RNA targeting with CRISPR-Cas13

Gliadin hydrolysates nanoparticles improve the bioavailability and antioxidant activity of berberine

Berberine (BBR) is an alkaloid with multiple physiological activities, but its low bioavailability limits its effectiveness in vivo. This study developed soluble nano delivery carriers using gliadin hydrolysates (GLH) to enhance BBR's bioavailability. The research evaluated the encapsulation efficiency, stability, release characteristics, and antioxidant capacities of GLH-BBR nanoparticles (GLH-BBR NPs) both in vitro and in vivo. Results showed that at a 5:1 GLH-to-BBR mass ratio, the encapsulation efficiency reached 74.95 %. GLH-BBR NPs increased DPPH radical scavenging from 19.19 % to 40.28 % and ABTS radical scavenging from 4.26 % to 60.96 %, compared to BBR alone. In vitro tests showed that GLH-BBR NPs inhibited BBR release during gastric digestion and promoted sustained release in the intestine. In addition, GLH-BBR NPs enhanced BBR's bioavailability and in vivo antioxidant activity. These findings support the development of sustainable peptide byproducts for high-quality delivery platforms.

CRISPR/CasRx-mediated RNA knockdown targeting β-catenin and Ihh signaling alleviates osteoarthritis

Osteoarthritis (OA) is a chronic degenerative joint disease. Currently, OA is incurable. Abnormal activation of canonical Wnt/β-catenin or Indian hedgehog (Ihh) signaling could lead to OA development and progression. This study aimed to determine if targeting β-catenin and Ihh signaling could yield an effective therapeutic intervention for OA disease. CRISPR/CasRx is a new RNA interference tool that can precisely and efficiently cleave single-strand RNAs. In this study, we screened CRISPR-derived RNA (crRNA) targeting Ctnnb1 and Smo in vitro and selected two optimal crRNAs for each gene. CasRx-mediated Ctnnb1 and Smo knockdown showed high efficiency and specificity with no obvious off-target effects in vitro. We then performed intra-articular injection of selected crRNAs driven by the adeno-associated virus into an OA mouse model. Micro-CT, histological, and histomorphometric analyses were conducted to evaluate the efficacy of CasRx approach on OA treatment. We found that the knockdown of Ctnnb1 and Smo decelerated pathological damage in the keen joint of the experimental OA mouse model. Our findings suggest that CasRx-mediated Ctnnb1 and Smo knockdown could be a potential strategy for OA treatment.

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.

Machine learning and statistical classification in CRISPR-Cas12a diagnostic assays

CRISPR-based diagnostics have gained increasing attention as biosensing tools able to address limitations in contemporary molecular diagnostic tests. To maximize the performance of CRISPR-based assays, much effort has focused on optimizing the chemistry and biology of the biosensing reaction. However, less attention has been paid to improving the techniques used to analyze CRISPR-based diagnostic data. To date, diagnostic decisions typically involve various forms of slope-based classification. Such methods are superior to traditional methods based on assessing absolute signals, but still have limitations. Herein, we establish performance benchmarks (total accuracy, sensitivity, and specificity) using common slope-based methods. We compare the performance of these benchmark methods with three different quadratic empirical distribution function statistical tests, finding significant improvements in diagnostic speed and accuracy when applied to a clinical data set. Two of the three statistical techniques, the Kolmogorov-Smirnov and Anderson-Darling tests, report the lowest time-to-result and highest total test accuracy. Furthermore, we developed a long short-term memory recurrent neural network to classify CRISPR-biosensing data, achieving 100 % specificity on our model data set. Finally, we provide guidelines on choosing the classification method and classification method parameters that best suit a diagnostic assay's needs.

A fluorescence biosensor for detecting LncRNA MALAT1 based on isothermal amplification by cyclic extension

BACKGROUND

Long non-coding RNA (lncRNA) Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1), a crucial regulator of gene expression, has emerged as a highly promising biomarker in the progression of various cancers. The clinical detection of lncRNA MALAT1 primarily relies on Reverse Transcription-Polymerase Chain Reaction (RT-PCR), which requires skilled operators and large, expensive thermal cycling equipment. These limitations have restricted the application of RT-PCR, particularly in resource-constrained settings.

RESULTS

In this study, we developed a novel signal amplification method, termed Isothermal Amplification by Cyclic Extension (IACE), based on the linear extension of a single-stranded DNA probe. IACE operates through the continuous extension of Probe 1 (a) into long single-stranded DNA with multiple repetitive sequences, facilitated by Probe 2 (a∗a∗) and Bst DNA polymerase. We found that the single-stranded DNA product of IACE could directly activate the CRISPR-Cas12a system without requiring a protospacer adjacent motif (PAM). By integrating IACE with a three-way junction structure and a nicking enzyme, we established a one-step signal amplification strategy for the detection of lncRNA MALAT1, achieving a detection limit as low as 37.5 fM using the CRISPR-Cas system.

SIGNIFICANCE

The biosensor developed in the present study simplifies workflows, minimizes contamination risks, and demonstrates exceptional detection performance in tumor patient samples, highlighting its potential to advance clinical tumor diagnostic approaches.

Split DNA Tetrahedron-Mediated Spatiotemporal-Hierarchy CRISPR Cascade Integrated with Au@Pt Nanolabels and Artificial Intelligence for a Cervical Cancer MicroRNA Bioassay

The screening and monitoring of microRNAs as cancer molecular biomarkers is clinically significant, but traditional methods lack sufficient sensitivity, accuracy, and convenience. The CRISPR-colorimetric lateral flow assay (CLFA) integration offers a promising and efficient solution; however, cumbersome preamplification and poor quantification hinder clinical adoption. In this study, we developed a one-step isothermal CRISPR-Cas cascaded sensing system that is preamplification-free. At its core is a designed and selected split DNA tetrahedron activator, employing spatiotemporal-hierarchy mechanisms to precisely bidirectionally drive the kinetics of two Cas enzymes, accelerating the activation of Cas13a while delaying the initiation of Cas12a, to achieve optimal balance. This system enables ultrasensitive, single-step, single-tube, and rapid detection of a cervical cancer relative biomarker, microRNA-21, achieving a limit of detection of 38 aM with a broad linear range. The CRISPR system is further integrated with CLFA enhanced by ultrathin platinum-protected gold nanolabels (Au@Pt, also named Au@s-Pt), along with a smartphone equipped with dual convolutional neural network models (YOLO v5 and MobileNet v3), enabling more precise, rapid quantification of target miRNA. Using this integrated platform, miRNA-21 levels in cervical cancer and precancerous samples can be accurately quantified with approximately 30 min at low cost and without the need for large, sophisticated instruments, with results showing good concordance with quantitative real-time polymerase chain reaction. This platform provides an efficient, highly sensitive, user-friendly, and quantifiable point-of-care testing solution.

CRISPR-Cas13a as a next-generation tool for rapid and precise plant RNA virus diagnostics

Plant viruses are among the most serious threats to global agriculture, causing significant yield losses and jeopardizing food security. Identifying these viruses is crucial to prevent widespread crop damage and ensure effective management. CRISPR-Cas13a, a subtype of the RNA-targeting Cas13 family, has emerged as a transformative tool in molecular diagnostics, specifically tailored to detect these plant RNA viruses with unparalleled precision. Unlike traditional methods such as ELISA and RT-PCR, which are often limited by sensitivity, equipment dependency, and long processing times, Cas13a offers exceptional specificity and attomolar-level sensitivity. Its RNA-guided collateral cleavage mechanism allows signal amplification, making it particularly suitable for field-deployable diagnostics. Recent advances in Cas13 engineering, including compact variants such as Cas13bt3 and Cas13Y, have further improved its delivery efficiency and minimized immune responses, enhancing its agricultural applications. Integration with amplification methods like LAMP and innovative biosensor platforms like graphene-based and electrochemical systems further enhances its diagnostic potential. While challenges remain, including off-target effects, reagent stability, and scalability, innovations in CRISPR RNA (crRNA) design, reagent encapsulation, and microfluidic technologies are actively addressing these barriers. CRISPR-Cas13a represents a cutting-edge solution for rapid, accurate, and accessible plant virus diagnostics, providing a powerful safeguard for crop yields and global food security.

A versatile CRISPR/Cas9 system off-target prediction tool using language model

Genome editing with the CRISPR/Cas9 system has revolutionized life and medical sciences, particularly in treating monogenic genetic diseases by enabling long-term therapeutic effects from a single intervention. However, the CRISPR/Cas9 system can tolerate mismatches and DNA/RNA bulges at target sites, leading to unintended off-target effects that pose challenges for gene-editing therapy development. Existing high-throughput detection and in silico prediction methods are often limited to specifically designed single guide RNAs (sgRNAs) and perform poorly on unseen sequences. To address these limitations, we introduce CCLMoff, a deep learning framework for off-target prediction that incorporates a pretrained RNA language model from RNAcentral. CCLMoff captures mutual sequence information between sgRNAs and target sites and is trained on a comprehensive, updated dataset. This approach enables accurate off-target identification and strong generalization across diverse NGS-based detection datasets. Model interpretation reveals the biological importance of the seed region, underscoring CCLMoff's analytical capabilities. The development of CCLMoff lays the foundation for a comprehensive, end-to-end sgRNA design platform, enhancing both the precision and efficiency of CRISPR/Cas9-based therapeutics. CCLMoff is a versatile tool and is publicly available at github.com/duwa2/CCLMoff .

Programmable RNA acetylation with CRISPR-Cas13

Recent studies claim that N4-acetylcytidine (ac4C) modification of RNA confers crucial regulatory roles, such as increasing translation efficiency and prolonging its half-life. However, the absence of methods for selectively acetylating specific RNA molecules hampers linking ac4C to cell physiology. Here, we developed an efficient molecular tool that incorporates ac4C on a specific transcript of interest. Through protein engineering, we developed a hyperactive variant of N-acetyltransferase 10 (NAT10), designated enhanced NAT10 (eNAT10). When fused to the programmable RNA-targeting protein dCas13, eNAT10 enables robust acetylation of various target RNAs in multiple contexts. RNA acetylation by dCas13-eNAT10 was highly dependent on co-transfected guide RNA, highlighting its specificity. We also describe the programmable RNA chemical modification in vivo using dual-adeno-associated virus. Using our system, we found that acetylation of RNA may modulate the subcellular localization of modified transcripts. We anticipate that our tool will facilitate numerous studies on ac4C functions across different cellular and disease contexts.

Current updates regarding biogenesis, functions and dysregulation of microRNAs in cancer: Innovative approaches for detection using CRISPR/Cas13‑based platforms (Review)

MicroRNAs (miRNAs) are short non‑coding RNAs, which perform a key role in cellular differentiation and development. Most human diseases, particularly cancer, are linked to miRNA functional dysregulation implicated in the expression of tumor‑suppressive or oncogenic targets. Cancer hallmarks such as continued proliferative signaling, dodging growth suppressors, invasion and metastasis, triggering angiogenesis, and avoiding cell death have all been demonstrated to be affected by dysregulated miRNAs. Thus, for the treatment of different cancer types, the detection and quantification of this type of RNA is significant. The classical and current methods of RNA detection, including northern blotting, reverse transcription‑quantitative PCR, rolling circle amplification and next‑generation sequencing, may be effective but differ in efficiency and accuracy. Furthermore, these approaches are expensive, and require special instrumentation and expertise. Thus, researchers are constantly looking for more innovative approaches for miRNA detection, which can be advantageous in all aspects. In this regard, an RNA manipulation tool known as the CRISPR and CRISPR‑associated sequence 13 (CRISPR/Cas13) system has been found to be more advantageous in miRNA detection. The Cas13‑based miRNA detection approach is cost effective and requires no special instrumentation or expertise. However, more research and validation are required to confirm the growing body of CRISPR/Cas13‑based research that has identified miRNAs as possible cancer biomarkers for diagnosis and prognosis, and as targets for treatment. In the present review, current updates regarding miRNA biogenesis, structural and functional aspects, and miRNA dysregulation during cancer are described. In addition, novel approaches using the CRISPR/Cas13 system as a next‑generation tool for miRNA detection are discussed. Furthermore, challenges and prospects of CRISPR/Cas13‑based miRNA detection approaches are described.

Targeting and engineering biomarkers for prostate cancer therapy

Prostate cancer (PCa) is the second most commonly occurring cancer among men worldwide. Although the clinical management of PCa has significantly improved, a number of limitations have been identified in both early diagnosis and therapeutic treatment. Because multiple studies show that prostate-specific antigen (PSA) screening frequently results in overdiagnosis and overtreatment, the use of PSA alone as a diagnostic marker for PCa screening has been controversial. For individuals with locally advanced or metastatic PCa, androgen deprivation therapy (ADT) is the standard initially successful treatment; nonetheless, the majority of patients will eventually develop lethal metastatic castration-resistant prostate cancer (CRPC). Alternative treatment options, including chemo-, immuno-,or radio-therapy, can only prolong the survival of CRPC patients for several months with the most developing resistance. Considering this background, there is an urgent need to discuss about selective prostate-specific biomarkers that can predict clinically relevant PCa diagnosis and to develop biomarker-driven treatments to counteract CRPC. This review addresses several PCa-specific biomarkers that will assist physicians in determining which patients are at risk of having high-grade PCa, focusing on the clinical relevance of these biomarker-based tests among PCa patients. Secondly, this review highlights the effective use of these markers as drug targets to develop precision medicine or targeted therapies to counteract CRPC. Altogether, translating this biomarker-based research into the clinic will pave the way for the effective execution of personalized therapies for the benefit of healthcare providers, the biopharmaceutical industry, and patients.

CRISPR-Cas applications in agriculture and plant research

Growing world population and deteriorating climate conditions necessitate the development of new crops with high yields and resilience. CRISPR-Cas-mediated genome engineering presents unparalleled opportunities to engineer crop varieties cheaper, easier and faster than ever. In this Review, we discuss how the CRISPR-Cas toolbox has rapidly expanded from Cas9 and Cas12 to include different Cas orthologues and engineered variants. We present various CRISPR-Cas-based methods, including base editing and prime editing, which are used for precise genome, epigenome and transcriptome engineering, and methods used to deliver the genome editors into plants, such as bacterial-mediated and viral-mediated transformation. We then discuss how promoter editing and chromosome engineering are used in crop breeding for trait engineering and fixation, and important applications of CRISPR-Cas in crop improvement, such as de novo domestication and enhancing tolerance to abiotic stresses. We conclude with discussing future prospects of plant genome engineering.

Amplification-free nucleic acids detection with next-generation CRISPR/dx systems

CRISPR-based diagnostics (CRISPR/Dx) have revolutionized the field of molecular diagnostics. It enables home self-test, field-deployable, and point-of-care testing (POCT). Despite the great potential of CRISPR/Dx in diagnoses of biologically complex diseases, preamplification of the template often is required for the sensitive detection of low-abundance nucleic acids. Various amplification-free CRISPR/Dx systems were recently developed to enhance signal detection at sufficient sensitivity. Broadly, these amplification-free CRISPR/Dx systems are classified into five groups depending on the signal enhancement strategies employed: CRISPR/Cas12a and/or CRISPR/Cas13a are integrated with: (1) other catalytic enzymes (Cas14a, Csm6, Argonaute, duplex-specific nuclease, nanozyme, or T7 exonuclease), (2) rational-designed oligonucleotides (multivalent aptamer, tetrahedral DNA framework, RNA G-quadruplexes, DNA roller machine, switchable-caged guide RNA, hybrid locked RNA/DNA probe, hybridized cascade probe, or "U" rich stem-loop RNA), (3) nanomaterials (nanophotonic structure, gold nanoparticle, micromotor, or microbeads), (4) electrochemical and piezoelectric plate biosensors (SERS nanoprobes, graphene field-effect transistor, redox probe, or primer exchange reaction), or (5) cutting-edge detection technology platforms (digital bioanalysis, droplet microfluidic, smartphone camera, or single nanoparticle counting). Herein, we critically discuss the advances, pitfalls and future perspectives for these amplification-free CRISPR/Dx systems in nucleic acids detection. The continued refinement of these CRISPR/Dx systems will pave the road for rapid, cost-effective, ultrasensitive, and ultraspecific on-site detection without resorting to target amplification, with the ultimate goal of establishing CRISPR/Dx as the paragon of diagnostics.

0.46 Terahertz wave irradiation inhibit transcription reaction in liposomes

Terahertz waves are absorbed by hydrogen bonds between water molecules and proteins, and low-frequency terahertz waves, in particular, have been reported to cause changes in protein function and inhibit cell division. In this study, we established an experimental system to irradiate liposomes containing T7 RNA polymerase for in vitro transcription reactions with terahertz waves in the absence of external fluid, and analyzed the resulting changes in transcription reaction efficiency. Terahertz wave irradiation at 460 GHz did not alter the shape of the liposomes, but the intraliposomal transcription reaction was non-thermally inhibited during irradiation, regardless of the energy per pulse. After irradiation, the transcription reaction efficiency was found to be higher than in non-irradiated samples. Since our experimental system allows for the analysis of a wide range of terahertz wave frequencies, pulse widths, pulse intervals, and energy levels, we can comprehensively explore the effects of terahertz waves on living organisms, an area that has been challenging to study in the past. This capability significantly broadens the potential applications of terahertz waves in future research.

Genetically Modified Animal-Derived Products: From Regulations to Applications

Biotechnological advances applied to the generation of genetically modified (GM) animals have shown the potential to develop innovative solutions for different challenges in key areas such as agriculture and human medicine. Despite its enormous potential, the deployment of genetic modification in animals, and its subsequent commercialization, does not meet the same public acceptance as GM plant-derived products, which are currently widely adopted around the world. In this review, we highlight the main examples of GM and gene-edited animal-derived products already approved by the FDA and discuss the regulatory context inherent to such processes, including the risk-based assessment analysis based on a case-by-case evaluation. Moreover, cases of GM animals already approved by other jurisdictions around the world are also discussed.

A targeted approach: Gene and RNA editing for neurodegenerative disease treatment

With the global aging trend, neurodegenerative diseases (NDs) have emerged as a significant public health concern in the 21st century, imposing substantial economic burdens on families and society. NDs are characterized by cognitive and motor decline, resulting from a combination of genetic and environmental factors. Currently, there is no cure for NDs. Gene and RNA editing therapies offer new possibilities for addressing NDs. Gene editing involves modifying mutant genes associated with NDs, while RNA editing can directly modify RNA molecules to regulate the protein translation process, potentially influencing the expression of genes related to NDs. In this review, we examined the historical evolution, mechanisms of action, applications in NDs, advantages and disadvantages, as well as ethical and safety considerations of gene and RNA editing. While gene and RNA editing technologies hold promise for treating NDs, further research and development are needed to address safety, efficacy, and treatment timing issues, ultimately offering improved treatment options for ND patients. Our review provides valuable insights for future gene and RNA editing applications in ND treatment.

Programmable control of spatial transcriptome in live cells and neurons

Spatial RNA organization has a pivotal role in diverse cellular processes and diseases1-4. However, functional implications of the spatial transcriptome remain largely unexplored due to limited technologies for perturbing endogenous RNA within specific subcellular regions1,5. Here we present CRISPR-mediated transcriptome organization (CRISPR-TO), a system that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of endogenous RNA localization in live cells. CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments, including the outer mitochondrial membrane, p-bodies, stress granules, telomeres and nuclear stress bodies, across various cell types. It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins, facilitating real-time manipulation and monitoring of RNA localization dynamics in living cells. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips, and co-transport with ribosomes, with β-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.

Application of CRISPR/Cas gene editing for infectious disease control in poultry

The poultry industry faces multifaceted challenges, including escalating demand for poultry products, climate change impacting feed availability, emergence of novel avian pathogens, and antimicrobial resistance. Traditional disease control measures are costly and not always effective, prompting the need for complementary methods. Gene editing (GE, also called genome editing) technologies, particularly CRISPR/Cas9, offer promising solutions. This article summarizes recent advancements in utilizing CRISPR/Cas GE to enhance infectious disease control in poultry. It begins with an overview of modern GE techniques, highlighting CRISPR/Cas9's advantages over other methods. The potential applications of CRISPR/Cas in poultry infectious disease prevention and control are explored, including the engineering of innovative vaccines, the generation of disease-resilient birds, and in vivo pathogen targeting. Additionally, insights are provided regarding regulatory frameworks and future perspectives in this rapidly evolving field.

Mpox diagnosis at POC

The increasing number of Monkeypox (Mpox) cases in non-endemic countries resulted in the WHO declaring a public health emergency of international concern. Accurate and timely diagnosis of Mpox has a critical role in containing the spread of infection. Diagnosis currently relies on PCR, which requires trained personnel and complex laboratory infrastructure. Thus, the development of point-of-care (POC) tools are essential to facilitate rapid, accurate, and user-friendly diagnosis. Here, we review POC diagnostic tools available for Mpox. We also discuss bottlenecks preventing the widespread implementation of POC platforms for Mpox diagnosis and potential strategies to address these limitations. Furthermore, we describe future directions, including the role of machine learning (ML) and deep learning (DL)-based models and the integration of integrated field-deployable platforms for Mpox diagnosis.

Cross-species tropism of AAV.CPP.16 in the respiratory tract and its gene therapies against pulmonary fibrosis and viral infection

Efficient gene delivery vectors are crucial for respiratory and lung disease therapies. We report that AAV.CPP.16, an engineered adeno-associated virus (AAV) variant derived from AAV9, efficiently transduces airway and lung cells in mice and non-human primates via intranasal administration. AAV.CPP.16 outperforms AAV6 and AAV9, two wild-type AAVs with demonstrated tropism for respiratory tissues, and efficiently targets key respiratory cell types. It supports gene supplementation and editing therapies in two clinically relevant mouse models of respiratory and lung diseases. A single intranasal dose of AAV.CPP.16 expressing a dual-target, vascular endothelial growth factor (VEGF)/transforming growth factor (TGF)-β1-neutralizing protein protected lungs from idiopathic pulmonary fibrosis, while a similar application of AAV.CPP.16 carrying an "all-in-one" CRISPR-Cas13d system inhibited transcription of the SARS-CoV-2-derived RNA-dependent RNA polymerase (Rdrp) gene. Our findings highlight AAV.CPP.16 as a promising vector for respiratory and lung gene therapy.

Pharmaceutical perspectives on oligonucleotide therapeutics and delivery systems

Gene therapy has a pivotal role in treating new diseases. In addition to the recent mRNA-based COVID-19 vaccines produced by Pfizer-BioNTech and Moderna against severe acute respiratory syndrome corona virus 2, several new gene therapies have recently been approved as effective treatments for fatal genetic disorders such as Duchenne's muscular dystrophy, familial transthyretin amyloidosis, hemophilia A, hemophilia B, spinal muscle atrophy, early cerebral autoleukodystrophy, and β-thalassemia. This review provides novel insights into RNA therapeutics focusing on endogenous RNA species, RNA structure and function, and chemical modifications that improve the stability and distribution of RNAs. Furthermore, it includes updated knowledge on clinically approved gene therapies rendering a comprehensive understanding of the biochemical basis and clinical application of gene therapies. SIGNIFICANCE STATEMENT: There have recently been significant advances in clinical translation of RNA therapeutics. This review discusses the diverse types of RNA species, RNA structure and function, backbone and chemical modifications to RNAs, and every RNA therapeutic approved for clinical use at the time of writing.

ADAR2-mediated Q/R editing of GluA2 in homeostatic synaptic plasticity

Homeostatic synaptic plasticity is a negative feedback mechanism through which neurons modify their synaptic strength to counteract chronic increases or decreases in activity. In response to activity deprivation, synaptic strength is enhanced by increasing the number of AMPA receptors (AMPARs), particularly Ca2+-permeable AMPARs, at the synapse. Here, we found that this increase in Ca2+-permeable AMPARs during homeostatic upscaling was mediated by decreased posttranscriptional editing of GRIA2 mRNA encoding the AMPAR subunit GluA2. In cultured neurons, activity deprivation resulted in increases in the amount of unedited GluA2, such that its ion channel pore contains a glutamine (Q) codon instead of arginine (R), and in the number of Ca2+-permeable AMPARs at the synapse. These effects were mediated by a splicing factor-dependent decrease in ADAR2 abundance and activity in the nucleus. Overexpression of ADAR2 or CRISPR-Cas13-directed editing of GluA2 transcripts blocked homeostatic upscaling in activity-deprived primary neurons. In mice, dark rearing resulted in decreased Q-to-R editing of GluA2-encoding transcripts in the primary visual cortex (V1), and viral overexpression of ADAR2 in the V1 blocked the induction of homeostatic synaptic plasticity. The findings indicate that activity-dependent regulation of GluA2 editing contributes to homeostatic synaptic plasticity.

Gene regulation technologies for gene and cell therapy

Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.

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.

Current updates on the structural and functional aspects of the CRISPR/Cas13 system for RNA targeting and editing: A next‑generation tool for cancer management (Review)

For centuries, a competitive evolutionary race between prokaryotes and related phages or other mobile genetic elements has led to the diversification of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR‑associated sequence (Cas) genome‑editing systems. Among the different CRISPR/Cas systems, the CRISPR/Cas9 system has been widely studied for its precise DNA manipulation; however, due to certain limitations of direct DNA targeting, off‑target effects and delivery challenges, researchers are looking to perform transient knockdown of gene expression by targeting RNA. In this context, the more recently discovered type VI CRISPR/Cas13 system, a programmable single‑subunit RNA‑guided endonuclease system that has the capacity to target and edit any RNA sequence of interest, has emerged as a powerful platform to modulate gene expression outcomes. All the Cas13 effectors known so far possess two distinct ribonuclease activities. Pre‑CRISPR RNA processing is performed by one RNase activity, whereas the two higher eukaryotes and prokaryotes nucleotide‑binding domains provide the other RNase activity required for target RNA degradation. Recent innovative applications of the type VI CRISPR/Cas13 system in nucleic acid detection, viral interference, transcriptome engineering and RNA imaging hold great promise for disease management. This genome editing system can also be employed by the Specific High Sensitivity Enzymatic Reporter Unlocking platform to identify any tumor DNA. The discovery of this system has added a new dimension to targeting, tracking and editing circulating microRNA/RNA/DNA/cancer proteins for the management of cancer. However, there is still a lack of thorough understanding of the mechanisms underlying some of their functions. The present review summarizes the recent updates on the type VI CRISPR/Cas system in terms of its structural and mechanistic properties and some novel applications of this genome‑editing tool in cancer management. However, some issues, such as collateral degradation of bystander RNA, impose major limitations on its in vivo application. Furthermore, additional challenges and future prospects for this genome editing system are described in the present review.

Advancing fish disease research through CRISPR-Cas genome editing: Recent developments and future perspectives

CRISPR-Cas genome editing technology has transformed genetic research, by enabling unprecedented precision in modifying DNA sequences across various organisms, including fish. This review explores the significant advancements and potential uses of CRISPR-Cas technology in the study and management of fish diseases, which pose serious challenges to aquaculture and wild fish populations. Fish diseases cause significant economic losses and environmental impacts, therefore effective disease control a top priority. The review highlights the pivotal role of CRISPR-Cas in identifying disease-associated genes, which is critical to comprehending the genetic causes of disease susceptibility and resistance. Some studies have reported key genetic factors that influence disease outcomes, using targeted gene knockouts and modifications to pave the way for the development of disease-resistant fish strains. The creation of such genetically engineered fish holds great promise for enhancing aquaculture sustainability by reducing the reliance on antibiotics and other conventional disease control measures. In addition, CRISPR-Cas has facilitated in-depth studies of pathogen-host interactions, offering new insights into the mechanisms by which pathogens infect and proliferate within their hosts. By manipulating both host and pathogen genes, this technology provides a powerful tool for uncovering the molecular underpinnings of these interactions, leading to the development of more effective treatment strategies. While CRISPR-Cas has shown great promise in fish research, its application remains limited to a few species, primarily model organisms and some freshwater fish. In addition, challenges such as off-target effects, ecological risks, and ethical concerns regarding the release of genetically modified organisms into the environment must be carefully addressed. This review also discusses these challenges and emphasizes the need for robust regulatory frameworks and ongoing research to mitigate risks. Looking forward, the integration of CRISPR-Cas with other emerging technologies, such as multi-omics approaches, promises to further advance our understanding and management of fish diseases. This review concludes by envisioning the future directions of CRISPR-Cas applications in fish health, underscoring its potential to its growing in the field.

The potential of advanced crop breeding technologies for sustainable food security

Considering the increasing demands of a growing global population, shortages of resources, and climate change, exploring the potential of modern plant breeding technology seems to be an important and feasible method for ensuring food security. The current review shed light on the dramatic application of modern plant breeding techniques, which not only increase yields of crops but also lead a way for sustainable agriculture and resilience in dealing with of environmental challenges. Modern plant breeding technologies, such as Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) genome editing tools, omics, marker-Assisted Selection (MAS), and RNA Interference (RNAi) for Crop Enhancement exhibited the potential to significantly enhance crop production and diversity. Modern plant breeding technologies offers a method for developing crops that are resistant to the effects of climate change, pests, and diseases, improving crop yield and nutritional quality while decreasing the demand for harmful pesticides. Finally, this review emphasizes the enormous potential of modern plant breeding methods in ensuring global food security, as well as the importance of continued research, collaboration, and strategic application for a resilient and sustainable agricultural future.

CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network

Cas proteins (CRISPR-associated protein) are the core components of the CRISPR-Cas system, playing critical roles in defending against foreign DNA and RNA invasions. Identifying Cas proteins can provide deeper insights into the immune mechanisms of the CRISPR-Cas system and help uncover the functional mechanisms of Cas proteins. In this study, we developed a computational tool named CasPro-ESM2, which combines the Pre-trained Protein Language Model ESM-2, multi-scale convolutional neural networks, and evolutionary information from protein sequences to identify Cas proteins. Experimental results demonstrate that CasPro-ESM2 outperforms existing models in Cas protein identification, achieving the highest values in metrics such as ACC, SP, SN, and MCC on two different datasets. Furthermore, we deployed this tool on a web server to enable direct access for users (http://www.bioai-lab.com/CasProESM-2).

CRISPR/Cas technologies for cancer drug discovery and treatment

Clustered regularly interspaced short palindromic repeats (CRISPR) tools are revolutionizing the establishment of genotype-phenotype relationships and are transforming cell- and gene-based therapies. In the field of oncology, CRISPR/CRISPR-associated protein 9 (Cas9), Cas12, and Cas13 have advanced the generation of cancer models, the study of tumor evolution, the identification of target genes involved in cancer growth, and the discovery of genes involved in chemosensitivity and resistance. Moreover, preclinical therapeutic strategies employing CRISPR/Cas have emerged. These include the generation of chimeric antigen receptor T (CAR-T) cells and engineered immune cells, and the use of precision anticancer gene-editing agents to inactivate driver oncogenes, suppress tumor support genes, and cull cancer cells in response to genetic circuit output. This review summarizes the collective impact that CRISPR technology has had on basic and applied cancer research, and highlights the promises and challenges facing its clinical translation.

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

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

CRISPR/Cas-mediated mRNA knockdown in the embryos of Xenopus tropicalis

The Xenopus tropicalis (Western clawed frog) is an important amphibian model for genetics, developmental and regenerative biology, due to its diploid genetic background and short generation time. CRISPR-Cas13 and CRISPR interference (CRISPRi) systems have recently been employed to suppress mRNA expression in many organisms such as yeast, plants, and mammalian cells. However, no systematic study of these two systems has been carried out in Xenopus tropicalis. Here, we show that CRISPRi rather than CRISPR-Cas13 is an effective and suitable approach to suppress specific mRNA transcription in Xenopus tropicalis embryos. We demonstrated that CRISPRi composed of dCas9 and KRAB-MeCP2 (dCas9-KM) can efficiently target exogenous and endogenous transcripts in Xenopus tropicalis embryos. Moreover, our data suggest that the new KRAB domain from ZIM3 protein (ZIM3-KRAB, ZIM3K) alone has a comparable transcript targeting capacity in Xenopus tropicalis embryos to the traditional fusion repressor KRAB-MeCP2 in which the KRAB domain from KOX1 protein. In conclusion, our results demonstrate that CRISPRi rather than CRISPR-Cas13 is an efficient knockdown platform to explore specific gene function in Xenopus tropicalis embryos.

Regulatory mechanisms of m6A RNA methylation in esophageal cancer: a comprehensive review

Esophageal cancer is an aggressively malignant neoplasm characterized by a high mortality rate. Frequently diagnosed at an advanced stage, it presents challenges for optimal therapeutic intervention due to its non-specific symptoms, resulting in lost opportunities for effective treatment, such as surgery, radiotherapy, chemotherapy and target therapy. The N6-methyladenosine (m6A) modification represents the most critical post-transcriptional modification of eukaryotic messenger RNA (mRNA). The reversible m6A modification is mediated by three regulatory factors: m6A methyltransferases, demethylating enzymes, and m6A recognition proteins. These components identify and bind to specific RNA methylation sites, thereby modulating essential biological functions such as RNA processing, nuclear export, stability, translation and degradation, which significantly influence tumorigenesis, invasion, and metastasis. Given the importance of m6A modification, this paper offers a comprehensive examination of the regulatory mechanisms, biological functions, and future therapeutic implications of m6A RNA methylation in the context of esophageal cancer.

Unraveling the future of genomics: CRISPR, single-cell omics, and the applications in cancer and immunology

The CRISPR system has transformed many research areas, including cancer and immunology, by providing a simple yet effective genome editing system. Its simplicity has facilitated large-scale experiments to assess gene functionality across diverse biological contexts, generating extensive datasets that boosted the development of computational methods and machine learning/artificial intelligence applications. Integrating CRISPR with single-cell technologies has further advanced our understanding of genome function and its role in many biological processes, providing unprecedented insights into human biology and disease mechanisms. This powerful combination has accelerated AI-driven analyses, enhancing disease diagnostics, risk prediction, and therapeutic innovations. This review provides a comprehensive overview of CRISPR-based genome editing systems, highlighting their advancements, current progress, challenges, and future opportunities, especially in cancer and immunology.

Integrating CRISPR-Cas12a with Aptamer as a Logic Gate Biosensing Platform for the Detection of CD33 and CD123

Molecular logic gates, as biomolecule-based computational systems, are highly suitable for multitarget detection due to their programmability and modularity. However, existing systems are primarily limited to nucleic acid detection and have not been widely applied to disease-related sensing, particularly for disease antigens. CD33 and CD123 are critical biomarkers for acute myeloid leukemia (AML), yet conventional detection methods rely on expensive equipment and complex procedures, limiting their accessibility and practicality. This study designs a DNA logic gate system integrating nucleic acid aptamers, catalytic hairpin assembly (CHA), and CRISPR-Cas12a, pioneering its use for AML antigen detection. The system comprises three modules: input recognition, signal amplification, and signal transduction. Nucleic acid aptamers specifically identify CD33 and CD123, while CHA enables efficient signal amplification and CRISPR-Cas12a generates a fluorescent output via trans-cleavage activity. The system operates stably at room temperature and implements multiple logic gate models, including YES, OR, AND, NOR, and INHIBIT, enabling the simultaneous detection of CD33 and CD123. Experimental results are visually distinguishable under blue light, and the system requires only standard fluorescence detection instruments. In serum samples, it exhibits excellent selectivity and stability, with a detection limit of 0.5 ng/mL. This study pioneers the application of logic gate technology for disease antigen detection, addressing a critical gap in AML biomarker sensing. Our study indicates that this logic detection platform, characterized by its simplicity in operation, high sensitivity, and versatility in logic functions, holds promise as a potent sensing system for the intelligent multiplex target detection of disease antigens, environmental pollutants, and heavy metals.

New Frontiers for the Early Diagnosis of Cancer: Screening miRNAs Through the Lateral Flow Assay Method

MicroRNAs (miRNAs), which circulate in the serum and plasma, play a role in several biological processes, and their levels in body fluids are associated with the pathogenesis of various diseases, including different types of cancer. For this reason, miRNAs are considered promising candidates as biomarkers for diagnostic purposes, enabling the early detection of pathological onset and monitoring drug responses during therapy. However, current methods for miRNA quantification, such as northern blotting, isothermal amplification, RT-PCR, microarrays, and next-generation sequencing, are limited by their reliance on centralized laboratories, high costs, and the need for specialized personnel. Consequently, the development of sensitive, simple, and one-step analytical techniques for miRNA detection is highly desirable, particularly given the importance of early diagnosis and prompt treatment in cases of cancer. Lateral flow assays (LFAs) are among the most attractive point-of-care (POC) devices for healthcare applications. These systems allow for the rapid and straightforward detection of analytes using low-cost setups that are accessible to a wide audience. This review focuses on LFA-based methods for detecting and quantifying miRNAs associated with the diagnosis of various cancers, with particular emphasis on sensitivity enhancements achieved through the application of different labels and detection systems. Early, non-invasive detection of these diseases through the quantification of tailored biomarkers can significantly reduce mortality, improve survival rates, and lower treatment costs.

Harnessing RNA base editing for diverse applications in RNA biology and RNA therapeutics

Recent advancements in molecular engineering have established RNA-based technologies as powerful tools for both fundamental research and translational applications. Among the various RNA-based technologies developed, RNA base editing has recently emerged as a groundbreaking advancement. It primarily involves the conversion of adenosine (A) to inosine (I) and cytidine (C) to uridine (U), which are mediated by ADAR and APOBEC enzymes, respectively. RNA base editing has been applied in both biological research and therapeutic contexts. It enables site-directed editing within target transcripts, offering reversible, dose-dependent effects, in contrast to the permanent or heritable changes associated with DNA base editing. Additionally, RNA editing-based profiling of RNA-binding protein (RBP) binding sites facilitates transcriptome-wide mapping of RBP-RNA interactions in specific tissues and at the single-cell level. Furthermore, RNA editing-based sensors have been utilized to express effector proteins in response to specific RNA species. As RNA base editing technologies continue to evolve, we anticipate that they will significantly drive advancements in RNA therapeutics, synthetic biology, and biological research.

Perturbation of mRNA splicing in liver cancer: insights, opportunities and challenges

Perturbation of mRNA splicing is commonly observed in human cancers and plays a role in various aspects of cancer hallmarks. Understanding the mechanisms and functions of alternative splicing (AS) not only enables us to explore the complex regulatory network involved in tumour initiation and progression but also reveals potential for RNA-based cancer treatment strategies. This review provides a comprehensive summary of the significance of AS in liver cancer, covering the regulatory mechanisms, cancer-related AS events, abnormal splicing regulators, as well as the interplay between AS and post-transcriptional and post-translational regulations. We present the current bioinformatic approaches and databases to detect and analyse AS in cancer, and discuss the implications and perspectives of AS in the treatment of liver cancer.

Targeted Control of Gene Expression Using CRISPR-Associated Endoribonucleases

CRISPR-associated endoribonucleases (Cas RNases) cleave single-stranded RNA in a highly sequence-specific manner by recognizing and binding to short RNA sequences known as direct repeats (DRs). Here, we investigate the potential of exploiting Cas RNases for the regulation of target genes with one or more DRs introduced into the 3' untranslated region, an approach we refer to as DREDGE (direct repeat-enabled downregulation of gene expression). The DNase-dead version of Cas12a (dCas12a) was identified as the most efficient among five different Cas RNases tested and was subsequently evaluated in doxycycline-regulatable systems targeting either stably expressed fluorescent proteins or an endogenous gene. DREDGE performed superbly in stable cell lines, resulting in up to 90% downregulation with rapid onset, notably in a fully reversible and highly selective manner. Successful control of an endogenous gene with DREDGE was demonstrated in two formats, including one wherein both the DR and the transgene driving expression of dCas12a were introduced in one step by CRISPR-Cas. Our results establish DREDGE as an effective method for regulating gene expression in a targeted, highly selective, and fully reversible manner, with several advantages over existing technologies.

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to identify the ancestors of the RNA-targeting CRISPR-Cas13 system. We find that Cas13 likely evolved from AbiF, which is encoded by an abortive infection-linked gene that is stably associated with a conserved non-coding RNA (ncRNA). We further characterize a miniature Cas13, classified here as Cas13e, which serves as an evolutionary intermediate between AbiF and other known Cas13s. Despite this relationship, we show that their functions substantially differ. Whereas Cas13e is an RNA-guided RNA-targeting system, AbiF is a toxin-antitoxin (TA) system with an RNA antitoxin. We solve the structure of AbiF using cryoelectron microscopy (cryo-EM), revealing basic structural alterations that set Cas13s apart from AbiF. Finally, we map the key structural changes that enabled a non-guided TA system to evolve into an RNA-guided CRISPR system.

Cytosolic CRISPR RNAs for efficient application of RNA-targeting CRISPR-Cas systems

Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) technologies have evolved rapidly over the past decade with the continuous discovery of new Cas systems. In particular, RNA-targeting CRISPR-Cas13 proteins are promising single-effector systems to regulate target mRNAs without altering genomic DNA, yet the current Cas13 systems are restrained by suboptimal efficiencies. Here, we show that U1 promoter-driven CRISPR RNAs (crRNAs) increase the efficiency of various applications, including RNA knockdown and editing, without modifying the Cas13 protein effector. We confirm that U1-driven crRNAs are exported into the cytoplasm, while conventional U6 promoter-driven crRNAs are mostly confined to the nucleus. Furthermore, we reveal that the end positions of crRNAs expressed by the U1 promoter are consistent regardless of guide sequences and lengths. We also demonstrate that U1-driven crRNAs, but not U6-driven crRNAs, can efficiently repress the translation of target genes in combination with catalytically inactive Cas13 proteins. Finally, we show that U1-driven crRNAs can counteract the inhibitory effect of miRNAs. Our simple and effective engineering enables unprecedented cytosolic RNA-targeting applications.

One-Step RAA and CRISPR-Cas13a Method for Detecting Influenza B Virus

We developed a sensitive and specific method based on recombinase-aided amplification (RAA) and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 13a (Cas13a). This method, named CRISPR-based Rapid and Efficient Test (CRISPRET), is designed for the early diagnosis of Influenza B (FluB) with the aim of shortening its transmission chain. We identified conserved regions in the Influenza B Virus (IBV) NS gene and designed forward and reverse primers along with crRNAs. We then established and optimised the reaction system, and Nucleic Acid Positive Reference Materials of IBV were used to evaluate the detection limit (DL) of CRISPRET. Additionally, we collected 257 clinical samples, comprising 127 samples from patients with IBV infection and 130 samples from healthy individuals, and subjected them to dual detection using CRISPRET and qPCR to evaluate the positive predictive value (PPV), negative predictive value (NPV), sensitivity and specificity of CRISPRET. We designed one forward primer, two reverse primers, and two crRNAs to establish and optimise the CRISPR ET. The method demonstrated the DL of 500 copies·μL-1 when assisted by appropriate equipment. Despite requiring auxiliary equipment and a 30-min reaction, the CRISPR ET method enables the detection of IBV nucleic acid within approximately the first 5 min, achieving high sensitivity (100%), specificity (97.69%), PPV (97.69%) and NPV (100%), with a concordance rate of 98.83% to qPCR. CRISPRET offers a simple, field-applicable, one-step method for the rapid detection of IBV. It has strong potential for field-testing applications and intelligent integration into existing diagnostic systems.

Dumbbell probe-bridged CRISPR/Cas13a and nicking-mediated DNA cascade reaction for highly sensitive detection of colorectal cancer-related microRNAs

Colorectal cancer (CRC) is a leading cause of cancer-related deaths globally, necessitating the development of sensitive and minimally invasive diagnostic approaches. In this study, we present a novel diagnostic strategy by integrating dumbbell probe-mediated CRISPR/Cas13a with nicking-induced DNA cascade reaction (DP-bridged Cas13a/NDCR) for highly sensitive microRNA (miRNA) detection. Target miRNA triggers Cas13a-mediated cleavage of the dumbbell probe, releasing an intermediate strand that hybridizes with a methylene blue-labeled hairpin probe on the electrode surface. Nicking enzyme cleaves the formed duplex DNA, triggering a cascade reaction that amplifies the electrochemical signal. Under optimized conditions, the method demonstrates a detection limit of 8.26 fM for miRNA-21, with reliable specificity and long-term stability. Furthermore, integration with machine learning models using multiple miRNA markers improved diagnostic accuracy, differentiating CRC from colorectal polyps and healthy controls with 100% accuracy in clinical validation cohorts. This study highlights the potential of DP-bridged Cas13a/NDCR as a sensitive and accurate diagnostic tool for CRC.

Implementation of RT-RAA and CRISPR/Cas13a for an NiV Point-of-Care Test: A Promising Tool for Disease Control

Nipah virus (NiV) is a severe zoonotic pathogen that substantially threatens public health. Pigs are the natural hosts of NiV and can potentially transmit this disease to humans. Establishing a rapid, sensitive, and accurate point-of-care detection method is critical in the timely identification of infected pig herds. In this study, we developed an NiV detection method based on reverse transcription-recombinase polymerase amplification (RT-RAA) and the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 13a (Cas13a) system for the precise detection of NiV. The highly conserved region of the NiV gene was selected as the detection target. We first designed eleven pairs of RT-RAA primers, and the optimal primer combination and reaction temperature were identified on the basis of RT-RAA efficiency. Additionally, the most efficient crRNA sequence was selected on the basis of the fluorescence signal intensity. The results revealed that the optimal reaction temperature for the developed method was 37 °C. The detection limit was as low as 1.565 copies/μL. Specificity testing revealed no cross-reactivity with nucleic acids from six common swine viruses, including Seneca virus A (SVA), foot-and-mouth disease virus (FMDV), classical swine fever virus (CSFV), porcine epidemic diarrhea virus (PEDV), African swine fever virus (ASFV), and pseudorabies virus (PRV). A validation test using simulated clinical samples revealed a 100% concordance rate. The detection results can be visualized via a fluorescence reader or lateral flow strips (LFSs). Compared with conventional detection methods, this RT-RAA-CRISPR/Cas13a-based method is rapid and simple and does not require scientific instruments. Moreover, the reagents can be freeze-dried for storage, eliminating the need for cold-chain transportation. This detection technology provides a convenient and efficient new tool for the point-of-care diagnosis of NiV and for preventing and controlling outbreaks.

AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack

Anti-CRISPR proteins (Acrs) inhibit CRISPR-Cas immune defenses, with almost all known Acrs acting on the Cas nuclease-CRISPR (cr)RNA ribonucleoprotein (RNP) complex. Here, we show that AcrVIB1 from Riemerella anatipestifer, the only known Acr against Cas13b, principally acts upstream of RNP complex formation by promoting unproductive crRNA binding followed by crRNA degradation. AcrVIB1 tightly binds to Cas13b but not to the Cas13b-crRNA complex, resulting in enhanced rather than blocked crRNA binding. However, the more tightly bound crRNA does not undergo processing and fails to activate collateral RNA cleavage even with target RNA. The bound crRNA is also accessible to RNases, leading to crRNA turnover in vivo even in the presence of Cas13b. Finally, cryoelectron microscopy (cryo-EM) structures reveal that AcrVIB1 binds a helical domain of Cas13b responsible for securing the crRNA, keeping the domain untethered. These findings reveal an Acr that converts an effector nuclease into a crRNA sink to suppress CRISPR-Cas defense.

RNA-targeted proteomics identifies YBX1 as critical for efficient HCMV mRNA translation

Viruses have evolved unique strategies to circumvent host control of protein synthesis and enable viral protein synthesis in the face of the host response. Defining the factors that regulate viral messenger RNA (mRNA) translation is thus critical to understand how viruses replicate and cause disease. To identify factors that might regulate viral mRNA translation, we developed a technique for identifying proteins associated with a native RNA expressed from its endogenous promoter and genomic locus. This approach uses a guide RNA to target dCas13b fused to a biotin ligase domain to a specific RNA, where it covalently labels proteins in close proximity. Using this approach, we identified multiple proteins associated with transcripts encoding the human cytomegalovirus (HCMV) IE1 and IE2 proteins and found that several associated proteins positively or negatively regulate HCMV replication. We confirmed that one such protein, the cellular Y-box binding protein 1 (YBX1), binds to HCMV immediate early mRNAs and is required for efficient viral protein expression and virus replication. Ablating YBX1 expression reduced the association of HCMV immediate early mRNAs with polysomes, demonstrating a role for YBX1 as a positive regulator of viral RNA translation. These results provide a powerful tool for unraveling RNA-protein interactions that can be used in a wide range of biological processes and reveal a role for YBX1 as a critical regulator of HCMV immediate early gene expression.

High-accuracy crRNA array assembly strategy for multiplex CRISPR

Simultaneous targeting of multiple loci with the CRISPR system, a tool known as multiplex CRISPR, offers greater feasibility for manipulating and elucidating the intricate and redundant endogenous networks underlying complex cellular functions. Owing to the versatility of continuously emerging Cas nucleases and the use of CRISPR arrays, multiplex CRISPR has been implemented in numerous in vitro and in vivo studies. However, a streamlined, practical strategy for CRISPR array assembly that is both convenient and accurate is lacking. Here, we present a novel, highly accurate, cost-, and time-saving strategy for CRISPR array assembly. Using this strategy, we efficiently assembled 12 CRISPR RNAs (crRNAs) (for AsCas12a) and 15 crRNAs (for RfxCas13d) in a single reaction. CRISPR arrays driven by Pol II promoters exhibited a distinct expression pattern compared with those driven by Pol III promoters, which could be exploited for specific distributions of CRISPR intensity. Improved approaches were subsequently designed and validated for expressing long CRISPR arrays. The study provides a flexible and powerful tool for the convenient implementation of multiplex CRISPR across DNA and RNA, facilitating the dissection of sophisticated cellular networks and the future realization of multi-target gene therapy.

Intelligent Design of Lipid Nanoparticles for Enhanced Gene Therapeutics

Lipid nanoparticles (LNPs) are an effective delivery system for gene therapeutics. By optimizing their formulation, the physiochemical properties of LNPs can be tailored to improve tissue penetration, cellular uptake, and precise targeting. The application of these targeted delivery strategies within the LNP framework ensures efficient delivery of therapeutic agents to specific organs or cell types, thereby maximizing therapeutic efficacy. In the realm of genome editing, LNPs have emerged as a potent vehicle for delivering CRISPR/Cas components, offering significant advantages such as high in vivo efficacy. The incorporation of machine learning into the optimization of LNP platforms for gene therapeutics represents a significant advancement, harnessing its predictive capabilities to substantially accelerate the research and development process. This review highlights the dynamic evolution of LNP technology, which is expected to drive transformative progress in the field of gene therapy.

CRISPR-Cas13d as a molecular tool to achieve targeted gene expression knockdown in chick embryos

The chick embryo is a classical model system commonly used in developmental biology due to its amenability to gene perturbation experiments. Pairing this powerful model organism with cutting-edge technology can significantly expand the range of experiments that can be performed. Recently, the CRISPR-Cas13d system has been successfully adapted for use in zebrafish, medaka, killifish, and mouse embryos to achieve targeted gene expression knockdown. Despite its success in other animal models, no prior study has explored the potential of CRISPR-Cas13d in the chick. Here, we present an adaptation of the CRISPR-Cas13d system to achieve targeted gene expression knockdown in the chick embryo. As proof-of-principle, we demonstrate the knockdown of PAX7, an early neural crest marker. Application of this adapted CRISPR-Cas13d technique resulted in effective knockdown of PAX7 expression and function, comparable to knockdown achieved by translation-blocking morpholino. CRISPR-Cas13d complements preexisting knockdown tools such as CRISPR-Cas9 and morpholinos, thereby expanding the experimental potential and versatility of the chick model system.

Lipid Nanoparticle-Mediated CRISPR-Cas13a Delivery for the Control of Bacterial Infection

Lipid nanoparticles (LNPs) can assist in the delivery of nucleic acid inside animal cells, as demonstrated by their use in COVID-19 vaccine development. However, LNPs applicable to bacteria have not been reported. Here, the screening of 511 LNPs containing random combinations of different lipid components identified two LNPs, LNP 496 and LNP 470, that efficiently delivered plasmids into Escherichia coli BW25113. Since Gram-negative bacteria have lipid bilayers, the bacteria are pretreated with LNP-helper that weakens the bacterial membrane. The cationic lipid DOTAP improved delivery of LNP-encapsulated plasmid DNA when present at a molar ratio of 10-25 mol% in the LNP. LNP encapsulation of the Cas13a/gRNA expression vector controlled infection by a clinical Escherichia strain in Galleria mellonela larvae and mouse infection models when used in combination with non-cytotoxic concentrations of polymyxin B, a bacterial membrane disruptor. Together, the results show that LNPs can be useful as a delivery platform for agents that counteract pathogenic bacterial infections.

Stretch-induced endogenous electric fields drive directed collective cell migration in vivo

Directed collective cell migration is essential for morphogenesis, and chemical, electrical, mechanical and topological features have been shown to guide cell migration in vitro. Here we provide in vivo evidence showing that endogenous electric fields drive the directed collective cell migration of an embryonic stem cell population-the cephalic neural crest of Xenopus laevis. We demonstrate that the voltage-sensitive phosphatase 1 is a key component of the molecular mechanism, enabling neural crest cells to specifically transduce electric fields into a directional cue in vivo. Finally, we propose that endogenous electric fields are mechanically established by the convergent extension movements of the ectoderm, which generate a membrane tension gradient that opens stretch-activated ion channels. Overall, these findings establish a role for electrotaxis in tissue morphogenesis, highlighting the functions of endogenous bioelectrical stimuli in non-neural contexts.