT162b2. This highlights the crucial role of spatial accessibility to ER-resident TENT5A in determining re-adenylation efficiency. In vivo, TENT5A is expressed in immune cells that take up mRNA vaccine, and TENT5A deficiency reduces specific immunoglobulin production for mRNA vaccines after immunization in mice. Overall, our findings reveal a principle for enhancing the efficacy of therapeutic mRNAs, paving the way for improvement.

Cyclic Acetal-Based Lipid Nanoparticles Deliver mRNA In Vivo for Tumor Immunotherapy

Lipid nanoparticle (LNP)-mRNA-based tumor immunotherapy needs to address challenges such as low efficacy of mRNA delivery, targeted protein expression, and compromised innate immunogenicity. Here, we screen a panel of 16 cyclic acetal-based ionizable lipid nanoparticles by in vitro and in vivo assays to develop a more effective and safer system specifically for tumor immunotherapy and mRNA delivery. Furthermore, by incorporating a cyclic acetal-based adjuvant lipid YK-TLR-001, two optimized cyclic acetal-based LNP formulations (YK-712 and YK-716) are demonstrated to enhance mRNA expression in the spleens and to induce exceptional maturation of antigen-presenting cells (APCs) and to promote antigen presentation. Moreover, animal studies treated with these formulations show activated cellular immunogenicity in healthy mice and inhibited tumor growth in the B16F10 melanoma model. Thus, the cyclic acetal-based LNPs with YK-TLR-001 present a promising direction in the design of mRNA vectors for the advancement of mRNA tumor immunotherapy.

Current Trends in Messenger RNA Technology for Cancer Therapeutics

Messenger RNA (mRNA)-based therapy has revolutionized cancer research by enabling versatile delivery systems for therapeutic applications. The future of mRNA-based cancer therapies shows promise amidst challenges such as delivery efficiency, immunogenicity, and tumor heterogeneity. Recent progress has adapted various strategies such as design flexibility, scalable production, and targeted delivery capabilities to enhance the potential in personalized cancer therapy. Further research to optimize delivery for enhanced outcomes and efficacy in solid tumors is warranted. Therefore, we aim to explore the current landscape and future prospects of mRNA technology across various therapeutic platforms.

Enhanced in vitro transfection efficiency of mRNA-loaded polyplexes into natural killer cells through osmoregulation

High expression of externally injected in vitro transcribed (IVT) mRNA in natural killer (NK) cells is a prerequisite for NK cell-mediated cell therapy. To enhance the transfection efficacy of IVT mRNA-loaded polyplexes, we exposed NK cells to a hypertonic condition during transfection, which facilitated endo/exocytosis to maintain the isotonic state of the cells. The transfection efficacy of IVT mRNA was significantly enhanced after 24 h, which was mainly due to the facilitated cellular uptake and endosomal escape of the polyplexes. Interestingly, osmotic alterations in NK cells significantly affect the expression levels of endosome-escape-related genes in ion channels. Treatment with a mild hypertonic condition exhibited negligible toxicity to NK cells, without disturbing the integrity of the cellular membranes or the innate cytotoxic abilities of NK cells against cancer cells. These results demonstrate that the hypertonic treatment of NK cells enhances the transfection efficacy of IVT mRNA to produce genetically engineered NK cells.

Exogenous RNA surveillance by proton-sensing TRIM25

Exogenous messenger RNAs (mRNAs) require cellular machinery for delivery and translation but also encounter inhibitory factors. To investigate their regulation, we performed genome-wide CRISPR screens with in vitro-transcribed mRNAs in lipid nanoparticles (LNPs). Heparan sulfate proteoglycans (HSPGs) and vacuolar adenosine triphosphatase (V-ATPase) were identified as mediators of LNP uptake and endosomal escape, respectively. TRIM25-an RNA binding E3 ubiquitin ligase-emerged as a key suppressor inducing turnover of both linear and circular mRNAs. The endoribonucleases N4BP1 and KHNYN, along with the antiviral protein ZAP, act redundantly in TRIM25-dependent surveillance. TRIM25 specifically targets mRNAs delivered by endosomes, and its RNA affinity increases at acidic pH, suggesting activation by protons released from ruptured endosomes. N1-methylpseudouridine modification reduces TRIM25's RNA binding, helping RNAs evade its suppressive effect. This study comprehensively maps cellular pathways regulating LNP-mRNAs, offering insights into RNA immunity and therapeutics.

The advent of clinical self-amplifying RNA vaccines

Self-amplifying RNA (saRNA) technology is an emerging platform for vaccine development, offering significant advantages over conventional mRNA vaccines. By enabling intracellular amplification of RNA, saRNA facilitates robust antigen expression at lower doses, thereby enhancing both immunogenicity and cost-effectiveness. This review examines the latest advancements in saRNA vaccine development, highlighting its applications in combating infectious diseases. This includes viral pathogens such as SARS-CoV-2, influenza, and emerging zoonotic threats. We discuss the design and optimization of saRNA vectors to maximize antigen expression while minimizing adverse immune responses. Recent studies demonstrating the safety, efficacy, and scalability of saRNA-based vaccines in clinical settings are also discussed. We address challenges related to delivery systems, stability, and manufacturing, along with novel strategies being developed to mitigate these challenges. As the global demand for rapid, flexible, and scalable vaccine platforms grows, saRNA presents a promising solution with enhanced potency and durability. This review emphasizes the transformative potential of saRNA vaccines to shape the future of immunization strategies, particularly in response to pandemics and other global health threats.

Key considerations for a prostate cancer mRNA vaccine

Prostate cancer has the second highest cancer mortality rate in the UK in males. Early prostate cancer is typically asymptomatic, with diagnosis at a locally advanced or metastatic stage. In addition, the inherent heterogeneity of prostate cancer tumours differs significantly in terms of genetic, molecular, and histological features. The successful treatment of prostate cancer is therefore exceedingly challenging. Immunotherapies, particularly therapeutic vaccines, have been widely used in preclinical and clinical studies to treat various cancers. Sipuleucel-T was the first cancer vaccine approved by the FDA for the treatment of asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC), ushering in a new era of immunotherapy. In this review, the latest immunotherapy strategies for prostate cancer are considered with key tumour-associated antigens (TAA) and tumour-specific antigens (TSA) highlighted. The key components of mRNA vaccines include in vitro transcription, stability, and immunogenicity. Finally, strategies to circumvent in vivo mRNA degradation and approaches to optimise in vitro transcription (IVT) process are also discussed.

Restoring Tumor Cell Immunogenicity Through Ion-Assisted p53 mRNA Domestication for Enhanced In Situ Cancer Vaccination Effect

The efficacy of in situ cancer vaccines (ISCVs) is hindered by the poor immunogenicity of tumor cells. Here, PRIZE, a P53-repair nanosystem based on a virus-mimicking nanostructure to deliver p53 mRNA and Zn (II) into tumor cells, domesticating tumor cells by restoring intracellular P53 levels to bolster their immunogenicity, is designed. PRIZE ensures precise delivery to tumor sites, stabilizes p53 mRNA with its biomineralized structure, and extends the half-life of P53. This research highlights that PRIZE can efficiently repair P53 abnormalities in 4T1 (P53-deficient) and MC38 (P53-mutant) cells, subsequently upregulating the expression of major histocompatibility complex (MHC) class I molecules and the surface co-stimulatory molecule CD80 on tumor cells, enhancing antigen presentation and transforming tumor cells into in situ antigen reservoirs. The co-delivered photothermal agent (ICG) can trigger immunogenic cell death under laser irradiation, effectively releasing tumor-associated antigens, and inducing the formation of ISCVs. Importantly, in P53 abnormal tumor mouse models, the induced ISCVs initiate the cancer immune cycle (CIC), demonstrating outstanding tumoricidal immunity and effectively thwarting tumor metastasis and postoperative recurrence, which provides valuable insights for advancing personalized cancer immunotherapy.

A review of advances in in vitro RNA preparation by ssRNAP

In vitro transcription (IVT) based on single-subunit RNA polymerase (ssRNAP) has enhanced the widespread application of RNA drugs in the biomedical field, showcasing unprecedented potential for disease prevention and treatment. While the classical enzyme T7 RNA polymerase (T7 RNAP) has driven significant progress in RNA production, several challenges persist. These challenges include the selectivity of the initiation nucleotide, low incorporation efficiency of modified nucleotides, limited processivity on certain templates, heterogeneity at the 3' end of RNA products, and high level of double-stranded RNA (dsRNA) byproducts. No review has systematically addressed the efforts to overcome these challenges. To fill this gap, we reviewed recent advances in engineering T7 RNAP variants and the discovery of novel ssRNAPs aimed at addressing the shortcomings of T7 RNAP. We also discussed the underlying mechanisms of ssRNAP-mediated byproduct formation, strategies to mitigate dsRNA production using modified nucleotides, and for the first time to sorted out the application of artificial intelligence in IVT. Overall, this review summarizes the advances in RNA synthesis via IVT and provides potential strategies for improving RNA products. We believe that ssRNAPs with more excellent performance will be on the stage of RNA synthesis in the near future to meet the growing demands of both scientific research and pharmaceutical industry.

Genetic editing of primary human dorsal root ganglion neurons using CRISPR-Cas9

CRISPR-Cas9 is now the leading method for genome editing and is advancing for the treatment of human disease. CRIPSR has promise in treating neurological diseases, but traditional viral-vector-delivery approaches have neurotoxicity limiting their use. Here we describe a simple method for non-viral transfection of primary human DRG (hDRG) neurons for CRISPR-Cas9 editing. We edited TRPV1, NTSR2, and CACNA1E using a lipofection method with CRISPR-Cas9 plasmids containing reporter tags (GFP or mCherry). Transfection was successfully demonstrated by the expression of the reporters two days post-administration. CRISPR-Cas9 editing was confirmed at the genome level with a T7-endonuclease-I assay; protein level with immunocytochemistry and Western blot; and functional level through capsaicin-induced Ca2+ accumulation in a high-throughput compatible fluorescent imaging plate reader (FLIPR) system. This work establishes a reliable, target specific, non-viral CRISPR-Cas9-mediated genetic editing in primary human neurons with potential for future clinical application for sensory diseases.

Polyplex Nanomicelle-Mediated Pgc-1α4 mRNA Delivery Via Hydrodynamic Limb Vein Injection Enhances Damage Resistance in Duchenne Muscular Dystrophy Mice

Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, leading to the absence of dystrophin and progressive muscle degeneration. Current therapeutic strategies, such as exon-skipping and gene therapy, face limitations including truncated dystrophin production and safety concerns. To address these issues, a novel mRNA-based therapy is explored using polyplex nanomicelles to deliver mRNA encoding peroxisome proliferator-activated receptor gamma coactivator 1 alpha isoform 4 (PGC-1α4) via hydrodynamic limb vein (HLV) administration. Using an in vivo muscle torque measurement technique, it is observed that nanomicelle-delivered Pgc-1α4 mRNA significantly improved muscle damage resistance and mitochondrial activity in mdx mice. Specifically, HLV administration of Pgc-1α4 mRNA in dystrophic muscles significantly relieved the torque reduction and myofiber injury induced by eccentric contraction (ECC), boosted metabolic gene expression, and enhanced muscle oxidative capacity. In comparison, lipid nanoparticles (LNPs), a widely used mRNA delivery system, does not achieve similar protective effects, likely due to their intrinsic immunogenicity. This foundational proof-of-concept study highlights the potential of mRNA-based therapeutics for the treatment of neuromuscular diseases such as DMD and demonstrates the capability of polyplex nanomicelles as a safe and efficient mRNA delivery system for therapeutic applications.

Cancer Vaccines: A Novel Revolutionized Approach to Cancer Therapy

Over the past few decades, there has been significant advancement in the field of tumor immunotherapy. For many years vaccination against infectious diseases have been available. On the other hand very few cancer vaccines have been approved for human use. Ideal Cancer vaccines are biological response modifier work by stimulating both humoral and cellular immunity while overcoming the immunological suppression found in tumor. Two types of cancer vaccine: Prophylactic and therapeutic cancer vaccines are recommended for clinical use of individuals. HPV and HBV vaccines are the two widely used preventive vaccine used for treatment of cervical and hepatocellular carcinoma respectively and are approved by Food and Drug Administration (FDA). In therapeutic vaccine only three are approved: Sipuleucel T-cell vaccine for treatment refractory prostatic cancer, BCG vaccine for early bladder cancer and T-VEC for inoperable melanoma. Active ingredient in all cancer vaccines is an antigen. Antigens used for formulating cancer vaccines along with adjuvants optimizes immunogenicity in it. Heterogeneity within and between cancer types, screening and identifying suitable antigen specific to tumors and selection of vaccine delivery platforms are challenges in the development of vaccines. Adoptive cell therapy, Chimeric antigen receptor T cell therapy are recent breakthrough for cancer treatment.

Folding of mRNA-DNA Origami for Controlled Translation and Viral Vector Packaging

mRNA is an important molecule in vaccine development and treatment of genetic disorders. Its capability to hybridize with DNA oligonucleotides in a programmable manner facilitates the formation of RNA-DNA origami structures, which can possess a well-defined morphology and serve as rigid supports for mRNA delivery. However, to date, comprehensive studies on the requirements for efficient folding of mRNA into distinct mRNA-DNA structures while preserving its translation functionality remain elusive. Here, the impact of design parameters on the folding of protein-encoding mRNA into mRNA-DNA origami structures is systematically investigated and the importance of the availability of ribosome-binding sequences on the translation efficiency is demonstrated. Furthermore, these hybrid structures are encapsulated inside virus capsids resulting in protecting them against nuclease degradation and also in enhancement of their cellular uptake. This multicomponent system therefore showcases a modular and versatile nanocarrier. The work provides valuable insight into the design of mRNA-DNA origami structures contributing to the development of mRNA-based gene delivery platforms.

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

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

Characterisation and analysis of mRNA critical quality attributes using liquid chromatography based methods

mRNA technology has been successfully deployed to rapidly develop and mass-manufacture vaccines. Beyond vaccines, RNA-based therapeutics have potential for treatments for infectious diseases, cancer, metabolic disorders, cardiovascular conditions and autoimmune diseases. mRNA based vaccines and therapeutics work by translating exogenous mRNA into the target protein. Analytical methods for mRNA characterisation, lot release and stability testing of mRNA drug substance and drug product must be developed and performed to monitor critical quality attributes (CQAs). mRNA is a highly polar molecule due to its extensive negatively charged phosphodiester backbone. Its single stranded nature forms dynamic alternative secondary structures that can generate potential sample heterogeneity, creating challenges for the analysis and characterisation of this large biomolecule. In this review, we describe current analytical methods, focussing on high performance liquid chromatography in conjunction with both UV detection and mass spectrometry for the analysis and characterisation of mRNA. In particular, we describe recent developments covering a wide range of methods centred on liquid chromatography for the analysis of important CQAs including mRNA identity, mRNA integrity, 5' capping efficiency and poly(A) tail length and heterogeneity.

Generation of tolerogenic antigen-presenting cells in vivo via the delivery of mRNA encoding PDL1 within lipid nanoparticles

Tolerogenic antigen-presenting cells (APCs) are promising as therapeutics for suppressing T cell activation in autoimmune diseases. However, the isolation and ex vivo manipulation of autologous APCs is costly, and the process is customized for each patient. Here we show that tolerogenic APCs can be generated in vivo by delivering, via lipid nanoparticles, messenger RNA coding for the inhibitory protein programmed death ligand 1. We optimized a lipid-nanoparticle formulation to minimize its immunogenicity by reducing the molar ratio of nitrogen atoms on the ionizable lipid and the phosphate groups on the encapsulated mRNA. In mouse models of rheumatoid arthritis and ulcerative colitis, subcutaneous delivery of nanoparticles encapsulating mRNA encoding programmed death ligand 1 reduced the fraction of activated T cells, promoted the induction of regulatory T cells and effectively prevented disease progression. The method may allow for the engineering of APCs that target specific autoantigens or that integrate additional inhibitory molecules.

Clinical development of therapeutic mRNA applications

mRNA therapeutics are emerging as a transformative approach in modern medicine, providing innovative, highly adaptable solutions for a wide range of diseases, from viral infections to cancer. Since the approval of the first mRNA therapeutic-the coronavirus disease 2019 vaccines in 2021-we have identified more than 70 current clinical trials utilizing mRNA for various diseases. We propose classifying mRNA therapeutics into four main categories: vaccines, protein replacement therapies, antibodies, and mRNA-based cell and gene therapies. Each category can be further divided into subcategories. Vaccines include those targeting viral antigens, bacterial or parasitic antigens, general and individualized cancer antigens, and self-antigens. Protein replacement therapies include maintenance therapeutics designed to treat genetic disorders and interventional therapeutics, where delivering therapeutic proteins could improve patient outcomes, such as vascular endothelial growth factor A for ischemic heart disease or proinflammatory cytokines in cancer. Therapeutic antibodies are based on mRNA sequences encoding the heavy and light chains of clinically relevant antibodies, enabling patient cells to produce them directly, bypassing the costly and complex process of manufacturing protein-ready antibodies. Another category of mRNA-based therapeutics encompasses cell and gene therapies, including CRISPR with mRNA-mediated delivery of Cas9 and the in vivo generation of cells expressing CAR through mRNA. We discuss examples of mRNA therapeutics currently in clinical trials within each category, providing a comprehensive overview of the field's progress and highlighting key advancements as of the end of 2024.

Buffer Specificity of Ionizable Lipid Nanoparticle Transfection Efficiency and Bulk Phase Transition

Lipid nanoparticles (LNPs) are efficient and safe carriers for mRNA vaccines based on advanced ionizable lipids. It is understood that the pH-dependent structural transition of the mesoscopic LNP core phase plays a key role in mRNA transfer. However, buffer-specific variations in transfection efficiency remain obscure. Here we analyze the effect of the buffer type on the transfection efficiency of LNPs. We find that LNPs formulated with the cationic ionizable lipids DLin-MC3-DMA (MC3), SM-102, and ALC-315 in citrate compared to phosphate and acetate buffers exhibit earlier onset and stronger mRNA-GFP expression in vitro. Using synchrotron small-angle X-ray scattering (SAXS) we determine the buffer specificity of the pH-dependent structure of ionizable lipid/cholesterol/water mesophases that serve as model systems for the LNP core phase. The results show that the phase transition from inverse micellar to inverse hexagonal with decreasing pH is shifted to a lower transition pH for acetate and phosphate compared with citrate buffer. Based on continuum theory and ion-specific adsorption obtained from all-atom MD simulations, we propose a mechanism for buffer specificity. Citrate stabilizes the inverse hexagonal phase thus shifting the formation of HII to a higher pH. By contrast, phosphate and acetate stabilize LII. It stands to reason that the inverse micellar to inverse hexagonal transition, which is facilitated in citrate buffer, enables a sensitized pH response of the LNP core phase. This, in turn, enhances endosomal release efficiency and accounts for the earlier onset of gene expression observed in LNPs prepared with citrate buffer.

Proceedings of the 2023 Annual Scientific Meeting of the French Society of Toxicologic Pathology (SFPT) on Preclinical Development and Therapeutic Applications of mRNA-Based Technologies

The 2023 annual scientific meeting of the French Society of Toxicologic Pathology (Société Française de Pathologie Toxicologique, SFPT), entitled "mRNA-based technologies: preclinical development and therapeutic applications," was held in Lyon (France) on May 25 to 26, 2023. The aim of the meeting was to discuss the biology, immunology, and preclinical development of messenger RNA (mRNA)-based vaccines and therapeutics, including immuno-oncology and rare diseases, as well as the regulatory aspect of the COVID-19 vaccines and an overview of the principles and applications of in situ hybridization techniques. This article presents the summary of five lectures along with selected figures, tables, and key literature references on this topic.

An epitope-directed mRNA vaccine inhibits tumor metastasis through the blockade of MICA/B α1/2 shedding

Antigenic peptide-based mRNA vaccines have been explored for immunotherapeutic use in various types of cancer because of their advantages in activating durable and specific immune responses. However, their role in modulating tumor metastasis is still unclear. Here, we identify a conserved linear epitope-based peptide, Ma3P, located in the proteolytic region of major histocompatibility complex (MHC) class I-related chain A (MICA) α3 and further design mCM10-L, an mRNA vaccine that encodes the carrier protein CRM197 and 10 tandem repeats of Ma3P. We demonstrate that vaccination with mCM10-L induces the production of specific antibodies that block MICA/B α1/2 shedding, activate CD8+ T cells and natural killer (NK) cells, and significantly inhibit MICA/B+ tumor metastasis in mice. Furthermore, mCM10-L stimulation triggers the production of specific antibodies to promote MICA/B-mediated immune killing in an in-vitro-interacting human organoid model and humanized mice. Our results indicate the potential clinical application prospects of the mCM10-L vaccine.

Lipid Nanoparticles for mRNA Delivery in Cancer Immunotherapy

Cancer immunotherapy is poised to be one of the major modalities for cancer treatment. Messenger RNA (mRNA) has emerged as a versatile and promising platform for the development of effective cancer immunotherapy. Delivery systems for mRNA therapeutics are pivotal for their optimal therapeutic efficacy and minimal adverse side effects. Lipid nanoparticles (LNPs) have demonstrated a great success for mRNA delivery. Numerous LNPs have been designed and optimized to enhance mRNA stability, facilitate transfection, and ensure intracellular delivery for subsequent processing. Nevertheless, challenges remain to, for example, improve the efficiency of endosomal escape and passive targeting. This review highlights key advancements in the development of mRNA LNPs for cancer immunotherapy. We delve into the design of LNPs for mRNA delivery, encompassing the chemical structures, characterization, and structure-activity relationships (SAR) of LNP compositions. We discuss the key factors influencing the transfection efficiency, passive targeting, and tropism of mRNA-loaded LNPs. We also review the preclinical and clinical applications of mRNA LNPs in cancer immunotherapy. This review can enhance our understanding in the design and application of LNPs for mRNA delivery in cancer immunotherapy.

Nucleic Acid Drugs in Radiotherapy

Radiotherapy remains a cornerstone of cancer treatment, using high-energy radiation to induce DNA damage in tumor cells, leading to cell death. However, its efficacy is often hindered by challenges such as radiation resistance and side effects. As a powerful class of functional molecules, nucleic acid drugs (NADs) present a promising solution to these limitations. Engineered to target key pathways like DNA repair and tumor hypoxia, NADs can enhance radiotherapy sensitivity. NADs can also serve as delivery vehicles for radiotherapy agents such as radionuclides, improving targeting accuracy and minimizing side effects. This review explores the role of NADs in optimizing radiotherapy, highlighting their mechanisms, clinical applications, and synergies with radiotherapy, ultimately offering a promising strategy for improving patient outcomes in cancer therapy.

Polyethylene glycol precipitation: fundamentals and recent advances

Downstream processing continues to face significant bottlenecks due to current purification technologies and improvements in upstream. Chromatography systems have been the primary method for purification due to their high yields and purities. However, the use of high-titer-producing strains has highlighted limitations in chromatographic steps, including mass transfer limitations, low capacity, and scalability issues. These challenges, combined with the growing interest in fully continuous manufacturing processes, have led to a widespread interest in alternative to affinity chromatography systems. Polyethylene glycol precipitation has been demonstrated to be a powerful, flexible, easily scalable, and titer-independent methodology for purifying therapeutic proteins such as monoclonal antibodies, achieving yields and purities comparable to chromatography systems. Furthermore, it also holds great potential for simplifying the current purification processes of new modalities and overcome current bottlenecks in downstream processing. Herein, we discuss the latest advances in polyethylene glycol precipitation as a purification technology and explore its future research directions and potential applications.

Research progress of mosquito-borne virus mRNA vaccines

In recent years, mRNA vaccines have emerged as a leading technology for preventing infectious diseases due to their rapid development and high immunogenicity. These vaccines encode viral antigens, which are translated into antigenic proteins within host cells, inducing both humoral and cellular immune responses. This review systematically examines the progress in mRNA vaccine research for major mosquito-borne viruses, including dengue virus, Zika virus, Japanese encephalitis virus, Chikungunya virus, yellow fever virus, Rift Valley fever virus, and Venezuelan equine encephalitis virus. Enhancements in mRNA vaccine design, such as improvements to the 5' cap structure, 5'UTR, open reading frame, 3'UTR, and polyadenylation tail, have significantly increased mRNA stability and translation efficiency. Additionally, the use of lipid nanoparticles and polymer nanoparticles has greatly improved the delivery efficiency of mRNA vaccines. Currently, mRNA vaccines against mosquito-borne viruses are under development and clinical trials, showing promising protective effects. Future research should continue to optimize vaccine design and delivery systems to achieve broad-spectrum and long-lasting protection against various mosquito-borne virus infections.

RNA Therapies in Cardio-Kidney-Metabolic Syndrome: Advancing Disease Management

Cardio-Kidney-Metabolic (CKM) Syndrome involves metabolic, kidney, and cardiovascular dysfunction, disproportionately affecting disadvantaged groups. Its staging (0-4) highlights the importance of early intervention. While current management targets hypertension, heart failure, dyslipidemia, and diabetes, RNA-based therapies offer innovative solutions by addressing molecular mechanisms of CKM Syndrome. Emerging RNA treatments, including antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs), show promise in slowing disease progression across CKM stages. For example, ASOs and siRNAs targeting ApoC-III and ANGPTL3 reduce triglycerides and LDL cholesterol, while siRNAs improve blood pressure control by targeting the renin-angiotensin-aldosterone system. Obesity treatments leveraging miRNAs and circRNAs tackle a key CKM risk factor. In heart failure and diabetes, RNA-based therapies improve cardiac function and glucose control, while early kidney disease trials show potential for RNAi in acute injury. Further research is essential to refine these therapies and ensure equitable access.

Structural and functional characterization of a histidylated liposome for mRNA delivery

The development of lipid-based mRNA delivery systems has significantly facilitated recent advances in mRNA-based therapeutics. Liposomes, as the pioneering class of mRNA vectors, continue to lead in clinical trials. We previously developed a histidylated liposome that demonstrated efficient nucleic acid delivery. In this study, the liposome preparation process was optimized by freeze-drying followed by extrusion to homogenize size distribution and improve storage stability. A comprehensive characterization of these LYX liposomes was performed, including evaluation in cellular and murine animal models. LYX liposomes can be stored for up to one year at 4 °C, maintaining a stable size (150 ± 10 nm) and polydispersity index (0.10 ± 0.02), while preserving their transfection efficacy. They exhibit high encapsulation efficacy (∼95 %) and protect mRNA from RNase degradation. Lamellar organization was confirmed by Small Angle X-ray Scattering and CryoTEM, and intracellular trafficking was examined using confocal microscopy. LYX-mRNA lipoplexes can transfect both cell lines and primary cells, albeit with a lower transfection efficacy compared to the commercial Lipofectamine MessengerMAX™ vector. Our data suggest that this could be attributed to slower cell uptake and reduced endosomal escape of LYX. LYX liposomes effectively delivered mRNA encoding therapeutic BMP2 and BMP9 molecules, producing significant amounts of functional proteins that successfully induced BMP signaling. In addition, in vivo studies demonstrated the potential of LYX lipoplexes when incorporated into hydrogels and implanted subcutaneously in mice. These findings provided evidence that LYX liposomes are a promising platform for mRNA delivery, offering versatility for multiple applications.

Cyclic Poly(2-methyl-2-oxazoline)-Lipid Conjugates Are Good Alternatives to Poly(ethylene glycol)-Lipids for Lipid Nanoparticle mRNA Formulation

Lipid nanoparticles (LNPs) with ionizable cationic lipids have revolutionized RNA drug delivery, playing a key role in the success of mRNA-based therapeutics, such as COVID-19 vaccines. A vital component of these LNPs is the poly(ethylene glycol) (PEG)-lipid conjugate, which enhances colloidal stability but may trigger the production of anti-PEG antibodies, resulting in accelerated blood clearance (ABC) and diminished therapeutic efficacy. In this study, we explored poly(2-methyl-2-oxazoline) (PMOXA) as an alternative stabilizing agent for mRNA LNPs. We synthesized both cyclic and linear PMOXA, conjugated them to dialkyl lipids, and created lipid-polymer amphiphiles. We systematically evaluated how polymer topology influenced the physicochemical properties of LNPs, including in vitro cellular uptake, transfection efficiency, and protein corona formation, and directly compared these properties with those of PEG-stabilized counterparts. In vivo experiments in mice further assessed the biodistribution and protein translation efficiency of these LNPs following intravenous administration. Our results showed that cyclic PMOXA conjugates not only matched but potentially surpassed the performance of PEG-based analogues, highlighting their promise as a superior alternative in mRNA-LNP formulations.

Evaluation of Lipid-Based Transfection in Primary Monocytes Within an Ex Vivo Whole-Blood Model

Transfection is a fundamental method in biomedical research to study intracellular molecular mechanisms by manipulating target protein expression. Various methods have been developed to deliver nucleic acids into the cells of interest in vitro, with chemical transfection by cationic lipids being the most widely used for RNA interference (RNAi). However, translating these in vitro results into in vivo remains a significant challenge. In this study, we established an ex vivo transfection model using cationic lipids in human whole blood. Three different lipid-based reagents were evaluated regarding toxicity, transfection efficiency, and immunogenicity across leukocyte populations using spectral flow cytometry. CD14+ monocytes were identified as the primary population to be transfected by cationic lipids in whole blood. To assess immunogenicity, the monocyte-specific activation markers CD80 and human leukocyte antigen DR isotype (HLA-DR) were analyzed upon transfection. Our results demonstrated that Lipofectamine RNAiMAX outperforms the other two reagents, showing low toxicity and high transfection efficiency in combination with a minimal potential for monocyte activation. Functional knockdown experiments using siRNA targeting CIITA and the microRNA mir-3972 targeting HLA-DRA showed dose-dependent suppression in HLA-DR expression. This study provides the framework for preliminary testing of RNAi in a physiologically relevant ex vivo model, enabling assessment of key endpoints such as toxicity, transfection efficiency, and immune activation potential of gene delivery systems.

Monitoring mRNA vaccine antigen expression in vivo using PET/CT

Noninvasive visualization of the distribution and persistence of mRNA vaccine antigen expression in mammalian systems has implications for the development and evaluation of future mRNA vaccines. Here, we genetically fuse E. coli dihydrofolate reductase (eDHFR) to the delta furin diproline modified SARS-CoV-2 spike glycoprotein (S2P∆f) mRNA vaccine and image its expression in female mice and male non-human primates using [18F]fluoropropyl-trimethoprim ([18F]FP-TMP). Whole body positron emission tomography (PET) imaging revealed transient expression of the vaccine antigen in the injection site and draining lymph nodes (dLNs). Fusion of eDHFR did not impact S2P immunogenicity and no humoral or cellular immune response was detected against eDHFR in either species. In this work, we show that eDHFR can be used as an mRNA-encoded PET reporter gene to monitor the spatiotemporal dynamics of mRNA vaccine antigen expression in vivo. This technique could be applied in clinical translation of future mRNA vaccines or therapeutics.

The Progress and Evolving Trends in Nucleic-Acid-Based Therapies

Nucleic-acid-based therapies have emerged as a pivotal domain within contemporary biomedical science, marked by significant advancements in recent years. These innovative treatments primarily operate through the precise binding of DNA or RNA molecules to discrete target genes, subsequently suppressing the expression of the target proteins. The spectrum of nucleic-acid-based therapies encompasses antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), etc. Compared to more traditional medicinal approaches, nucleic-acid-based therapies stand out for their highly targeted action on specific genes, as well as their potential for chemical modification to improve resistance to nucleases, ensuring sustained therapeutic activity and mitigating immunogenicity concerns. Nevertheless, these molecules' limited cellular permeability necessitates the deployment of delivery vectors to enhance their intracellular uptake and stability. As nucleic-acid-based therapies progressively display promising pharmacodynamic profiles, there has been a burgeoning interest in these treatments for applications in clinical research. This review aims to summarize the variety of nucleic acid drugs and their mechanisms, evaluate the present status in research and application, discourse on prospective trends, and potential challenges ahead. These innovative therapeutics are anticipated to assume a pivotal role in the management of a wide array of diseases.

DRAG: design RNAs as hierarchical graphs with reinforcement learning

The rapid development of RNA vaccines and therapeutics puts forward intensive requirements on the sequence design of RNAs. RNA sequence design, or RNA inverse folding, aims to generate RNA sequences that can fold into specific target structures. To date, efficient and high-accuracy prediction models for secondary structures of RNAs have been developed. They provide a basis for computational RNA sequence design methods. Especially, reinforcement learning (RL) has emerged as a promising approach for RNA design due to its ability to learn from trial and error in generation tasks and work without ground truth data. However, existing RL methods are limited in considering complex hierarchical structures in RNA design environments. To address the above limitation, we propose DRAG, an RL method that builds design environments for target secondary structures with hierarchical division based on graph neural networks. Through extensive experiments on benchmark datasets, DRAG exhibits remarkable performance compared with current machine-learning approaches for RNA sequence design. This advantage is particularly evident in long and intricate tasks involving structures with significant depth.

Ultrasound-Enhanced Spleen-Targeted mRNA Delivery via Fluorinated PEGylated Lipid Nanoparticles for Immunotherapy

Lipid nanoparticles (LNPs) based messenger RNA (mRNA) therapeutics hold immense promise for treating a wide array of diseases, while their nonhepatic organs targeting and insufficient endosomal escape efficiency remain challenges. For LNPs, polyethylene glycol (PEG) lipids have a crucial role in stabilizing them in aqueous medium, but they severely hinder cellular uptake and reduce transfection efficiency. In this study, we designed ultrasound (US)-assisted fluorinated PEGylated LNPs (F-LNPs) to enhance spleen-targeted mRNA delivery and transfection. Through liquid-to-gas phase transition, we enabled the controlled shedding of fluorinated PEG lipids from F-LNPs, facilitating cellular uptake, membrane fusion, and mRNA release. In vivo results demonstrated that US-assisted F-LNPs increased mRNA transfection approximately 4.0-fold in the spleen following intravenous administration. Notably, the F-LNPs achieved effective mRNA delivery to antigen-presenting cell subsets, such as dendritic cells, macrophages, and B cells. The targeted delivery of full-length ovalbumin-encoding mRNA vaccine induced significant CD8+ T cell response and exhibited excellent therapeutic effect against the ovalbumin-transduced B16F10 tumor model. These findings establish a novel strategy for spleen-specific mRNA delivery through the combination of fluorinated PEG lipids and US treatment, which holds substantial promise for enhancing the efficacy of immunotherapy, potentially broadening the scope of clinical applications for mRNA-based therapy.

Engineered mitochondria in diseases: mechanisms, strategies, and applications

Mitochondrial diseases represent one of the most prevalent and debilitating categories of hereditary disorders, characterized by significant genetic, biological, and clinical heterogeneity, which has driven the development of the field of engineered mitochondria. With the growing recognition of the pathogenic role of damaged mitochondria in aging, oxidative disorders, inflammatory diseases, and cancer, the application of engineered mitochondria has expanded to those non-hereditary contexts (sometimes referred to as mitochondria-related diseases). Due to their unique non-eukaryotic origins and endosymbiotic relationship, mitochondria are considered highly suitable for gene editing and intercellular transplantation, and remarkable progress has been achieved in two promising therapeutic strategies-mitochondrial gene editing and artificial mitochondrial transfer (collectively referred to as engineered mitochondria in this review) over the past two decades. Here, we provide a comprehensive review of the mechanisms and recent advancements in the development of engineered mitochondria for therapeutic applications, alongside a concise summary of potential clinical implications and supporting evidence from preclinical and clinical studies. Additionally, an emerging and potentially feasible approach involves ex vivo mitochondrial editing, followed by selection and transplantation, which holds the potential to overcome limitations such as reduced in vivo operability and the introduction of allogeneic mitochondrial heterogeneity, thereby broadening the applicability of engineered mitochondria.

Poly(β-amino ester) polymer library with monomer variation for mRNA delivery

Non-viral vectors for mRNA delivery primarily include lipid nanoparticles (LNPs) and polymers. While LNPs are known for their high mRNA delivery efficiency, they can induce excessive immune responses and cause off-target effects, potentially leading to side effects. In this study, we aimed to explore polymer-based mRNA delivery systems as a viable alternative to LNPs, focusing on their mRNA delivery efficiency and potential application in mRNA vaccines. We created a library of poly(β-amino ester) (PBAE) polymers by combining various amine monomers and acrylate monomers. Through screening this polymer library, we identified specific polymer nanoparticles (PNPs) that demonstrated high mRNA expression efficiency, with sustained mRNA expression for up to two weeks. Furthermore, the PNPs showed mRNA expression only at the injection site and did not exhibit liver toxicity. Additionally, when assessing immune activation, the PNPs significantly induced T-cell immune activation and were effective in the plaque reduction neutralization test. These results suggest that polymer-based mRNA delivery systems not only hold potential for use in mRNA vaccines but also show promise for therapeutic applications.

Engineering EVs-Mediated mRNA Delivery Regulates Microglia Function and Alleviates Depressive-Like Behaviors

The development of new non-neurotransmitter drugs is an important supplement to the clinical treatment of major depressive disorder. The latest development of mRNA therapy provides the possibility for the treatment of some major diseases. The endoplasmic reticulum (ER) and mitochondria constitute a highly interconnected set of fundamental organelles within cells. The interconnection between them forms specific microdomains that play pivotal roles in calcium signaling, mitochondrial dynamics, inflammation, and autophagy. Perturbations in ER-mitochondrial connections may contribute to the progression of neurological disorders and other diseases. Herein, an extracellular vesicles-based delivery system, grounded in mRNA gene therapy and integrated with nanomedicine technology is devised. This system is engineered to traverse the blood-brain barrier and specifically target the central nervous system (CNS), facilitating the simultaneous delivery of mRNA drugs and metallic nanozymes into the brain. This dual-pronged approach, targeting ER and mitochondrial crosstalk, inhibits microglial overactivation, promotes M2 polarization of microglia, and suppresses the NF-κB signaling pathway. Consequently, it significantly alleviates Lipopolysaccharides-induced neuroinflammatory responses and ameliorates anxiety- and depression-like behaviors. This study demonstrates a novel antidepressant therapeutic strategy and establishes a new paradigm for mRNA gene therapy in CNS diseases.

Orthogonal RNA replication enables directed evolution and Darwinian adaptation in mammalian cells

Directed evolution in mammalian cells offers a powerful approach for advancing synthetic biology applications. However, existing mammalian-based directed evolution methods face substantial bottlenecks, including host genome interference, small library size and uncontrolled mutagenesis. Here we engineered an orthogonal alphaviral RNA replication system to evolve RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in proliferating mammalian cells. This system generates a large, continuously diversified library of replicative RNAs through replicase-limited mode of replication and inducible mutagenesis. Using REPLACE, we engineered fluorescent proteins and transcription factors. Notably, cells equipped with REPLACE can undergo Darwinian adaptation, allowing them to evolve in response to both cell-extrinsic and cell-intrinsic challenges. Collectively, this work establishes a powerful platform for advancing mammalian synthetic biology and cell engineering applications through directed evolution.

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

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

Nano Approaches to Nucleic Acid Delivery: Barriers, Solutions, and Current Landscape

Nucleic acid (NA) therapy holds tremendous potential for treating a wide range of genetic diseases by the delivery of therapeutic genes into target cells. However, significant challenges exist in safely and effectively delivering these genes to their intended locations. Viral vectors, though efficient, pose risks such as immunogenicity and mutagenesis. This has resulted in growing interest in non-viral, nanoparticle-based NA delivery systems. This review article describes various physiological barriers to NA delivery and explores nanoparticle-based NA delivery systems, including bioengineered nanoparticles, peptides, lipid nanoparticles, and polymeric nanoparticles, highlighting their unique features to overcome in vivo barriers for NA delivery. While these nanoparticle-based NA delivery systems offer a promising alternative to viral vectors, challenges related to cytotoxicity, reproducible synthesis, and cost need to be addressed. The current clinical landscape of NA delivery is also discussed, emphasizing the need for safer, scalable, and cost-effective solutions. Nanoparticles represent a promising future in NA therapy, with the possibility of developing clinically relevant, non-toxic, stable, and non-immunogenic delivery vehicles, paving the way for broader therapeutic applications and improved clinical outcomes.

Harnessing Synthetic Riboswitches for Tunable Gene Regulation in Mammalian Cells

RNA switches regulated by specific inducer molecules have become a powerful synthetic biology tool for precise gene regulation in mammalian systems. The engineered RNA switches can be integrated with natural RNA-mediated gene regulatory functions as a modular and customizable approach to probe and control cellular behavior. RNA switches have been used to advance synthetic biology applications, including gene therapy, bio-production, and cellular reprogramming. This review explores recent progress in the design and functional implementation of synthetic riboswitches in mammalian cells based on diverse RNA regulation mechanisms by highlighting recent studies and emerging technologies. We also discuss challenges such as off-target effects, system stability, and ligand delivery in complex biological environments. In conclusion, this review emphasizes the potential of synthetic riboswitches as a platform for customizable gene regulation in diverse biomedical applications.