CRISPR-Cas guides the future of genetic engineering

RT-RPA-assisted scaffold RNA transcription amplification activation Cas12a trans-cleavage strategy for one-pot miRNA detection

Split crRNA is utilized in the CRISPR system as a highly specific and sensitive tool for nucleic acid identification in molecular diagnostics. Here, we introduce a novel one-pot RT-RPA-assisted Scaffold RNA Transcription Amplification Activation Cas12a Trans-cleavage (ScRNA-TAAT) strategy for miRNA detection. Capable of completing miRNA detection in 50 min with a detection limit of 2.66 aM. The miRNA was amplified into double-stranded DNA amplicons with a T7 promoter using RT-RPA, which is subsequently transcribed into RNA trigger. A split T7 promoter extension sequence with template binds to the RNA trigger, assembly a three-way linker to initiate transcription of the scaffold RNA. The three-way linker with sticky ends joins to its RNA products, assembling a DNA-RNA complex that acts as both a spacer RNA and an activator. Simultaneously, the DNA-RNA hybrid complexes and scaffold RNA could replace the split crRNA and combined with Cas12a, forming an active ribonucleoprotein (RNP) complex with trans-cleavage activity comparable to that of the wild-type Cas12a RNP. Furthermore, we have successfully integrated the ScRNA-TAAT strategy into lateral flow analysis, enabling the visual detection of miRNAs. The assay's exceptional specificity and universality are highlighted by its application to complex biological matrices, including serum and cell lysates. The simplicity, sensitivity, and adaptability of the ScRNA TAAT assay render it a promising candidate for point-of-care testing and high sensitivity in molecular diagnostics.

Engineering adeno-associated viral vectors for CRISPR/Cas based in vivo therapeutic genome editing

The recent approval of the first gene editing therapy for sickle cell disease and transfusion-dependent beta-thalassemia by the U.S. Food and Drug Administration (FDA) demonstrates the immense potential of CRISPR (clustered regularly interspaced short palindromic repeats) technologies to treat patients with genetic disorders that were previously considered incurable. While significant advancements have been made with ex vivo gene editing approaches, the development of in vivo CRISPR/Cas gene editing therapies has not progressed as rapidly due to significant challenges in achieving highly efficient and specific in vivo delivery. Adeno-associated viral (AAV) vectors have shown great promise in clinical trials as vehicles for delivering therapeutic transgenes and other cargos but currently face multiple limitations for effective delivery of gene editing machineries. This review elucidates these challenges and highlights the latest engineering strategies aimed at improving the efficiency, specificity, and safety profiles of AAV-packaged CRISPR/Cas systems (AAV-CRISPR) to enhance their clinical utility.

CRISPR/Cas9-directed epigenetic editing in colorectal cancer

Colorectal cancer (CRC) remains a leading cause of cancer-related illness and death worldwide, arising from a complex interplay of genetic predisposition, environmental influences, and epigenetic dysregulation. Among these factors, epigenetic modifications-reversible and heritable changes in gene expression-serve as crucial regulators of CRC progression. Understanding these modifications is essential for identifying potential biomarkers for early diagnosis and developing targeted therapeutic strategies. Epigenetic drugs (epidrugs) such as DNA methyltransferase inhibitors (e.g., decitabine) and bromodomain inhibitors (e.g., JQ1) have shown promise in modulating aberrant epigenetic changes in CRC. However, challenges such as drug specificity, delivery, and safety concerns limit their clinical application. Advances in CRISPR-Cas9-based epigenetic editing offer a more precise approach to modifying specific epigenetic markers, presenting a potential breakthrough in CRC treatment. Despite its promise, CRISPR-based epigenome editing may result in unintended genetic modifications, necessitating stringent regulations and safety assessments. Beyond pharmacological interventions, lifestyle factors-including diet and gut microbiome composition-play a significant role in shaping the epigenetic landscape of CRC. Nutritional and microbiome-based interventions have shown potential in preventing CRC development by maintaining intestinal homeostasis and reducing tumor-promoting epigenetic changes. This review provides a comprehensive overview of epigenetic alterations in CRC, exploring their implications for diagnosis, prevention, and treatment. By integrating multi-omics approaches, single-cell technologies, and model organism studies, future research can enhance the specificity and efficacy of epigenetic-based therapies. Shortly, a combination of advanced gene-editing technologies, targeted epidrugs, and lifestyle interventions may pave the way for more effective and personalized CRC treatment strategies.

Synthetic CRISPR Networks Driven by Transcription Factors via Structure-Switching DNA Translators

CRISPR-Cas systems have advanced many domains in life sciences, enabling diverse applications in gene editing, diagnostics, and biosensing. Here, we introduce a platform that leverages transcription factors (TFs) to regulate CRISPR-Cas12a trans-cleavage activity via engineered DNA translators. These dynamic DNA structures respond to TF binding by switching conformations, modulating Cas12a activity. Using TATA-binding protein and Myc-Max as TF models, we optimized DNA translators for precise and tunable control with rapid response kinetics. We demonstrated the platform's specificity and versatility by integrating TF-induced regulation into synthetic biology networks, including the activation of a fluorogenic RNA aptamer (Mango III) and the creation of an artificial multimolecular communication pathway between Cas12a and Cas13a. This work establishes TFs as effective regulators of CRISPR-Cas systems, enabling novel protein-nucleic acid communication channels, showing potential for novel synthetic biology applications.

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

Genome-wide CRISPR-Cas9 screens have untangled regulatory networks driving diverse biological processes. Their success relies on interrogating specific molecular phenotypes and distinguishing key regulators from background effects. Here, we realize these goals by optimizing CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) to dramatically improve the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely matched promoters. We use our improved CiBER-seq to accurately capture known components of well-studied RNA and protein quality control systems. These results demonstrate the precision and versatility of CiBER-seq for dissecting cellular pathways.

A CRISPR/Cas12a-Assisted SERS Nanosensor for Highly Sensitive Detection of HPV DNA

The lack of timely and effective screening and diagnosis is a major contributing factor to the high mortality rate of cervical cancer in low-income countries and resource-limited regions. Therefore, the development of a rapid, sensitive, and easily deployable diagnostic tool for HPV DNA is of critical importance. In this study, we present a novel high-sensitivity and high-specificity detection method for HPV16 and HPV18 by integrating the CRISPR/Cas12a system with surface-enhanced Raman scattering (SERS) technology. This method leverages the trans-cleavage activity of the CRISPR/Cas12a system, which cleaves biotin-modified spherical nucleic acids (Biotin-SNA) in the presence of target DNA, releasing free Biotin-DNA. The released Biotin-DNA preferentially binds to streptavidin-modified magnetic beads (SAV-MB), reducing the capture of Biotin-SNA by SAV-MB and thereby significantly enhancing detection sensitivity. This method offers the potential for point-of-care diagnostics as it operates efficiently at 37 °C without the need for thermal cycling. Using standard DNA samples, we demonstrated that this biosensor achieved detection limits as low as 209 copies/μL and 444 copies/μL within 95 min. When combined with recombinase polymerase amplification (RPA), the sensor demonstrated enhanced sensitivity, enabling detection of target DNA at concentrations as low as 1 copy/μL within approximately 50 min. Furthermore, validation with clinical samples confirmed the feasibility and practical applicability of this method. This novel SERS-based sensor offers a new and effective tool in the prevention and detection of cervical cancer.

Modulating binding affinity of aptamer-based loading constructs enhances extracellular vesicle-mediated CRISPR/Cas9 delivery

The CRISPR/Cas9 toolbox consists of modular nucleases that can be employed to efficiently modify genomic sequences with high specificity. However, delivery of the large Cas9-sgRNA ribonucleoprotein (RNP) complexes remains challenging due to their immunogenicity, size, and overall negative charge. An approach to overcome these limitations is the use of extracellular vesicles (EVs) as intracellular delivery vehicles. EVs exhibit the natural ability to carry and deliver RNA and proteins across biological barriers, and can be engineered to load and deliver a variety of biotherapeutic molecules. Previous studies have shown that efficient EV-mediated cargo delivery does not only require active loading strategies, but also benefits from strategies to release cargo from the EV membrane. Here, we load Cas9 RNP complexes into EVs by expressing sgRNAs containing MS2 aptamers (MS2-sgRNAs), alongside Cas9 and a fusion protein of CD63 and tandem MS2 coat proteins (MCPs). We demonstrate that efficient Cas9 RNP delivery can also be facilitated by modulating the binding affinity between MS2 aptamers and the MCPs. To study the effect of altering the binding affinity between the MS2 hairpin and the MCP on Cas9 RNP delivery, various mutations affecting the binding affinity were made in both the interacting MS2-hairpin and the RNA-binding domain of the MCPs. Comparing Cas9 RNP delivery of the modulated MS2-sgRNAs revealed that adapting binding affinity highly affects functional RNP delivery. Mutations resulting in high affinity did not facilitate efficient RNP delivery unless combined with a photo-inducible release strategy, showing that cargo release was a limiting factor in RNP delivery. Mutations that decreased affinity resolved this issue, resulting in Cas9 RNP delivery without the requirement of additional release strategies. However, further decreasing affinity resulted in decreased Cas9 gene-editing efficiency due to decreased levels of Cas9 RNP loading into EVs. A similar effect on functional delivery was seen after modification of the RNA-binding domain of the MCPs. Our results demonstrate that EVs are capable of functional Cas9-sgRNA complex delivery, and that modulation of binding affinity can be used to increase efficient functional delivery with non-covalent loading constructs, without the need for additional engineering strategies for cargo release.

Lipopeptide-mediated delivery of CRISPR/Cas9 ribonucleoprotein complexes for gene editing and correction

CRISPR/Cas gene editing is a highly promising technology for the treatment and even potential cure of genetic diseases. One of the major challenges for its therapeutic use is finding safe and effective vehicles for intracellular delivery of the CRISPR/Cas9 ribonucleoprotein (RNP) complex. In this study, we tested and characterized a series of novel fatty acid-modified versions of a previously reported Cas9 RNP carrier, consisting of a complex of the cell-penetrating peptide (CPP) LAH5 with Cas9 RNP and homology-directed DNA repair templates. Comparative experiments demonstrated that RNP/peptide nanocomplexes showed various improvements depending on the type of fatty acid modification. These improvements included enhanced stability in serum, improved membrane disruption capability and increased transfection efficacy. Cas9 RNP/oleic acid LAH5 peptide nanocomplexes showed the overall best performance for both gene editing and correction. Moreover, Cas9 RNP/oleic acid LAH5 nanocomplexes significantly protected the Cas9 protein cargo from enzymatic protease digestion. In addition, in vivo testing demonstrated successful gene editing after intramuscular administration. Despite the inherent barriers of the tightly organized muscle tissues, we achieved approximately 10 % gene editing in the skeletal muscle tissues when targeting the CAG-tdTomato locus in the transgenic Ai9 Cre-LoxP reporter mouse strain and 7 % gene editing when targeting the Ccr5 gene, without any observable short-term toxicity. In conclusion, the oleic acid-modified LAH5 peptide is an effective delivery platform for direct Cas9/RNP delivery, and holds great potential for the development of new CRISPR/Cas9-based therapeutic applications for the treatment of genetic diseases.

Advancements in autism spectrum disorder research --from mechanisms to interventions

This review summarizes recent advancements in the research of autism spectrum disorders (ASD), emphasizing genetic underpinnings and their implications for neurodevelopment and cognitive functions. It explores both syndromic and nonsyndromic ASD, highlighting the discovery of critical ASD-related genes and their mechanistic roles as revealed by studies using genetically engineered mouse and non-human primate models. While these models have shed light on the potential of synaptic dysfunction to disrupt brain development, they also underscore the challenges of replicating complex cognitive dysfunctions observed in ASD. Recent successes in gene therapy, particularly through innovative approaches like gene replacement and base editing, offer promising pathways for addressing genetic anomalies in ASD. These therapeutic strategies, underscored by clinical trials and cutting-edge genetic manipulation techniques, pave the way for potential interventions that could profoundly impact ASD management and treatment.

Single and combinatorial gene inactivation in Aspergillus niger using selected as well as genome-wide gRNA library pools

Aspergillus niger is a saprotroph, a pathogen, an endophyte, a food spoiler and an important cell factory. Only a minor fraction of its genes has been experimentally characterized. We here set up a CRISPR/Cas9 mutagenesis screen for functional gene analysis using co-transformation of a pool of gene editing plasmids that are maintained under selection pressure and that each contain a gRNA. First, a pool of gRNA vectors was introduced in A. niger targeting five genes with easy selectable phenotypes. Transformants were obtained with all possible single, double, triple, quadruple and quintuple gene inactivation phenotypes. Their genotypes were confirmed using the gRNA sequences in the transforming vector as barcodes. Next, a gRNA library was introduced in A. niger targeting > 9600 genes. Gene nsdC was identified as a sporulation gene using co-transformation conditions that favored uptake of one or two gRNA construct(s) from the genome-wide vector pool. Together, CRISPR/Cas9 vectors with a (genome-wide) pool of gRNAs can be used for functional analysis of genes in A. niger with phenotypes that are the result of the inactivation of a single or multiple genes.

Microbial cell factories for bioconversion of lignin to vanillin - Challenges and opportunities: A review

The bioconversion of lignin into vanillin via microbial cell factories offers a promising and sustainable route for producing high-value aromatic compounds from the abundant and underutilized byproducts of plant biomass. This review comprehensively explores the synthesis, structural characteristics, and diverse industrial applications of lignin, while addressing the inherent challenges posed by its complex structure in bioconversion processes. It examines the potential of microbial cell factories for lignin degradation, emphasizing the latest advancements in genetic engineering and metabolic optimization strategies that enhance microbial efficiency in lignin degradation and vanillin biosynthesis. It further assesses the economic feasibility of lignin-to-vanillin conversion by discussing key factors influencing cost-effectiveness and scalability, highlighting the transformative potential for producing high-value aromatic compounds in an environmentally sustainable manner. The review also highlights ongoing research efforts to develop robust microbial strains and optimize metabolic pathways for improved vanillin yield. By integrating multidisciplinary approaches, this review highlights the transformative potential of microbial cell factories to valorize lignin, offering a sustainable pathway for the production of vanillin and related aromatic compounds.

Histone demethylase KDM6B promotes glioma cell proliferation by increasing PDGFRA expression via chromatin loop formation

OBJECTIVES

Changes in gene expression pattern play an essential role in promoting the process of cancer. For example, platelet-derived growth factor receptor alpha (PDGFRA) is overexpressed in many cancers, including gliomas. Abnormal histone methylation is a typical characteristics of glioma, and our previous studies have shown that histone lysine demethylase 6B (KDM6B) is involved in glioma development by regulating the expression of specific oncogenes. In this study, the regulatory effect and underlying mechanism of KDM6B on PDGFRA expression were investigated.

METHODS

The expression information of KDM6B and PDGFRA in patients with glioma was analyzed in GEPIA database. The expression or activity of KDM6B was regulated with CRISPR interference/activation (CRISPRi/a) assays, gene knockdown and specific inhibitor. Cell proliferation was determined using cell counting kit assay. Chromatin immunoprecipitation assay (ChIP) and ChIP-loop assays were used to determine the H3K27me3 status in the PDGFRA promoter and DNA-DNA interactions mediated by KDM6B.

RESULTS

The expression of KDM6B and PDGFRA expression is positively correlated in gliomas. CRISPRi/a assays indicated that KDM6B has a positive regulatory role in PDGFRA expression in glioma cells and can promote glioma cell proliferation. KDM6B knockdown and inhibitor assays further proved that KDM6B promotes PDGFRA expression. ChIP assays indicated KDM6B reduces H3K27me3 level in the PDGFRA promoter. The ChIP-loop assays showed KDM6B increases the formation of chromatin loops, which facilitates the proximity of enhancer and promoter.

CONCLUSION

This study reveals a new epigenetic mechanism of PDGFRA overexpression in glioma cells, that is, KDM6B catalyzes the demethylation of H3K27me3 and induces chromatin loop formation to activate PDGFRA expression. This study is of great significance for the understanding of glioma development and the application of new treatment strategies, such as radiation therapy combined with epigenetic therapy.

Trans-cleavage activity of Cas12a effectors can be unleashed by both double-stranded DNA and single-stranded RNA targeting in absence of PAM

CRISPR-Cas12a is a powerful tool in nucleic acid detection, but the relationship between its trans-cleavage activity and protospacer adjacent motif (PAM) sequences remains incompletely understood. In this study, we synthesized diverse PAM-sequence substrates and conducted systematic cis-cleavage and trans-cleavage experiments with three Cas12a orthologs. We found that double-stranded DNA (dsDNA) can activate Cas12a's trans-cleavage activity even without PAM and this activation occurring independently of cis-cleavage. Notably, our results also revealed that single-stranded RNA (ssRNA) can directly initiate the trans-cleavage activity of Cas12a.We also experimentally validated the feasibility of CRISPR-Cas12a in detecting target dsDNA lacking PAM sequences, including identifying mutated sites in clinical samples. Structural prediction using AlphaFold 3 revealed the potential mechanism of Cas12a's PAM-independent trans-cleavage. Our research expands the understanding of Cas12a's trans-cleavage mechanism and demonstrates its potential for nucleic acid detection beyond PAM-dependent targets. This discovery broadens the application scope of Cas12a, providing new opportunities for developing highly sensitive and versatile diagnostic platforms.

The Fomivirsen, Patisiran, and Givosiran Odyssey: How the Success Stories May Pave the Way for Future Clinical Translation of Nucleic Acid Drugs

Over the past 25 years, the approval of several nucleic acid-based drugs by the US Food and Drug Administration (FDA) has marked a significant milestone, establishing nucleic acid drugs as a viable therapeutic modality. These groundbreaking discoveries are the result of some crucial points in the timeline of nucleic acid drug development. The inventions used in fomivirsen (Vitravene; Isis Pharmaceuticals) development paved the road for structural backbone modifications as well as nucleobase and sugar modifications. The approval of patisiran (Onpattro; Alnylam) demonstrated an effective and safe delivery system for small interfering RNA (siRNA), extending potential applications to other nucleic acids such as messenger RNA (mRNA). Givosiran (Givlaari; Alnylam) further revolutionized the field with a carrier-free, targeted platform, utilizing N-Acetylgalactosamine (GalNAc)-siRNA conjugates to enable efficient delivery, expanding therapeutic applications beyond rare genetic disorders to more common conditions such as hyperlipidemia and hypertension. In this review paper, we highlight the evolution of nucleic acid-based drug development, focusing on the pioneering agents fomivirsen, patisiran, and givosiran, and discuss the ongoing challenges in advancing these therapeutics and vaccines.

Hi-TARGET: a fast, efficient and versatile CRISPR type I-B genome editing tool for the thermophilic acetogen Thermoanaerobacter kivui

BACKGROUND

Due to its ability to grow fast on CO2, CO and H2 at high temperatures and with high energy efficiency, the thermophilic acetogen Thermoanaerobacter kivui could become an attractive host for industrial biotechnology. In a circular carbon economy, diversification and upgrading of C1 platform feedstocks into value-added products (e. g., ethanol, acetone and isopropanol) could become crucial. To that end, genetic and bioprocess engineering tools are required to facilitate the development of bioproduction scenarios. Currently, the genome editing tools available for T. kivui present some limitations in speed and efficiency, thus restricting the development of a powerful strain chassis for industrial applications.

RESULTS

In this study, we developed the versatile genome editing tool Hi-TARGET, based on the endogenous CRISPR Type I-B system of T. kivui. Hi-TARGET demonstrated 100% efficiency for gene knock-out (from both purified plasmid and cloning mixture) and knock-in, and 49% efficiency for creating point mutations. Furthermore, we optimized the transformation and plating protocol and increased transformation efficiency by 245-fold to 1.96 × 104 ± 8.7 × 103 CFU μg-1. Subsequently, Hi-TARGET was used to demonstrate gene knock-outs (pyrE, rexA, hrcA), a knock-in (ldh::pFAST), a single nucleotide mutation corresponding to PolCC629Y, and knock-down of the fluorescent protein pFAST. Analysis of the ∆rexA deletion mutant created with Hi-TARGET revealed that the transcriptional repressor rexA is likely involved in the regulation of the expression of lactate dehydrogenase (ldh). Following genome engineering, an optimized curing procedure for edited strains was devised. In total, the time required from DNA to a clean, edited strain is 12 days, rendering Hi-TARGET a fast, robust and complete method for engineering T. kivui.

CONCLUSIONS

The CRISPR-based genome editing tool Hi-TARGET developed for T. kivui can be used for scarless deletion, insertion, point mutation and gene knock-down, thus fast-tracking the generation of industrially-relevant strains for the production of carbon-negative chemicals and fuels as well as facilitating studies of acetogen metabolism and physiology.

Natronobacterium gregoryi Argonaute inhibits class 1 integron integrase-mediated excision and integration

Argonaute (Ago) proteins, ubiquitous in all domains of life, serve as key components in defense against foreign nucleic acids. While eukaryotic Agos (eAgos) are well characterized for guide RNA-mediated RNA targeting, prokaryotic Agos (pAgos) exhibit diverse functions, particularly in protecting bacteria from invasive DNA. The previous study identified Class 1 integron integrase (IntI-1), a tyrosine site-specific recombinase involved in horizontal transfer of antibiotic resistance genes, as a potential interaction partner of Natronobacterium gregoryi Argonaute (NgAgo), a member of pAgos. Here, we demonstrated that this interaction was direct, depended on the PIWI domain, and was independent of the catalytic activity of NgAgo. Notably, no interaction occurred between NgAgo and Cre (another tyrosine site-specific recombinase), highlighting the specificity of NgAgo-IntI-1 interaction. Furthermore, NgAgo could inhibit binding of IntI-1 to its target DNA, and then impede IntI-1-mediated integration and excision. Consistent with the above finding, few pAgos could be found in prokaryotic genomes containing IntI, whereas IntI showed significant co-occurrence with another bacterial defense system, CRISPR-Cas. In summary, our study elucidated a novel defense mechanism of pAgos through interaction with IntI-1 for inhibiting IntI-1-mediated gene excision/integration process.

Innovative Chemical Strategies for Advanced CRISPR Modulation

ConspectusOver the past decade, RNA-guided gene editing technologies, particularly those derived from CRISPR systems, have revolutionized life sciences and opened unprecedented opportunities for therapeutic innovation. Despite their transformative potential, achieving precise control over the activity and specificity of these molecular tools remains a formidable challenge, requiring advanced and innovative regulatory strategies. We and others have developed new approaches that integrate chemical ingenuity with bioorthogonal techniques to achieve remarkable precision in CRISPR regulation. One key innovation lies in the chemical modulation of guide RNA (gRNA), significantly expanding the CRISPR toolkit. Strategies such as CRISPR-ON and CRISPR-OFF switches rely on selective chemical masking and demasking of gRNA. These approaches use either bulky chemical groups to preemptively mask RNA or minor, less obstructive groups to fine-tune its function, followed by bioorthogonal reactions to restore or suppress activity. These methodologies have proven to be pivotal for controlled gene editing and expression, addressing the challenges of precision, reversibility, and dynamic regulation.Parallel to these advances, the development of mesoporous metal-organic frameworks (MOFs) has emerged as a promising solution for RNA deprotection and activation. By serving as catalytic tools, MOFs enhance the versatility and efficiency of CRISPR systems, pushing their applications beyond the conventional boundaries. In addition, the synthesis of novel small molecules for regulating CRISPR-Cas9 activity marks a critical milestone in the evolution of gene therapy protocols. Innovative RNA structural control strategies have also emerged, particularly through the engineering of G-quadruplex (G4) motifs and G-G mismatches. These methods exploit the structural propensities of engineered gRNAs, employing small-molecule ligands to induce specific conformational changes that modulate the CRISPR activity. Whether stabilizing G4 formation or promoting G-G mismatches, these strategies demonstrate the precision and sophistication required for the molecular-level control of gene editing.Further enhancing these innovations, techniques like host-guest chemistry and conditional diacylation cross-linking have been developed to directly alter gRNA structure and function. These approaches provide nuanced, reversible, and safe control over CRISPR systems, advancing both the precision and reliability of gene editing technologies. In conclusion, this body of work highlights the convergence of chemistry, materials science, and molecular biology to create integrative solutions for gene editing. By combination of bioorthogonal chemistry, RNA engineering, and advanced materials, these advancements offer unprecedented accuracy and control for both fundamental research and therapeutic applications. These innovations not only advance genetic research but also contribute to developing safer and more effective gene editing strategies, moving us closer to realizing the full potential of these technologies.

CRISPR-Cas Systems: A Functional Perspective and Innovations

Adaptation is a fundamental tenet of evolutionary biology and is essential for the survival of all organisms, including prokaryotes. The evolution of clustered regularity exemplifies this principle of interspaced short palindromic repeats (CRISPR) and associated proteins (Cas), an adaptive immune system that confers resistance to viral infections. By integrating short segments of viral genomes into their own, bacteria and archaea develop a molecular memory that enables them to mount a rapid and targeted response upon subsequent viral challenges. The fortuitous discovery of this immune mechanism prompted many studies and introduced researchers to novel tools that could potentially be developed from CRISPR-Cas and become clinically relevant as biotechnology rapidly advances in this area. Thus, a deeper understanding of the underpinnings of CRISPR-Cas and its possible therapeutic applications is required. This review analyses the mechanism of action of the CRISPR-Cas systems in detail and summarises the advances in developing biotechnological tools based on CRISPR, opening the field for further research.

Cuproptosis and its potential role in musculoskeletal disease

Cuproptosis, a recently identified form of copper-dependent cell death, arises from intracellular copper dyshomeostasis. As an essential trace element, copper plays a critical role in bioenergetic metabolism, redox regulation, and synaptic transmission. However, excessive copper exerts cytotoxic effects through multiple pathways, including increased reactive oxygen species (ROS) production, apoptotic cascade activation, necrotic membrane rupture, inflammatory responses, and mitochondrial dysfunction. Distinct from other cell death mechanisms, cuproptosis is characterized by copper ion binding to acetylated mitochondrial respiratory chain proteins, leading to pathogenic protein aggregation, iron-sulfur cluster depletion, and cellular collapse. Emerging evidence underscores aberrant copper accumulation and resultant proteotoxic stress as pivotal contributors to the pathogenesis of multiple musculoskeletal pathologies, including osteoporosis, osteoarthritis, sarcopenia, osteosarcoma, intervertebral disc degeneration, spinal cord injury, and biofilm-associated orthopedic infections. Understanding the spatiotemporal regulation of cuproptosis may provide novel opportunities for advancing diagnostic and therapeutic approaches in orthopedic medicine. This review synthesizes current insights into the molecular mechanisms of cuproptosis, its pathogenic role in musculoskeletal diseases, and the potential for biomarker-driven therapeutic interventions.

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.

Probiotics and prebiotics: new treatment strategies for oral potentially malignant disorders and gastrointestinal precancerous lesions

Oral potentially malignant disorders (OPMDs) and gastrointestinal precancerous lesions (GPLs) are major public health concerns because of their potential to progress to cancer. Probiotics, prebiotics, and engineered probiotics can positively influence the prevention and management of OPMDs and GPLs. This review aims to comprehensively review the application status of probiotics, prebiotics and engineered probiotics in OPMDs and GPLs, explore their potential mechanisms of action, and anticipate their future clinical use.

Editing gliA, gliP and gliZ of Aspergillus fumigatus Using CRISPR/Cas System Renders Fungus Incapable to Produce Gliotoxin

Aspergillus fumigatus is a saprophytic fungus that causes respiratory infections in human, animals, and birds. This fungus produces gliotoxin which is a secondary metabolite that triggers pathogenicity. Gliotoxin is encoded by a 13-gene cluster including gliA, gliP and gliZ. The purpose of this study was to determine whether the fungus produces gliotoxin after these genes are edited using CRISPR/Cas system. For this, crRNAs for gliA, gliP and gliZ were designed using EuPaGDT, while tracrRNA and Cas9 protein were purchased ready-made. These crRNAs were individually annealed with the tracrRNA to make three gRNAs which were then individually combined with the Cas9 to make three ribonucleoprotein (RNP) complexes. A. fumigatus protoplasts were enzymatically generated and transfected with each of the RNP complexes (group 1) in PEGylated conditions. Non-treated protoplasts were simultaneously run as control (group 2). Transfected protoplasts showed reduced growth on SDA plates as compared to their control. Gliotoxin extraction through thin-layer chromatography was carried out for both the groups which showed the absence of gliotoxin in group 1. Sequencing results confirmed the indels in target genes which shows that the CRISPR/Cas9 system effectively targeted A. fumigatus' gliotoxin-related genes that rendered fungus incapable to produce gliotoxin. This work may pave the way to develop effective strategies to control the infections caused by A. fumigatus.

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.

Spy-ing on nucleic acids: Atomic resolution of the S. pyogenes CRISPR-Cas9 surveillance state

In a recent issue of Cell Chemical Biology, De Paula et al.1 report an extensive methyl-TROSY solution NMR study of the CRISPR-Cas9 holoenzyme. Studying millisecond-to-second protein dynamics using individual domain constructs of Cas9 coupled to structural interrogations of the full-length enzyme, the authors describe the Cas9 "surveillance state," a molecular mechanism driving the discrimination between on- and off-target DNA.

Design of lipid nanoparticle (LNP) containing genetic material CRISPR/Cas9 for familial hypercholesterolemia

Familial hypercholesterolemia is a genetic disorder caused by mutations in the low- density lipoprotein receptor gene (LDLR) and the current treatment still focuses on symptom management. The aim of this study was to develop a lipid nanoparticle (LNP)- based delivery system for the CRISPR/Cas9 component in correcting LDLR gene mutations. LNPs were prepared using an ultrasonic-solvent emulsification technique by varying the surfactant: oil ratio (SOR), homogenization speed and time, and sonication time. Next, the LNP surface was modified by adding DSPE-PEG2000-NH2 and polyethyleneimine. The next stage is to design the single guide RNA (sgRNA) and Donor DNA wildtype (Donor DNA wt). This genetic material was complexed with LNP and then transfected into Hepa1-6 LDLR mt cells, an in vitro representation of cells suffering from familial hypercholesterolemia. This optimization process produced LNPs with a particle size of 118.6 ± 0.8  nm and a polydispersity index of 0.34 ± 0.03. The LNP surface modification resulted in a zeta potential of +7.5  mV. A transmission electron microscope (TEM) analysis showed spherical morphology with size distribution following a regular pattern. LNP cell viability tests showed good biocompatibility at concentrations <15  mM with a half-maximal inhibitory concentration (IC50) value of 27.7  mM. The dominant cellular uptake mechanism of LNP was through the clathrin-mediated endocytosis (CME) pathway. The Hepa1-6 LDLR mt cell model was successfully produced with the transfecting agent Lipofectamine 3000 by homology-directed repair (HDR) mechanism. The LNP-genetic material complex with a ratio of sgRNA:Cas9:Donor DNA wt (1:1:0.04) showed an increase in LDLR gene expression of 3.3 ± 0.2 times and LDLR protein levels reached 12.95 ± 0.25  ng/mL on day 4 after transfection. The results of this study indicate that the developed LNP-based delivery system has the potential for gene therapy applications in familial hypercholesterolemia.

Application of Multiple Base-Editing Mediated by Polycistronic tRNA-gRNA-Processing System in Pig Cells

Gene edited pigs have extensive and important application value in the fields of agriculture and biomedicine. With the increasing demand in medical research and agricultural markets, more and more application scenarios require gene edited pigs to possess two or even more advantageous phenotypes simultaneously. The current production of multi gene edited pigs is inefficient, time-consuming, and costly, and there is an urgent need to develop efficient and accurate multi gene editing application technologies. The polycistronic tRNA-gRNA-processing system (PTG), developed based on endogenous tRNA self-processing systems, has been shown to exhibit efficient multi gene editing in plants. This study aims to combine a PTG strategy with multiple gRNA production functions with an adenine base editor (ABE) to test its feasibility for efficient and precise multi gene base editing in pig cells. The results indicate that the PTG based integrated ABE plasmid can perform efficient base editing at multiple gene loci in pig cells. And while the gene editing efficiency was significantly improved, no indel and sgRNA dependent off target effects caused by DSB were detected. This work permit will provide a solid foundation for the production of multi gene edited pigs with agricultural and medical applications.

Application of pre-amplification-based CRISPR-Cas nanostructured biosensors for bacterial detection

Bacterial infections are one of the primary triggers of global disease outbreaks. Traditional detection methods, such as bacterial culture and PCR, while reliable, are limited by their time-consuming procedures and operational complexity. In recent years, the CRISPR-Cas system has demonstrated significant potential in gene editing and diagnostics due to its high specificity and precision, offering innovative solutions for bacterial detection. By integrating pre-amplification techniques, the CRISPR-Cas system has substantially enhanced detection sensitivity, particularly excelling in detecting low-concentration target bacteria. This review summarizes the principles and application examples of CRISPR-Cas-based fluorescence, electrochemical, lateral flow, and colorimetric nanostructured biosensors developed over the past three years, categorizing them according to their recognition methods (e.g. bacterial genomes, aptamers, antibodies). It systematically explores the broad application prospects of these sensors in medical diagnostics, environmental monitoring, and food safety assessment. Additionally, this review discusses future research directions and potential development prospects, providing new insights and technical support for the rapid diagnosis and treatment of bacterial infections.

Therapeutic Targeting in Ovarian Cancer: Nano-Enhanced CRISPR/Cas9 Gene Editing and Drug Combination Therapy

Ovarian cancer is the third most common gynecological cancer worldwide. Due to the high recurrence rate of advanced-stage ovarian cancer, often resulting from drug-resistant and refractory disease, various treatment strategies are under investigation. Genome editing of therapeutic target genes holds promise in enhancing cancer treatment efficacy by elucidating gene functions and mechanisms involved in cancer progression. The CRISPR/Cas9 system, in particular, shows great potential in ovarian cancer gene therapy and drug development. Targeting therapeutic genes such as BRCA1/2, P53, Snai1 etc, could improve the therapeutic strategy in ovarian cancer. CRISPR/Cas9 is a powerful gene-editing tool that there are many on-going clinical trials to treat various diseases including cancer. Nano-based delivery systems for CRISPR/Cas9 offer further therapeutic benefits, leveraging the unique properties of nanoparticles to improve delivery efficiency. Nano-based delivery systems could enhance the stability of CRISPR/Cas9 delivery formats (such as plasmid, mRNA, etc) and improve the delivery precision of delivery to target tumors. Additionally, combining CRISPR/Cas9 with targeted drug treatments, especially those aimed at genes associated with drug resistance, may significantly improve therapeutic outcomes in ovarian cancer. In this review, we discuss therapeutic target genes and their mechanisms in ovarian cancer, advances in nano-based CRISPR/Cas9 delivery, and the therapeutic potential of combining CRISPR/Cas9 with drug treatments for ovarian cancer.

Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates

The sequence specificity and programmability of DNA binding and cleavage have enabled widespread applications of CRISPR-Cas12a in genetic engineering. As an RNA-guided CRISPR endonuclease, Cas12a engages a 20-base pair (bp) DNA segment by forming a three-stranded R-loop structure in which the guide RNA hybridizes to the DNA target. Here we use single-molecule torque spectroscopy to investigate the dynamics and mechanics of R-loop formation of two widely used Cas12a orthologs at base-pair resolution. We directly observe kinetic intermediates corresponding to a ~5 bp initial RNA-DNA hybridization and a ~17 bp intermediate preceding R-loop completion, followed by transient DNA unwinding that extends beyond the 20 bp R-loop. The complex multistate landscape of R-loop formation is ortholog-dependent and shaped by target sequence, mismatches, and DNA supercoiling. A four-state kinetic model captures essential features of Cas12a R-loop dynamics and provides a biophysical framework for understanding Cas12a activity and specificity.

The evolving landscape of NF gene therapy: Hurdles and opportunities

Neurofibromatosis type 1 (NF1)- and NF2-related schwannomatosis are rare autosomal dominant monogenic disorders characterized by a predisposition for nerve-associated tumors. Current treatments focus on symptomatic management, but advancements in the gene therapy field present unique opportunities to treat the genetic underpinnings and develop curative therapies for NF. Approaches such as nonsense suppression agents and oligonucleotide therapies are becoming more mature and have emerging preclinical data in the context of NF. Furthermore, there has been progress in developing gene therapy vectors that can be delivered locally into tumors to ablate or shrink their size. While still a nascent research area, gene addition and gene repair strategies hold tremendous promise for the prevention and treatment of NF-related tumors. These technologies will also require parallel development of delivery vectors able to target the Schwann cells from which tumors most commonly arise. This review seeks to contextualize these advancements and which hurdles remain for their clinical adoption.

Discovery of the widespread site-specific single-stranded nuclease family Ssn

Site-specific endonucleases that exclusively cut single-stranded DNA have hitherto never been described and constitute a barrier to the development of ssDNA-based technologies. We identify and characterize one such family, from the GIY-YIG superfamily, of widely distributed site-specific single-stranded nucleases (Ssn) exhibiting unique ssDNA cleavage properties. By first comprehensively studying the Ssn homolog from Neisseria meningitidis, we demonstrate that it interacts specifically with a sequence (called NTS) present in hundreds of copies and surrounding important genes in pathogenic Neisseria. In this species, NTS/Ssn interactions modulate natural transformation and thus constitute an additional mechanism shaping genome dynamics. We further identify thousands of Ssn homologs and demonstrate, in vitro, a range of Ssn nuclease specificities for their corresponding sequence. We demonstrate proofs of concept for applications including ssDNA detection and digestion of ssDNA from RCA. This discovery and its applications set the stage for the development of innovative ssDNA-based molecular tools and technologies.

RNAi and genome editing of sugarcane: Progress and prospects

Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan-genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods-biolistic gene transfer or Agrobacterium-mediated transformation-coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture-free technologies, such as spray-induced gene silencing, virus-induced gene silencing, or virus-induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.

High-Efficiency Genome Editing in Naturally Isolated Aeromonas hydrophila and Edwardsiella Piscicida Using the CRISPR-Cas9 System

Aeromonas hydrophila and Edwardsiella piscicida are significant bacterial pathogens in aquaculture, causing severe diseases and tremendous economic losses worldwide. Additionally, both of them can act as opportunistic pathogens in humans, leading to severe infections. Efficient genome editing tools for these pathogens are essential for understanding their pathogenic mechanisms and physiological behaviors, enabling the development of targeted strategies to control and mitigate their effects. In this study, we adapted the CRISPR-Cas9 system for high-efficiency, marker-less genome editing in multiple naturally isolated strains of these two aquaculture pathogens. We developed a streamlined procedure that successfully generated deletion mutants of the aerA gene (encoding for aerolysin, a pore-forming toxin that plays a critical role in the pathogenicity) and the gfp insertion mutants in three naturally isolated A. hydrophila strains. Additionally, we deleted five putative hemolysin-encoding genes in both A. hydrophila ML10-51K and its ∆aerA derivative. The same system was also applied to the naturally isolated E. piscicida S11-285 strain, successfully deleting the ssaV gene (a component of the Type III Secretion System-a critical virulence mechanism in many pathogenic bacteria). The methodologies developed herein could be broadly applied to other pathogenic strains from natural environments, providing valuable tools for studying bacterial pathogenesis and aiding in the development of effective control strategies.

BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library

CRISPR/Cas base editors offer precise conversion of single nucleotides without inducing double-strand breaks. This technology finds extensive applications in gene therapy, gene function analysis, and other domains. However, a crucial challenge lies in selecting the appropriate guide RNAs (gRNAs) for base editing. Although various gRNAs design tools exist, creating a simplified base-editing library with diverse protospacer adjacent motifs (PAM) sequences for gRNAs screening remains a challenge. We present a user-friendly web tool, BES-Designer ( https://bes-designer.aielab.net ), for gRNAs design based on base editors, aimed at streamlining the creation of a base-editing library. BES-Designer incorporates our proposed rules for target sequence simplification, helping researchers narrow down the scope of biological experiments in the lab. It allows users to design target sequences with various PAMs and editing types simultaneously, and prioritize them in the simplified base-editing library. This tool has been experimentally proven to achieve a 30% simplification efficiency on the base-editing-library.

CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model

Astrocytes promote neuroinflammation and neurodegeneration in multiple sclerosis (MS) through cell-intrinsic activities and their ability to recruit and activate other cell types. In a genome-wide CRISPR-based forward genetic screen investigating regulators of astrocyte proinflammatory responses, we identified the C-type lectin domain-containing 16A gene (CLEC16A), linked to MS susceptibility, as a suppressor of nuclear factor-κB (NF-κB) signaling. Gene and small-molecule perturbation studies in mouse primary and human embryonic stem cell-derived astrocytes in combination with multiomic analyses established that CLEC16A promotes mitophagy, limiting mitochondrial dysfunction and the accumulation of mitochondrial products that activate NF-κB, the NLRP3 inflammasome and gasdermin D. Astrocyte-specific Clec16a inactivation increased NF-κB, NLRP3 and gasdermin D activation in vivo, worsening experimental autoimmune encephalomyelitis, a mouse model of MS. Moreover, we detected disrupted mitophagic capacity and gasdermin D activation in astrocytes in samples from individuals with MS. These findings identify CLEC16A as a suppressor of astrocyte pathological responses and a candidate therapeutic target in MS.

Engineering live cell surfaces with polyphenol-functionalized nanoarchitectures

Cell surface functionalization has emerged as a powerful strategy for modulating cellular behavior and expanding cellular capabilities beyond their intrinsic biological limits. Natural phenolic molecules present as 'green' and versatile building blocks for constructing cell-based biomanufacturing and biotherapeutic platforms. Due to the abundant catechol or galloyl groups, phenolic molecules can dynamically and reversibly bind to versatile substrates via multiple molecular interactions. A range of self-assembled cytoadhesive polyphenol-functionalized nanoarchitectures (cytoPNAs) can be formed via metal coordination or macromolecular self-assembly that can rapidly attach to cell surfaces in a cell-agnostic manner. Additionally, the cytoPNAs attached on the cell surface can also provide active sites for the conjunction of bioactive payloads, further expanding the structural repertoire and properties of engineered cells. This Perspective introduces the wide potential of cytoPNA-mediated cell engineering in three key applications: (1) creating inorganic-organic biohybrids as cell factories for efficient production of high-value chemicals, (2) constructing engineered cells for cell-based therapies with enhanced targeting specificity and nano-bio interactions, and (3) encapsulating microbes as biotherapeutics for the treatment of gastrointestinal tract-related diseases. Collectively, the rapid, versatile, and modular nature of cytoPNAs presents a promising platform for next-generation cell engineering and beyond.

Rapid Enzymatic Assay for Antiretroviral Drug Monitoring Using CRISPR-Cas12a-Enabled Readout

Maintaining the efficacy of human immunodeficiency virus (HIV) medications is challenging among children because of dosing difficulties, the limited number of approved drugs, and low rates of medication adherence. Drug level feedback (DLF) can support dose optimization and timely interventions to prevent treatment failure, but current tests are heavily instrumented and centralized. We developed the REverse transcriptase ACTivity crispR (REACTR) for rapid measurement of HIV drugs based on the extent of DNA synthesis by HIV reverse transcriptase. CRISPR-Cas enzymes bind to the synthesized DNA, triggering collateral cleavage of quenched reporters and generating fluorescence. We measured azidothymidine triphosphate (AZT-TP), a key drug in pediatric HIV treatment, and investigated the impact of assay time and DNA template length on REACTR's sensitivity. REACTR selectively measured clinically relevant AZT-TP concentrations in the presence of genomic DNA and peripheral blood mononuclear cell lysate. REACTR has the potential to enable rapid point-of-care HIV DLF to improve pediatric HIV care.

Dynamic sampling of a surveillance state enables DNA proofreading by Cas9

CRISPR-Cas9 has revolutionized genome engineering applications by programming its single-guide RNA, where high specificity is required. However, the precise molecular mechanism underscoring discrimination between on/off-target DNA sequences, relative to the guide RNA template, remains elusive. Here, using methyl-based NMR to study multiple holoenzymes assembled in vitro, we elucidate a discrete protein conformational state which enables recognition of DNA mismatches at the protospacer adjacent motif (PAM)-distal end. Our results delineate an allosteric pathway connecting a dynamic conformational switch at the REC3 domain, with the sampling of a catalytically competent state by the HNH domain. Our NMR data show that HiFi Cas9 (R691A) increases the fidelity of DNA recognition by stabilizing this "surveillance state" for mismatched substrates, shifting the Cas9 conformational equilibrium away from the active state. These results establish a paradigm of substrate recognition through an allosteric protein-based switch, providing unique insights into the molecular mechanism which governs Cas9 selectivity.

Expanding the horizon of CAR T cell therapy: from cancer treatment to autoimmune diseases and beyond

Chimeric antigen receptor (CAR)-T-cell therapy has garnered significant attention for its transformative impact on the treatment of hematologic malignancies such as leukemia and lymphoma. Despite its remarkable success, challenges such as resistance, limited efficacy in solid tumors, and adverse side effects remain prominent. This review consolidates recent advancements in CAR-T-cell therapy and explores innovative engineering techniques and strategies to overcome the immunosuppressive tumor microenvironment (TME). We also discuss emerging applications beyond cancer, including autoimmune diseases and chronic infections. Future perspectives highlight the development of more potent CAR-T cells with increased specificity and persistence and reduced toxicity, providing a roadmap for next-generation immunotherapies.

CrRNA Conformation-Engineered CRISPR-Cas12a System for Robust and Ultrasensitive Nucleic Acid Detection

Despite the widespread application of the CRISPR-Cas12a system in vitro diagnostics due to its high programmability and distinctive trans-cleavage activity, the susceptibility of its crRNA component to degradation and sensitivity to storage and working conditions poses a significant challenge to improving the practical efficacy of these diagnostic systems. Here, we show that engineered crRNA with a covalently closed circular structure (C-crRNA) can replace traditional linear crRNA to form functional complexes with Cas12a protein, significantly enhancing the anti-interference ability of the CRISPR-Cas12a system while maintaining its sensitivity and specificity. Based on this finding, a circular crRNA-mediated CRISPR molecular diagnostic (CRCD) toolkit is developed and successfully integrated with a standard nucleic acid amplification technique to detect synthesized Human Papillomavirus type 16 (HPV-16) plasmids down to 10 aM sensitivity levels. Furthermore, the CRCD system is applied for ultrasensitive detection of 40 HPV-16 and 40 influenza A viruses in clinical samples, with results consistent with those from PANTHER detection and quantitative real-time polymerase chain reaction (qRT-PCR). In conclusion, this strategy introduces a novel paradigm for engineering crRNA to program Cas12a, which has the potential to revolutionize the use of crRNA in CRISPR-based molecular diagnostics.

A Novel Quantification Method for Gene-Edited Animal Detection Based on ddPCR

As gene-editing technologies continue to evolve, gene-edited products are making significant strides. These products have already been commercialized in the United States and Japan, prompting global attention to their safety and regulatory oversight. However, the detection of gene editing still relies on qPCR, and there is a lack of quantitative detection methods to quantify gene-editing components in products. To ensure consumer safety and transparency, we developed a novel droplet digital PCR (ddPCR)-based detection method for gene-edited products. Primers and probes were designed targeting the editing sites of MSTN-edited cattle, and the method was evaluated for specificity, sensitivity, real sample testing, and detection thresholds. Our results demonstrate that this ddPCR method is highly specific, with a detection limit of 5 copies/µL, and it successfully detected MSTN edits in all 11 tested samples. Tests using both actual gene-edited cattle samples and plasmid DNA at concentrations of 5%, 1%, and 0.01% yielded consistent results, indicating the method's suitability for real-world applications. This ddPCR assay provides a sensitive and specific tool for detecting MSTN gene-edited cattle and determining the presence of gene-edited products, offering crucial support for regulatory monitoring of gene-edited animal-derived foods.

PAM-adjacent DNA flexibility tunes CRISPR-Cas12a off-target binding

Cas12a is a class 2 type V CRISPR-associated nuclease that uses an effector complex comprised of a single protein activated by a CRISPR-encoded small RNA to cleave double-stranded DNA at specific sites. Cas12a processes unique features as compared to other CRISPR effector nucleases such as Cas9, and has been demonstrated as an effective tool for manipulating complex genomes. Prior studies have indicated that DNA flexibility at the region adjacent to the protospacer-adjacent-motif (PAM) contributes to Cas12a target recognition. Here, we adapted a SELEX-seq approach to further examine the connection between PAM-adjacent DNA flexibility and off-target binding by Cas12a. A DNA library containing DNA-DNA mismatches at PAM + 1 to + 6 positions was generated and subjected to binding in vitro with FnCas12a in the absence of pairing between the RNA guide and DNA target. The bound and unbound populations were sequenced to determine the propensity for off-target binding for each of the individual sequences. Analyzing the position and nucleotide dependency of the DNA-DNA mismatches showed that PAM-dependent Cas12a off-target binding requires unpairing of the protospacer at PAM + 1 and increases with unpairing at PAM + 2 and + 3. This revealed that PAM-adjacent DNA flexibility can tune Cas12a off-target binding. The work adds support to the notion that physical properties of the DNA modulate Cas12a target discrimination, and has implications on Cas12a-based applications.

Using CRISPR for viral nucleic acid detection

Pathogenic microorganisms, such as viruses, have threatened human health and will continue to contribute to future epidemics and pandemics, highlighting the importance of developing effective diagnostics. To contain viral outbreaks within populations, fast and early diagnosis of infected individuals is essential. Although current standard methods are highly sensitive and specific, like RT-qPCR, some can have slow turnaround times, which can hinder the prevention of viral transmission. The discovery of CRISPR-Cas systems in bacteria and archaea initially revolutionized the world of genome editing. Intriguingly, CRISPR-Cas enzymes also have the ability to detect nucleic acids with high sensitivity and specificity, which sparked the interest of researchers to also explore their potential in diagnosis of viral pathogens. In particular, the CRISPR-Cas13 system has been used as a tool for detecting viral nucleic acids. Cas13's capability to detect both target RNA and non-specific RNAs has led to the development of detection methods that leverage these characteristics through designing specific detection read-outs. Optimization of viral sample collection, amplification steps and the detection process within the Cas13 detection workflow has resulted in assays with high sensitivity, rapid turnaround times and the capacity for large-scale implementation. This review focuses on the significant innovations of various CRISPR-Cas13-based viral nucleic acid detection methods, comparing their strengths and weaknesses while highlighting Cas13's great potential as a tool for viral diagnostics.

Entropy-driven amplification reaction and the CRISPR/Cas12a system form the basis of an electrochemical biosensor for E.coli-specific detection

We present an innovative biosensor designed for the precise identification of Escherichia coli (E.coli), a predominant pathogen responsible for gastrointestinal infections. E.coli is prevalent in environments characterized by substandard water quality and can lead to severe diarrhea, especially in hospital settings. The device employs entropy-driven reactions to synthesize copious amounts of double-stranded DNA (dsDNA), which, upon binding with crRNA, triggers the CRISPR/Cas12a system's cleavage mechanism. This process results in the separation of a ferrocene (Fc)-tagged DNA strand from the electrode, enhancing the electrochemical signal for E.coli's rapid and accurate detection. Our tests confirm the biosensor's ability to quantify E.coli across a dynamic range from 100 to 10 million CFU/mL, achieving a detection threshold of just over 5 CFU/mL. The development of this electrochemical biosensor highlights its exceptional selectivity, high sensitivity, and user-friendly interface for E.coli detection. It stands as a significant step forward in pathogen detection technology, promising new directions for identifying various bacterial infections through the CRISPR/Cas mechanism.

Targeted correction of megabase-scale CNTN6 duplication in induced pluripotent stem cells and impacts on gene expression

Copy number variations of the human CNTN6 gene, resulting from megabase-scale microdeletions or microduplications in the 3p26.3 region, are frequently implicated in neurodevelopmental disorders such as intellectual disability and developmental delay. However, duplication of the full-length human CNTN6 gene presents with variable penetrance, resulting in phenotypes that range from neurodevelopmental disorders to no visible pathologies, even within the same family. Previously, we obtained a set of induced pluripotent stem cell lines derived from a patient with a CNTN6 gene duplication and from two healthy donors. Our findings demonstrated that CNTN6 expression in neurons carrying the duplication was significantly reduced. Additionally, the expression from the CNTN6 duplicated allele was markedly lower compared to the wild-type allele. Here, we first introduce a system for correcting megabase-scale duplications in induced pluripotent stem cells and secondly analyze the impact of this correction on CNTN6 gene expression. We showed that the deletion of one copy of the CNTN6 duplication did not affect the expression levels of the remaining allele in the neuronal cells.

Using Quantitative Trait Locus Mapping and Genomic Resources to Improve Breeding Precision in Peaches: Current Insights and Future Prospects

Modern breeding technologies and the development of quantitative trait locus (QTL) mapping have brought about a new era in peach breeding. This study examines the complex genetic structure that underlies the morphology of peach fruits, paying special attention to the interaction between genome editing, genomic selection, and marker-assisted selection. Breeders now have access to precise tools that enhance crop resilience, productivity, and quality, facilitated by QTL mapping, which has significantly advanced our understanding of the genetic determinants underlying essential traits such as fruit shape, size, and firmness. New technologies like CRISPR/Cas9 and genomic selection enable the development of cultivars that can withstand climate change and satisfy consumer demands with unprecedented precision in trait modification. Genotype-environment interactions remain a critical challenge for modern breeding efforts, which can be addressed through high-throughput phenotyping and multi-environment trials. This work shows how combining genome-wide association studies and machine learning can improve the synthesis of multi-omics data and result in faster breeding cycles while preserving genetic diversity. This study outlines a roadmap that prioritizes the development of superior cultivars utilizing cutting-edge methods and technologies in order to address evolving agricultural and environmental challenges.

Advancements in Lactiplantibacillus plantarum: probiotic characteristics, gene editing technologies and applications

The exploration of microorganisms in fermented products has become a pivotal area of scientific research, primarily due to their widespread availability and profound potential to improve human health. Among these, Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) stands out as a versatile lactic acid bacterium, prevalent across diverse ecological niches. Its appeal extends beyond its well-documented probiotic benefits to include the remarkable plasticity of its genome, which has captivated both scientific and industrial stakeholders. Despite this interest, substantial challenges persist in fully understanding and harnessing the potential of L. plantarum. This review aims to illuminate the probiotic attributes of L. plantarum, consolidate current advancements in gene editing technologies, and explore the multifaceted applications of both wild-type and genetically engineered strains.

One-for-all gene inactivation via PAM-independent base editing in bacteria

Base editing is preferable for bacterial gene inactivation without generating double-strand breaks, requiring homology recombination, or highly efficient DNA delivery capability. However, the potential of base editing is limited by the adjoined dependence on the editing window and protospacer adjacent motif. Herein, we report an unconstrained base-editing system to enable the inactivation of any genes of interest in bacteria. We employed a dCas9 derivative, dSpRY, and activation-induced cytidine deaminase to build a protospacer adjacent motif-independent base editor. Then, we programmed the base editor to exclude the START codon of a gene of interest instead of introducing premature STOP codons to obtain a universal approach for gene inactivation, namely XSTART, with an overall efficiency approaching 100%. By using XSTART, we successfully manipulated the amino acid metabolisms in Escherichia coli, generating glutamine, arginine, and aspartate auxotrophic strains. While we observed a high frequency of off-target events as a trade-off for increased efficiency, refining the regulatory system of XSTART to limit expression levels reduced off-target events by over 60% without sacrificing efficiency, aligning our results with previously reported levels. Finally, the effectiveness of XSTART was also demonstrated in probiotic E. coli Nissle 1917 and photoautotrophic cyanobacterium Synechococcus elongatus, illustrating its potential in reprogramming diverse bacteria.

Prime Editing of Mouse Primary Neurons

Prime editing is a hybrid genome editing technology that introduces small edits on the genome with high precision. It combines nickase Cas9 with reverse transcriptase to prime and synthesizes edited DNA from RNA, reducing unintended insertions and deletions on the genome. This protocol describes the design of prime editing guide RNAs (pegRNAs), cloning of plasmids, nucleofection of mouse primary neurons, and preparation for next-generation sequencing. Directions are given for pegRNA and PE3b gRNA design and construction using PegAssist, a publicly available webtool and plasmid set. Prime editing in neurons allows genome manipulation while maintaining endogenous gene expression, making it ideal for studying protein structure/function relationships and pathogenic variants in a native neuronal context.