@article {pmid40456962,
year = {2026},
author = {Yu, J and Jin, J and Kwon, E and Jang, H and Choi, SK and Kim, D and Kim, C and Son, S and Yoon, KJ and Heo, WD},
title = {Programmable RNA acetylation with CRISPR-Cas13.},
journal = {Nature chemical biology},
volume = {22},
number = {6},
pages = {969-982},
pmid = {40456962},
issn = {1552-4469},
mesh = {Acetylation ; *CRISPR-Cas Systems/genetics ; *RNA/metabolism/chemistry/genetics ; Humans ; Cytidine/analogs & derivatives/metabolism/chemistry ; Acetyltransferases/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; HEK293 Cells ; N-Terminal Acetyltransferases ; },
abstract = {Recent studies claim that N[4]-acetylcytidine (ac[4]C) 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 ac[4]C to cell physiology. Here, we developed an efficient molecular tool that incorporates ac[4]C 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 ac[4]C functions across different cellular and disease contexts.},
}

Acetylation
*CRISPR-Cas Systems/genetics
*RNA/metabolism/chemistry/genetics
Humans
Cytidine/analogs & derivatives/metabolism/chemistry
Acetyltransferases/genetics/metabolism
RNA, Guide, CRISPR-Cas Systems/genetics/metabolism
HEK293 Cells
N-Terminal Acetyltransferases

@article {pmid41378919,
year = {2026},
author = {Hirata, S and Ozono, T and Kawai, K and Machida, C and Kobayashi, K and Ikeda, Y and Nishimura, T and Kaya, H},
title = {Development of a simple and locus-restricted DNA methylation editing system using direct fusion of a nickase-type SpCas9 and DNA methylation-related enzymes in Arabidopsis thaliana.},
journal = {Plant & cell physiology},
volume = {67},
number = {5},
pages = {739-751},
doi = {10.1093/pcp/pcaf162},
pmid = {41378919},
issn = {1471-9053},
support = {25NIBB333//NIBB Collaborative Research Program/ ; 24NIBB322//NIBB Collaborative Research Program/ ; 23NIBB307//NIBB Collaborative Research Program/ ; 22NIBB306//NIBB Collaborative Research Program/ ; 21-209//NIBB Collaborative Research Program/ ; 20-328//NIBB Collaborative Research Program/ ; 19-331//NIBB Collaborative Research Program/ ; //Okayama University Institute of Plant Science and Resource (IPSR)/ ; 25K01988//Japan Society for the Promotion of Science/ ; 21K06233//Japan Society for the Promotion of Science/ ; //The United Graduate School of Agricultural Sciences/ ; JPMJSP2162//Japan Science and Technology Agency/ ; },
mesh = {*Arabidopsis/genetics/metabolism ; *DNA Methylation/genetics ; Arabidopsis Proteins/genetics/metabolism ; *Gene Editing/methods ; Gene Expression Regulation, Plant ; *Deoxyribonuclease I/metabolism/genetics ; Promoter Regions, Genetic/genetics ; Epigenome Editing ; CRISPR-Cas Systems/genetics ; *CRISPR-Associated Protein 9/metabolism/genetics ; Transcription Factors/genetics/metabolism ; Plants, Genetically Modified ; Homeodomain Proteins ; },
abstract = {DNA methylation is an important epigenetic modification that regulates gene expression and supports genome stability. DNA methylation editing technology differs from conventional genome editing technology, which introduces mutations into genes, in that it enables changing gene expression without altering the base sequence. In this study, we attempted simple and locus-restricted DNA methylation editing in Arabidopsis thaliana using fusion proteins directly linking a nickase-type SpCas9 protein with DNA methylation-related enzymes. First, fusion of the human Ten-eleven translocation methyl cytosine dioxygenase 1 (TET1) catalytic domain (TET1cd) to nSpCas9 led to removing 5-methylcytosine in the FLOWERING LOCUS WA (FWA) promoter region of the wild-type plant, resulting in increased expression of the FWA gene and consequently, a late-flowering phenotype. Conversely, fusion of a mutant form of the bacterial DNA methyltransferase MQ1 (MQ1v) to nSpCas9 induced de novo DNA methylation in the fwa101-D mutant, in which the FWA promoter region is hypomethylated, and suppressed FWA gene expression, resulting in an early-flowering phenotype compared with the fwa101-D mutant. Of particular importance, our nSpCas9 system achieves targeted DNA methylation editing within a genomic window of ~10-20 kb. The nSpCas9 system features a compact and simplified vector structure due to the DNA methylation-related enzyme directly fusing to nSpCas9. Furthermore, sgRNA can be easily replaced, making it highly flexible. We propose a new method for targeted epigenome editing technology in plants, paving the way for innovative strategies in both basic research on epigenetics and crop development through epigenome editing.},
}

*Arabidopsis/genetics/metabolism
*DNA Methylation/genetics
Arabidopsis Proteins/genetics/metabolism
*Gene Editing/methods
Gene Expression Regulation, Plant
*Deoxyribonuclease I/metabolism/genetics
Promoter Regions, Genetic/genetics
Epigenome Editing
CRISPR-Cas Systems/genetics
*CRISPR-Associated Protein 9/metabolism/genetics
Transcription Factors/genetics/metabolism
Plants, Genetically Modified
Homeodomain Proteins

@article {pmid41645451,
year = {2026},
author = {Sun, Y and Yan, N and Feng, H and Lu, H and Zuo, Z and Zhou, C and Zuo, E},
title = {Therapeutic adenine base editor with minimized off-target effects.},
journal = {Protein & cell},
volume = {17},
number = {6},
pages = {543-559},
pmid = {41645451},
issn = {1674-8018},
support = {B2502040//Shenzhen Medical Research Fund/ ; 32371549//National Natural Science Foundation of China/ ; 32101223//National Natural Science Foundation of China/ ; W2533083//National Natural Science Foundation of China/ ; Y2024QC32//Agricultural Science and Technology Innovation Program/ ; CAAS-CSIAF-202401//Agricultural Science and Technology Innovation Program/ ; CAAS-BRC-AFIS-2025-03//Agricultural Science and Technology Innovation Program/ ; CAAS-SCAB-202301//Agricultural Science and Technology Innovation Program/ ; 2021M693452//China Postdoctoral Science Foundation/ ; 2022A1515012142//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Animals ; Humans ; *Adenine/metabolism ; Mice ; *Tyrosinemias/genetics/therapy ; *Aminohydrolases/genetics/metabolism ; Polymorphism, Single Nucleotide ; *Genetic Therapy/methods ; *CRISPR-Cas Systems ; },
abstract = {Genome-wide off-target effect poses a safety risk for clinical use of adenine base editor (ABE), among which ABE8e is one of the most efficient. Genome-wide off-target analysis by two-cell embryo injection (GOTI) analysis showed that the rate of genome-wide single-nucleotide variants (SNVs) in ABE8e-edited cells was ∼30-fold higher than that of spontaneous SNVs in control cells, indicating prevalent off-target effects of ABE8e, but no off-target effect for ABE7.10, from which ABE8e was derived. We performed saturation mutagenesis of eight amino acid sites of the deaminase (TadA8e) within ABE8e and obtained ABE8eY149V that exhibited high editing efficiency without detectable off-target effect. Furthermore, TadA8eY149V could be fused with other Cas homologs (PAM-relaxed SpRY, hypercompact SaKKH, or IscB) to expand its target range. Finally, ABE8eY149V editing of hydroxyphenylpyruvate dioxygenase (Hpd) gene prevented lethality in hereditary tyrosinemia type I mice. The high efficiency and fidelity of ABE8eY149V suggest its potential application in ABE-based gene therapies.},
}

Animals
Humans
*Adenine/metabolism
Mice
*Tyrosinemias/genetics/therapy
*Aminohydrolases/genetics/metabolism
Polymorphism, Single Nucleotide
*Genetic Therapy/methods
*CRISPR-Cas Systems

@article {pmid41914542,
year = {2026},
author = {He, S and Connerty, P and de Weck, A},
title = {CRISPR-Cas9 Genome-Wide Screening in Paediatric Cancer: Functional Genomics for Target Discovery and the Improvement of Existing Therapies.},
journal = {Medicinal research reviews},
volume = {46},
number = {4},
pages = {989-1004},
doi = {10.1002/med.70046},
pmid = {41914542},
issn = {1098-1128},
support = {RG23-08//Cancer Council NSW/ ; RG212077//Cancer Institute NSW/ ; 2021/CBG003//Cancer Institute NSW Research Capacity Building/ ; //Sydney Partnership for Health, Education, Research and Enterprise/ ; },
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Neoplasms/genetics/therapy ; *Genomics/methods ; Drug Discovery ; Child ; Animals ; *Genome-Wide Association Study ; },
abstract = {CRISPR-Cas9 genome-wide screening has been instrumental towards identifying novel targets for drug discovery in cancer research. However, much of this research has centred specifically on adult cancers, with paediatric cancers being underserviced by current research and screening. With contemporary evidence increasingly highlighting the differences in biology between adult and children's cancers, more research has gradually occurred investigating dependencies and mechanisms of resistance in paediatric cancers through the use of CRISPR-Cas9 genome-wide screens. This review collates and summarises the experimental genome-wide screens that have been performed specifically in paediatric cancer models, and highlights the versatility of this technology and the knowledge gained through this research.},
}

Humans
*CRISPR-Cas Systems/genetics
*Neoplasms/genetics/therapy
*Genomics/methods
Drug Discovery
Child
Animals
*Genome-Wide Association Study

@article {pmid41985988,
year = {2026},
author = {Yeo, JH and Kim, HH and Oh, SH and Lee, J},
title = {Highly efficient and scarless genome editing via essential-gene-coupled homology-directed repair.},
journal = {Genome research},
volume = {36},
number = {6},
pages = {1187-1198},
doi = {10.1101/gr.281194.125},
pmid = {41985988},
issn = {1549-5469},
mesh = {*Gene Editing/methods ; Humans ; CRISPR-Cas Systems ; *Recombinational DNA Repair ; DNA Breaks, Double-Stranded ; HEK293 Cells ; },
abstract = {Homology-directed repair (HDR) enables precise genome editing; however, its application in mammalian cells is limited by low efficiency owing to competition from error-prone repair pathways and intrinsically restricted HDR activity. Existing HDR-enhancement strategies, including small-molecule treatments and marker-based selection, are constrained by cytotoxicity, genomic scarring, and inconsistent performance. Here, we present essential-gene-supported scarless HDR (ESS-HDR), a robust, drug- and marker-free platform that selectively enriches HDR-proficient cells. By leveraging essential-gene coediting, ESS-HDR enables precise and scarless genome modification with enhanced efficiency. CRISPR-Cas9 induces double-strand breaks at both the target locus and an essential gene, accompanied by two donor templates: one introducing the desired edit and the other restoring essential-gene function. Only cells that undergo accurate HDR at the essential locus survive, providing endogenous selection without exogenous markers. Single-cell clone analysis confirms that enrichment of HDR-proficient cells enhances editing at the target locus. Using ssODN donors carrying a 1 nucleotide substitution or a 10 nucleotide insertion, ESS-HDR increases HDR efficiencies by sevenfold to 16-fold in HEK293 cells and 41-fold in primary epidermal keratinocytes compared with conventional single-site HDR. With plasmid donors targeting TUBA1B, LMNB1, or ACTB, ESS-HDR improves knock-in efficiencies by sixfold to 34-fold across HEK293, U2OS, and HeLa cells. ESS-HDR also outperforms chemical enhancers including RS-1, SCR7, nocodazole, and AZD7648. Together, these findings establish ESS-HDR as a broadly applicable strategy for efficient, scarless genome editing without external selection markers.},
}

*Gene Editing/methods
Humans
CRISPR-Cas Systems
*Recombinational DNA Repair
DNA Breaks, Double-Stranded
HEK293 Cells

@article {pmid42134990,
year = {2026},
author = {An, K and Prillo, S and Wu, W and Kristanto, I and Jones, MG and Song, YS and Yosef, N},
title = {Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.},
journal = {Genome research},
volume = {36},
number = {6},
pages = {1199-1208},
doi = {10.1101/gr.280564.125},
pmid = {42134990},
issn = {1549-5469},
mesh = {*CRISPR-Cas Systems ; Animals ; *Algorithms ; Mice ; *Cell Lineage/genetics ; *Phylogeny ; Lung Neoplasms/genetics ; },
abstract = {CRISPR-Cas9-based lineage tracing technologies have enabled the reconstruction of single-cell phylogenies from transcriptional readouts. However, developing tree-reconstruction algorithms with theoretical guarantees in this setting is challenging. In this work, we derive a reconstruction algorithm with theoretical guarantees using Neighbor-Joining (NJ) on distances that are moment-matched to estimate the true tree distances. We develop a series of tools to analyze this algorithm and prove its theoretical guarantees. When the parameters of the data generating process are known and there is no missing data, our results align with established results from common evolutionary models, such as Cavender-Farris-Neyman and Jukes-Cantor. However, to account for the realistic case where the parameters of the data generating process are not known and there is missing data, we develop new theory that shows for the first time that it is still possible to obtain reconstruction guarantees in the CRISPR-Cas9 case and in other models of evolution. Empirically, we show on both simulated lineage tracing data and on real data from a mouse model of lung cancer the improved performance of our method as compared to the traditional use of NJ.},
}

*CRISPR-Cas Systems
Animals
*Algorithms
Mice
*Cell Lineage/genetics
*Phylogeny
Lung Neoplasms/genetics

@article {pmid42138212,
year = {2026},
author = {Xu, B and Tian, S and Yang, N and Cai, J and Yi, Q and Wang, Y and Ou, X and Jin, Y and Bai, S and Xue, J and Wang, J},
title = {Re-Engineering CRISPR-Cas12a into a Multimodal Biosensing Platform with Programmable Precursor crRNA.},
journal = {Analytical chemistry},
volume = {98},
number = {21},
pages = {15709-15719},
doi = {10.1021/acs.analchem.6c01251},
pmid = {42138212},
issn = {1520-6882},
mesh = {*Biosensing Techniques/methods ; *CRISPR-Cas Systems/genetics ; Humans ; *CRISPR-Associated Proteins/genetics/metabolism ; *RNA/analysis/genetics ; *Bacterial Proteins/genetics/metabolism ; *Endodeoxyribonucleases/genetics/metabolism ; },
abstract = {The CRISPR-Cas12a system has emerged as a powerful tool for molecular diagnostics due to its trans-cleavage activity. However, its utility in point-of-care testing is constrained by several inherent limitations: strict dependence on DNA for activation, compromised specificity against single-stranded DNA targets, and a basal catalytic rate often insufficient for direct detection. Here, we engineered a class of programmable precursor CRISPR RNAs (pcRNAs), which re-engineer Cas12a into a multimodal biosensing platform. Our platform enables Cas12a to respond to diverse programmable inputs, including direct RNA detection without reverse transcription, and features a built-in autocatalytic circuit for signal amplification. It demonstrates programmable high specificity, discriminating single-nucleotide variants in DNA with selectivity up to 908.7, and achieves high sensitivity by directly detecting synthetic circHER2 RNA, with a detection limit of 0.5 aM. The robust performance of the platform is validated through the quantitative assessment of circHER2 levels in breast cancer cell lines within complex cellular lysates. By employing a modular nucleic acid design strategy, this work breaks the intrinsic functional constraints of Cas12a and establishes a generalizable framework for the development of next-generation intelligent and programmable molecular diagnostic and sensing systems.},
}

*Biosensing Techniques/methods
*CRISPR-Cas Systems/genetics
Humans
*CRISPR-Associated Proteins/genetics/metabolism
*RNA/analysis/genetics
*Bacterial Proteins/genetics/metabolism
*Endodeoxyribonucleases/genetics/metabolism

@article {pmid42190604,
year = {2026},
author = {Kim, JH and Cho, HJ and Lee, HM},
title = {Leveraging CRISPR/Cas9 for optimized adoptive T cell therapies: From molecular engineering to clinical manufacturing.},
journal = {Biochemical and biophysical research communications},
volume = {826},
number = {},
pages = {154003},
doi = {10.1016/j.bbrc.2026.154003},
pmid = {42190604},
issn = {1090-2104},
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Immunotherapy, Adoptive/methods ; *Gene Editing/methods ; *T-Lymphocytes/immunology/transplantation ; Animals ; *Neoplasms/therapy/immunology/genetics ; Receptors, Chimeric Antigen/genetics/immunology ; Genetic Engineering/methods ; },
abstract = {Cancer immunotherapy is rapidly evolving from pharmacologic immune modulation to adoptive cell therapy (ACT). In ACT, T cells are expanded and genetically engineered ex vivo to achieve long-lasting antitumor activity. The primary ACT platforms-tumor-infiltrating lymphocytes (TIL), chimeric antigen receptor (CAR) T cells, and T-cell receptor (TCR) T cells-rely on T-cell effector function but differ in their mechanisms of antigen recognition, HLA dependence, and engineering requirements, leading to unique clinical strengths and limitations. CRISPR/Cas9 genome editing provides precise knock-out (KO) and knock-in (KI) strategies, allowing for multiplex editing and functional modulation across the genome. In the context of ACT manufacturing, CRISPR/Cas9 addresses critical challenges such as T-cell exhaustion, graft-versus-host disease (GvHD), and ensuring product consistency and quality. This article explores how CRISPR/Cas9 can be utilized to overcome the limitations of ACT and summarizes the current clinical landscape of CRISPR-engineered ACT products. Finally, we discuss the ongoing challenges associated with CRISPR-based genome editing and propose potential solutions.},
}

Humans
*CRISPR-Cas Systems/genetics
*Immunotherapy, Adoptive/methods
*Gene Editing/methods
*T-Lymphocytes/immunology/transplantation
Animals
*Neoplasms/therapy/immunology/genetics
Receptors, Chimeric Antigen/genetics/immunology
Genetic Engineering/methods

@article {pmid42226661,
year = {2026},
author = {Guo, A and Bell, AG and Myhrvold, C},
title = {Towards deployable CRISPR-based nucleic acid detection.},
journal = {Progress in biomedical engineering (Bristol, England)},
volume = {8},
number = {2},
pages = {},
pmid = {42226661},
issn = {2516-1091},
mesh = {Humans ; Nucleic Acid Amplification Techniques/methods ; SARS-CoV-2/genetics/isolation & purification ; *COVID-19/diagnosis/virology ; *CRISPR-Cas Systems ; Molecular Diagnostic Techniques/methods ; Point-of-Care Systems ; *COVID-19 Nucleic Acid Testing/methods ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Rapid Diagnostic Tests ; },
abstract = {Deployable diagnostics are necessary for the control and treatment of infectious diseases, with significant unmet needs revealed during the COVID-19 pandemic. Nucleic acid diagnostics remain among the most sensitive and specific forms of detection, yet their reliance on laboratory equipment and trained personnel limits their deployment in resource limited settings. CRISPR-based diagnostics are uniquely positioned to enable rapid, affordable, and highly accurate nucleic acid testing at both the point-of-care and the point-of-need. In this review, we discuss advances toward deployable CRISPR-based diagnostics. We begin by examining innovations in sample processing methods, emphasizing strategies that reduce equipment requirements and enhance compatibility across diverse sample types and pathogens. We then explore developments in one-pot isothermal and amplification-free approaches, comparing the benefits and tradeoffs associated with each, as well as multiplexing strategies for simultaneous detection of multiple pathogens. Finally, we consider additional factors that impact assay deployability, including reagent lyophilization to minimize cold chain dependence and readout technologies that enable detection in resource-limited settings. We conclude by outlining remaining challenges and opportunities for future progress.},
}

Humans
Nucleic Acid Amplification Techniques/methods
SARS-CoV-2/genetics/isolation & purification
*COVID-19/diagnosis/virology
*CRISPR-Cas Systems
Molecular Diagnostic Techniques/methods
Point-of-Care Systems
*COVID-19 Nucleic Acid Testing/methods
*Clustered Regularly Interspaced Short Palindromic Repeats
Rapid Diagnostic Tests

@article {pmid42226679,
year = {2026},
author = {Han, L and Wu, N and Li, Q and Li, Y and Zhang, Y and Chen, X and Zhou, H and Chen, F and Sun, T},
title = {Xylt2 Knockout Eliminates O-Xylosylation and Enhances Bone Morphogenetic Protein 2 Production in Chinese Hamster Ovary Cells.},
journal = {Biotechnology journal},
volume = {21},
number = {6},
pages = {e70256},
doi = {10.1002/biot.70256},
pmid = {42226679},
issn = {1860-7314},
mesh = {Animals ; CHO Cells ; Cricetulus ; *Pentosyltransferases/genetics/metabolism ; UDP Xylose-Protein Xylosyltransferase ; *Bone Morphogenetic Protein 2/genetics/metabolism/biosynthesis ; Gene Knockout Techniques ; Humans ; CRISPR-Cas Systems ; Recombinant Proteins/genetics/metabolism ; Cricetinae ; Protein Processing, Post-Translational ; Heparan Sulfate Proteoglycans/metabolism ; },
abstract = {O-xylosylation of glycine-serine (GS) linkers in multispecific antibodies or fusion proteins introduces product heterogeneity, posing critical challenges for biomanufacturing quality control and elevating potential immunogenicity risks. This post-translational modification is primarily catalyzed by xylosyltransferase 2 (Xylt2) in chinese hamster ovary (CHO) cells. To address this, we generated Xylt2-deficient CHO cells via both clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) and zinc finger nuclease (ZFN)-mediated gene knockout, which resulted in the complete elimination of O-xylosylation as verified by mass spectrometry in a GS linker-containing bispecific antibody. Furthermore, because heparan sulfate proteoglycans (HSPGs), key cell-surface receptors for ligand binding and internalization, rely on O-xylosylation for their proper biosynthesis and function, the Xylt2 knockout also enhanced the titer of human bone morphogenetic protein 2 (hBMP2), which undergoes HSPG-dependent cellular uptake, with up to a 2.5-fold increase from 9.62 to 34.09 µg/mL in engineered cells compared to wild-type CHO controls. Collectively, our results demonstrate that Xylt2-deficient cell lines provide a genetic approach to produce recombinant proteins without O-xylosylation, as well as for enhancing the titer of hBMP2.},
}

Animals
CHO Cells
Cricetulus
*Pentosyltransferases/genetics/metabolism
UDP Xylose-Protein Xylosyltransferase
*Bone Morphogenetic Protein 2/genetics/metabolism/biosynthesis
Gene Knockout Techniques
Humans
CRISPR-Cas Systems
Recombinant Proteins/genetics/metabolism
Cricetinae
Protein Processing, Post-Translational
Heparan Sulfate Proteoglycans/metabolism

@article {pmid42234680,
year = {2026},
author = {Hemberg, M and Hansen, AL and Storgaard, J and Blay-Cadanet, J and Pedersen, A and Thielke, AL and Holm, CK},
title = {MAVS is important for antiviral defense against influenza A virus in a human respiratory epithelium model.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350839},
doi = {10.1371/journal.pone.0350839},
pmid = {42234680},
issn = {1932-6203},
mesh = {Humans ; *Adaptor Proteins, Signal Transducing/genetics/metabolism ; *Influenza A virus/physiology/immunology ; *Respiratory Mucosa/virology/immunology/metabolism ; *Influenza, Human/immunology/virology ; Virus Replication ; Interferon Type I ; CRISPR-Cas Systems ; Interferons/metabolism ; Cells, Cultured ; Animals ; },
abstract = {The respiratory epithelium is an important immunological barrier and the first line of defense against influenza A virus (IAV). In mice and in various cellular systems, induction of type I interferons (IFNα/β) during IAV infections is known to depend on cytosolic RNA sensors retinoic acid-induced gene I (RIG-I) and melanoma differentiation-association gene 5 (MDA5) and their common adaptor protein mitochondrial antiviral-signaling adaptor protein (MAVS). Until now, it has not been possible to directly assess the importance of MAVS for induction of IFNs and for resistance to IAV infection in primary human respiratory epithelium. Here, we used CRISPR-Cas9 to establish MAVS-deficient cultures of primary human respiratory epithelium using the air-liquid interphase culture system. Using this setup, we show that MAVS is indeed required for the induction of type I and type III IFNs and subsequently for the induction of IFN-stimulated genes in response to IAV infection in this respiratory epithelium model. Finally, we demonstrate that MAVS is important for restricting viral replication in this model. In conclusion, this study demonstrates that MAVS plays a non-redundant protective role during IAV infection in primary human respiratory epithelium.},
}

Humans
*Adaptor Proteins, Signal Transducing/genetics/metabolism
*Influenza A virus/physiology/immunology
*Respiratory Mucosa/virology/immunology/metabolism
*Influenza, Human/immunology/virology
Virus Replication
Interferon Type I
CRISPR-Cas Systems
Interferons/metabolism
Cells, Cultured
Animals

@article {pmid41674084,
year = {2026},
author = {Ghosh, PK and Biswas, S and Malaker, R and Pham, H and Septiningsih, EM and Ravelombola, W},
title = {Optimization of CRISPR/Cas9-mediated CtPDS knockout in guar protoplasts.},
journal = {The plant genome},
volume = {19},
number = {1},
pages = {e70177},
doi = {10.1002/tpg2.70177},
pmid = {41674084},
issn = {1940-3372},
support = {//Texas A&M Institute for Advancing Health through Agriculture/ ; //Texas A&M Advancing Discovery to Market/ ; GSC2024075//Texas Department of Agriculture/ ; 58-6046-2-008//USDA-ARS Germplasm Evaluation/ ; 58-6046-3-005//USDA-ARS Germplasm Evaluation/ ; },
mesh = {*CRISPR-Cas Systems ; *Protoplasts/metabolism ; *Gene Editing/methods ; *Cyamopsis/genetics ; *Plant Proteins/genetics ; Gene Knockout Techniques/methods ; },
abstract = {Guar (Cyamopsis tetragonoloba L. Taub.) is a climate-resilient legume with industrial and agricultural applications. Recently, gene editing has emerged as a key genetic tool for crop improvement. Despite its recent increasing value as a commodity for various uses, there is no documented report of gene editing work in guar to date. In this study, we present the first optimized protocol for protoplast-based clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) genome editing in guar. The most intact and viable protoplasts were observed in the cotyledons of 6-day-old seedlings that were isolated using the tape-sandwich method. Enzymatic digestion with 1.5% cellulase RS and 0.3% pectinase in 600 mM mannitol, followed by 10 min of vacuum infiltration, increased protoplast release and viability. Polyethylene glycol (PEG)-mediated transformation had been tailored using 40% PEG for 5 min with green fluorescent protein plasmid, and the cestrum yellow leaf curling virus promoter at room temperature showed the highest transient expression efficiency (∼57%). A multiplexed CRISPR/Cas9 construct was designed to target the Cyamopsis tetragonoloba phytoene desaturase (CtPDS) gene in guar. Polymerase chain reaction amplification and Sanger sequencing of transfected protoplasts confirmed highly efficient editing, with fragment deletions ranging from 714 to 1061 bp in CtPDS. Overall, we achieved 100% editing efficiency, as all successfully transformed samples showed CRISPR/Cas9-induced mutations. These findings establish a reliable, transient protoplast system for functional genomics and targeted trait improvement in guar, providing a key foundation for future crop improvement.},
}

*CRISPR-Cas Systems
*Protoplasts/metabolism
*Gene Editing/methods
*Cyamopsis/genetics
*Plant Proteins/genetics
Gene Knockout Techniques/methods

@article {pmid41674090,
year = {2026},
author = {Han, K and Xie, B and Luo, C and Luo, Y and Yang, M and Lei, L and Jia, MA and Xu, T},
title = {Identification of a novel BBWV2 isolate and a sensitive and rapid RT-RPA-CRISPR/Cas12a-LFD detection method development.},
journal = {Pest management science},
volume = {82},
number = {6},
pages = {5255-5265},
doi = {10.1002/ps.70635},
pmid = {41674090},
issn = {1526-4998},
support = {//Guizhou Provincial Innovation Talents Team/ ; //the Guizhou Province Key Core Technology Research Project for Mountain Agriculture/ ; //the Plateau Characteristic Vegetable Industry Technology System Program of Guizhou Province/ ; //Special Program of China National Tobacco Corporation/ ; //National Natural Science Foundation of China/ ; //Guizhou Provincial Science and Technology Foundation/ ; //Provincial College Students' innovation and entrepreneurship training program/ ; },
mesh = {*Plant Diseases/virology ; *CRISPR-Cas Systems ; *Capsicum/virology ; *Nucleic Acid Amplification Techniques/methods ; China ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Broad bean wilt virus 2 (BBWV2) is a major viral pathogen causing significant economic losses in vegetable production. Existing detection methods often lack the speed, sensitivity, or simplicity required for effective on-site field diagnosis. This study aimed to identify a novel BBWV2 isolate and develop a rapid, equipment-free visual detection method suitable for field applications.

RESULTS: A novel BBWV2 isolate (BBWV2-GZCa) was identified and characterized from pepper in Guizhou Province, China. We developed a one-step visual detection assay by integrating reverse transcription-recombinase polymerase amplification (RT-RPA) with a CRISPR/Cas12a system, enabling readout via fluorescence or lateral flow dipstick (LFD). The assay demonstrated a detection limit of 7.5 copies/μL, which is 10[5] times more sensitive than conventional RT-PCR. It showed no cross-reactivity with other common pepper viruses and achieved 100% accuracy when validated using 20 field-collected samples.

CONCLUSION: The entire detection process can be completed within one hour without specialized equipment, requiring only visual interpretation. This RT-RPA-CRISPR/Cas12a-LFD method provides a rapid, highly sensitive, specific, and user-friendly platform for on-site detection of BBWV2, offering a practical tool for early diagnosis and disease management in agricultural settings. © 2026 Society of Chemical Industry.},
}

*Plant Diseases/virology
*CRISPR-Cas Systems
*Capsicum/virology
*Nucleic Acid Amplification Techniques/methods
China
Sensitivity and Specificity

@article {pmid41674223,
year = {2026},
author = {Goudar, P and Hall, A},
title = {The influence of GMO media strategies on public perceptions of CRISPR crop technologies in Southern Ontario.},
journal = {GM crops & food},
volume = {17},
number = {1},
pages = {2620131},
pmid = {41674223},
issn = {2164-5701},
mesh = {Ontario ; *Public Opinion ; *Plants, Genetically Modified/genetics ; Humans ; Gene Editing ; *Crops, Agricultural/genetics ; *CRISPR-Cas Systems ; Adult ; Surveys and Questionnaires ; Male ; Female ; Middle Aged ; },
abstract = {Genetically modified organisms (GMOs) have often divided public opinion, one factor influencing perceptions of GMO technologies has been misunderstood or poorly communicated scientific messaging. However, advancements in gene editing tools like CRISPR/Cas9 offer new crop modification possibilities, prompting different regulatory frameworks than traditional GMO technologies. This research examines public understanding of GMOs, awareness of CRISPR crops, and how prior experiences with GMOs shape perceptions of new genetic technologies. A mixed-methods approach was employed, combining a public survey of adults in the Greater Toronto-Hamilton area and interviews with science journalists. Results show hesitance toward GMOs and CRISPR crops, with acceptance most impacted by consumer behavior and cost. Key interview themes include journalist's concerns about levels of public education, the role of social media, and the cost of goods. Our findings suggest increased transparency and effective communication could improve public acceptance of GMOs and CRISPR crops. While CRISPR crops do not come under the GMO regulatory framework in Canada, our findings show that the public does not recognize this distinction. Without increased transparency and more effective communication CRISPR crops may become widely associated with the negative media frames that have shaped perceptions of GMOs.},
}

Ontario
*Public Opinion
*Plants, Genetically Modified/genetics
Humans
Gene Editing
*Crops, Agricultural/genetics
*CRISPR-Cas Systems
Adult
Surveys and Questionnaires
Male
Female
Middle Aged

@article {pmid41674382,
year = {2026},
author = {Zhang, Y and Xu, Y and Ding, Z and Cheng, Y and Gao, Y and Ye, J and Zhang, H and Li, P and Wu, H},
title = {Machine learning-optimized long single-stranded DNA synthesis technology empowers high-precision diagnostic-therapeutic integration in living cells.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
pmid = {41674382},
issn = {1362-4962},
support = {2021YFC2100600//National Key Research and Development Program of China/ ; 31872608//National Natural Science Foundation of China/ ; 31872608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Single-Stranded/chemistry/genetics/chemical synthesis/biosynthesis ; Humans ; *Machine Learning ; Gene Editing/methods ; Nanotechnology/methods ; DNA-Directed DNA Polymerase/metabolism ; CRISPR-Cas Systems ; },
abstract = {While DNA nanotechnology holds transformative potential across biomedical and information storage applications, current technologies face critical limitations in synthesizing long single-stranded DNA (ssDNA) with high purity and homogeneity. To address these challenges, we developed Ouroborosyn-ssDNA, a nicking enzymatic assisted replication (NEAR) platform that synergizes enzymatic engineering with computational optimization. By integrating phi29 DNA polymerase and Nb.BbvCI nickase in formate-based buffers, we achieved extended ssDNA synthesis up to 15 000 nt while preserving sequence fidelity, resulting in a 4.73-fold yield enhancement compared to commercial buffers. Notably, machine learning-guided parameter optimization identified magnesium ion dynamics and thermal modulation as pivotal determinants of enzymatic efficiency. Furthermore, solid-phase synthesis using thiol-gold immobilized templates demonstrated 86.38% purification recovery via automated magnetic bead systems, enabling scalable production. To validate functional utility, we engineered six-helix bundle DNA origami-CRISPR complexes that achieved nucleolin-targeted genome editing in cervical cancer cells, coupling GFP-based diagnostics with therapeutic E7 oncogene disruption. These advancements directly overcome key limitations in enzymatic stochasticity and product heterogeneity through buffer engineering and computational optimization, establishing a scalable pathway for applications in precision nanomedicine, synthetic biology, and molecular data storage. This integrated strategy advances DNA nanotechnology from proof-of-concept studies toward standardized biomanufacturing of sequence-defined macromolecular architectures.},
}

*DNA, Single-Stranded/chemistry/genetics/chemical synthesis/biosynthesis
Humans
*Machine Learning
Gene Editing/methods
Nanotechnology/methods
DNA-Directed DNA Polymerase/metabolism
CRISPR-Cas Systems

@article {pmid41674468,
year = {2026},
author = {Takeda, T and Aso, M and Ueda, H and Yuzawa, S},
title = {Direct Pathway Synthesis and Editing (DiPaSE): A One-Pot DNA Assembly Method for Accurate and Efficient Refactoring of High-GC Biosynthetic Gene Clusters.},
journal = {ACS synthetic biology},
volume = {15},
number = {3},
pages = {1221-1230},
doi = {10.1021/acssynbio.5c00934},
pmid = {41674468},
issn = {2161-5063},
mesh = {*Multigene Family/genetics ; *Gene Editing/methods ; Streptomyces/genetics/metabolism ; *Biosynthetic Pathways/genetics ; CRISPR-Cas Systems/genetics ; Base Composition/genetics ; Genome, Bacterial ; Escherichia coli/genetics ; Biological Products/metabolism ; },
abstract = {Natural products (NPs) produced by actinobacteria, particularly Streptomyces species, represent a rich source of bioactive compounds and have yielded many clinically important compounds. Actinobacterial genomes are characterized by high GC content and typically harbor 20-40 biosynthetic gene clusters (BGCs) per genome, which encode diverse NPs such as polyketides, peptides, and glycosides. CRISPR/Cas-based genome editing has emerged as a promising tool to activate silent BGCs and engineer NP biosynthesis. However, the efficiency of multiplex editing drastically decreases as the number of targeted sites increases. Here, we report a novel one-pot DNA assembly method, termed direct pathway synthesis and editing (DiPaSE), for the efficient synthesis and multiplex editing of long, high-GC BGCs. DiPaSE accurately assembles multiple high-GC DNA fragments up to 60 kb and enables simultaneous deletions and insertions within a target BGC without compromising the assembly efficiency. Using this approach, we identified functions of previously uncharacterized genes in the aureothin BGC and significantly enhanced the titer of the corresponding NP. The workflow employs conventional polymerase chain reaction, type IIP restriction enzymes, commercially available DNA assembly reagents, and Escherichia coli, providing a simple, cost-effective, and broadly applicable platform for genome mining, BGC refactoring, and rational design of artificial biosynthetic pathways.},
}

*Multigene Family/genetics
*Gene Editing/methods
Streptomyces/genetics/metabolism
*Biosynthetic Pathways/genetics
CRISPR-Cas Systems/genetics
Base Composition/genetics
Genome, Bacterial
Escherichia coli/genetics
Biological Products/metabolism

@article {pmid41674724,
year = {2026},
author = {Baum, R and Telugu, N and Bruyneel, AAN and Kay, M and Nair, P and Perea-Gil, I and Termglinchan, V and Bharucha, N and Lee, E and Mercola, M and Diecke, S and Karakikes, I},
title = {CRISPR-MiX: A pooled single-stranded donor strategy to enhance HDR efficiency in human iPSCs.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {1},
pages = {102820},
pmid = {41674724},
issn = {2162-2531},
abstract = {CRISPR-Cas9 is widely used to model genetic disorders by introducing or correcting disease-associated mutations in induced pluripotent stem cells (iPSCs) through homology-directed repair (HDR). However, HDR efficiency in iPSCs remains low and is highly dependent on the target locus. Here, we developed CRISPR-MiX, an improved protocol to enhance HDR efficiency in human iPSCs. Using a GFP-to-BFP reporter system, we identified key single-stranded oligodeoxynucleotide (ssODN) donor design parameters, including homology arm symmetry, CRISPR/Cas-blocking mutations, and strand complementarity, which significantly influence HDR outcomes. We applied this approach to introduce pathogenic variants into five genes related to genetic cardiomyopathies. Quantitative analysis of HDR events showed that both the target locus and ssODN design strongly affect HDR efficiency. To address the locus- and design-specific limitations, we established CRISPR-MiX, a pooled ssODN-based method for scarless genome editing using ribonucleoproteins (RNPs) that does not require selection. CRISPR-MiX consistently improved HDR efficiency across multiple loci. This strategy offers a simple, robust, and versatile approach for precise genome engineering in iPSCs, supporting broad applications in disease modeling and functional genomics.},
}

@article {pmid41674784,
year = {2025},
author = {Yashooa, RK and Nabi, AQ and Smail, SW and Azeez, SS and Nooh, WA and Mustafa, SA and Al-Farha, AA and Capitanio, N and Shekha, MS},
title = {CRISPR-Cas technologies in neurodegenerative disorders: mechanistic insights, therapeutic potential, and translational challenges.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1737468},
pmid = {41674784},
issn = {1664-2295},
abstract = {CRISPR-Cas genome-editing technologies have emerged as powerful tools for precise DNA and RNA modulation, offering promising therapeutic strategies for neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). This review critically evaluates current CRISPR/Cas applications in neurodegeneration, with emphasis on mechanistic insights, therapeutic outcomes, and translational feasibility. Preclinical and early translational studies demonstrate that CRISPR-Cas platforms can correct pathogenic mutations, suppress toxic gene expression, and restore neuronal function. Advanced modalities, including base and prime editing, CRISPRi/a, and RNA-targeting Cas systems, improve precision and reduce genomic damage, which is particularly advantageous in post-mitotic neurons. Emerging CRISPR-based diagnostics (e.g., SHERLOCK and DETECTR), AI-assisted sgRNA design, and machine-learning approaches for predicting off-target effects further enhance the safety, stratification, and monitoring of CRISPR therapeutics. In parallel, patient-derived brain organoids and assembloids provide scalable human-relevant platforms for mechanistic studies and preclinical validation. Despite this progress, major challenges remain, including efficient delivery across the blood-brain barrier, immune responses, long-term safety, and ethical and regulatory considerations. Overall, CRISPR-Cas technologies hold strong potential as disease-modifying interventions for neurodegenerative disorders, provided that advances in delivery systems, artificial intelligence integration, and regulatory oversight continue to evolve toward clinical translation.},
}

@article {pmid41676858,
year = {2026},
author = {Niu, Y and Wu, S and Su, J},
title = {Harnessing CRISPR/Cas systems for food safety detection: biosensor design and emerging applications for food safety detection.},
journal = {Analytical methods : advancing methods and applications},
volume = {18},
number = {8},
pages = {1559-1582},
doi = {10.1039/d5ay01791b},
pmid = {41676858},
issn = {1759-9679},
mesh = {*CRISPR-Cas Systems ; *Biosensing Techniques/methods ; *Food Safety/methods ; Humans ; Foodborne Diseases ; Food Microbiology/methods ; Food Contamination/analysis ; },
abstract = {Food safety has become a critical global concern, with foodborne diseases affecting approximately 600 million people annually and causing 420 000 deaths each year, posing significant risks to human health and well-being. Rapid, efficient, and reliable detection methods are essential to mitigate these risks. Traditional detection methods, such as PCR and culture-based assays, while widely used, often face challenges related to speed, accuracy, and portability. Over the past 5 years (2020-2025), the (CRISPR)/Cas system has emerged as a powerful tool for food safety detection due to its high sensitivity, specificity, and versatility. This review highlights recent advances in CRISPR/Cas-based biosensors and their applications in food safety. First, we discuss the key challenges in food safety detection and the design principles of CRISPR/Cas biosensors. Next, we comprehensively summarize their applications in detecting foodborne pathogens (viruses and bacteria), food fraud, genetically modified organisms (GMOs), toxins, heavy metals, antibiotic residues, and pesticides. Finally, we address the current limitations and future prospects of CRISPR/Cas biosensors, providing insights into their potential for next-generation food safety solutions.},
}

*CRISPR-Cas Systems
*Biosensing Techniques/methods
*Food Safety/methods
Humans
Foodborne Diseases
Food Microbiology/methods
Food Contamination/analysis

@article {pmid41677799,
year = {2026},
author = {Boubakri, H},
title = {CRISPR-Cas9-mediated genome editing in fungi: applications, challenges, and future directions.},
journal = {Journal of applied microbiology},
volume = {137},
number = {3},
pages = {},
doi = {10.1093/jambio/lxag046},
pmid = {41677799},
issn = {1365-2672},
mesh = {*Gene Editing/methods/trends ; *CRISPR-Cas Systems ; *Fungi/genetics ; *Genome, Fungal ; },
abstract = {The clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been shown to be an effective genome-editing tool in many organisms, including fungi. It enables precise modifications to the DNA of fungal species, facilitating advancements in research, agriculture, and biotechnology. CRISPR-Cas9-edited non-pathogenic antagonists have emerged as a promising alternative for biocontrol. Several filamentous fungi have been engineered to produce secondary metabolites. Furthermore, the CRISPR-Cas9 system has been used to improve the quality of several edible fungi. However, the application of CRISPR-Cas9 technology for fungal genome editing is still facing some challenges that researchers must address. This review highlights the major approaches and applications of genome editing in fungi, as well as the associated challenges.},
}

*Gene Editing/methods/trends
*CRISPR-Cas Systems
*Fungi/genetics
*Genome, Fungal

@article {pmid41678334,
year = {2026},
author = {Wang, Y and Su, X and Chen, Y and Chen, Y and Shi, C and Liu, F and Ye, Y and Sun, P and Tan, M and Yu, M and Wang, Y and Xie, S and Liu, J and Yan, Q and Sun, Q and Neculai, D and Liu, W and Shao, J and Liu, Y and Lin, W and Lin, A},
title = {A CRISPR-based mitochondrial gene therapy tool derived by engineering guide RNAs.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116958},
doi = {10.1016/j.celrep.2026.116958},
pmid = {41678334},
issn = {2211-1247},
mesh = {Humans ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Mitochondria/genetics/metabolism ; *Genetic Therapy/methods ; DNA, Mitochondrial/genetics ; *CRISPR-Cas Systems/genetics ; Animals ; *Mitochondrial Diseases/genetics/therapy ; RNA, Long Noncoding/genetics/metabolism ; Gene Editing/methods ; Mice ; RNA-Binding Proteins/metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; },
abstract = {Mitochondrial genetic diseases arise from mitochondrial DNA (mtDNA) defects, which gene therapy tools may rectify. However, delivering single-guide RNAs (sgRNAs) into mitochondria remains a challenge limiting CRISPR-mediated mtDNA therapy. Here, through network analysis of mitochondrion-localized long noncoding RNAs (lncRNAs) and RNA-binding proteins (RBPs), we found that lncRNA RP11-46H11.3 translocates into mitochondria via binding mitochondria-associated RBPs using its key RNA recognition motifs (RRMs); its derived 30 nt ST2-RNA mitochondrial targeting sequence (RMTS) showed the highest mitochondrial localization efficiency. We engineered the RMTS-CRISPR tool by fusing ST2-RMTS to sgRNA, verifying its ability to target and cleave mtDNA. Strikingly, our results demonstrated that RMTS-CRISPR could achieve heteroplasmic mtDNA shifting efficiencies of up to 26.37% in m.3243A>G mutant cell models and 26.79% in vivo, offering a technological approach for the correction of heterogeneous mtDNA mutations. Taken together, our findings reveal a CRISPR-based mitochondrial gene intervention strategy that may have applications in mitochondrial disorders.},
}

Humans
*RNA, Guide, CRISPR-Cas Systems/genetics/metabolism
*Mitochondria/genetics/metabolism
*Genetic Therapy/methods
DNA, Mitochondrial/genetics
*CRISPR-Cas Systems/genetics
Animals
*Mitochondrial Diseases/genetics/therapy
RNA, Long Noncoding/genetics/metabolism
Gene Editing/methods
Mice
RNA-Binding Proteins/metabolism
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics

@article {pmid41678341,
year = {2026},
author = {Wang, Z and Wang, Y and Ji, Q},
title = {Bacterial Cofactors for CRISPR Activation.},
journal = {Biochemistry},
volume = {65},
number = {5},
pages = {501-504},
doi = {10.1021/acs.biochem.5c00738},
pmid = {41678341},
issn = {1520-4995},
mesh = {*CRISPR-Cas Systems ; *Thioredoxins/metabolism/chemistry ; *CRISPR-Associated Proteins/metabolism/chemistry/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Bacterial Proteins/metabolism/chemistry ; *Endodeoxyribonucleases/metabolism/chemistry ; *Coenzymes/metabolism ; *Bacteria/metabolism/genetics ; },
abstract = {Anti-CRISPR (Acr) proteins have long exemplified the viral counterattack against CRISPR-Cas immunity. By contrast, comparatively little is known about host proteins that may increase Cas effector activity. Recent work on a compact type V nuclease, Cas12p, demonstrates that this phage-associated effector depends on the bacterial thioredoxin TrxA for efficient DNA cleavage. TrxA binds a dedicated thioredoxin-binding (TB) domain on Cas12p through a redox-sensitive interaction, promoting an active conformation competent for DNA cleavage. This finding adds to a small but growing set of CRISPR activators and highlights that CRISPR-Cas systems are not static defense modules but dynamic networks shaped by auxiliary factors that can fine-tune their activity.},
}

*CRISPR-Cas Systems
*Thioredoxins/metabolism/chemistry
*CRISPR-Associated Proteins/metabolism/chemistry/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats
*Bacterial Proteins/metabolism/chemistry
*Endodeoxyribonucleases/metabolism/chemistry
*Coenzymes/metabolism
*Bacteria/metabolism/genetics

@article {pmid41678468,
year = {2026},
author = {Mendoza-Garcia, P and Keith, B and Nordberg, M and Quist, E and Ferrás, C and Hamza, GM and Elgendy, R and Ashenden, SK and Chi, J and van Zuydam, NR and Hattersley, N and Zhang, X},
title = {Omics-aided design genome editing strategy for challenging human immortalized cell models.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0341124},
pmid = {41678468},
issn = {1932-6203},
mesh = {Humans ; *Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; MCF-7 Cells ; Hep G2 Cells ; DNA End-Joining Repair ; Proliferating Cell Nuclear Antigen/genetics/metabolism ; Genomics/methods ; Gene Knock-In Techniques ; },
abstract = {CRISPR-Cas9 has become a popular genome editing tool for biomedical research and drug development due to its capability to enable precise correction or integration of genetic mutations in the genome. However, precise genome editing competency varies dramatically between cell types depending on their capabilities for DNA damage. In this proof-of-concept study, we took the example of HepG2 and MCF7 to show that omics profiling identifies bottlenecks that are associated with poor precise knock-in (KI) efficiency in hard-to-engineer cells. These bottlenecks include previously described factors such as the predominance of non-homologous end joining (NHEJ) repair and impaired homologous recombination (HR) capability, but also reveals apoptotic priming status of the cells as a limiting factor. Upon further comparative analysis between HepG2 and MCF7 cells, we pinpointed and validated the proliferating cell nuclear antigen (PCNA) as a target to overexpress to enhance precise KI efficiency in MCF7. Overall, we describe how employing a multi-omics approach to characterize cell models of interest can facilitate an in-depth understanding of their editability molecular signature, empowering us to manipulate the activity of key pathways for precise editing, and therefore increase efficiency of desired editing outcomes.},
}

Humans
*Gene Editing/methods
*CRISPR-Cas Systems/genetics
MCF-7 Cells
Hep G2 Cells
DNA End-Joining Repair
Proliferating Cell Nuclear Antigen/genetics/metabolism
Genomics/methods
Gene Knock-In Techniques

@article {pmid41678638,
year = {2026},
author = {El-Brolosy, MA and Oak, A and Hoang, AT and Damergi, Y and Fischer, A and Saunders, RA and Luo, J and Balabaki, A and Guez, J and Whitfield, TW and Goldman, SR and Latifkar, A and Lu, YR and Stainier, DYR and Karczewski, KJ and Corradin, O and Weissman, JS},
title = {Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6786},
pages = {eaea1272},
doi = {10.1126/science.aea1272},
pmid = {41678638},
issn = {1095-9203},
mesh = {Humans ; CRISPR-Cas Systems ; *Cytoplasm/metabolism ; *Protein Biosynthesis ; *RNA Stability ; *RNA, Messenger/metabolism/genetics ; *RNA-Binding Proteins/metabolism/genetics ; *Transcription, Genetic ; HEK293 Cells ; },
abstract = {Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmically generated mRNA fragments affect nuclear transcription remains poorly understood. Using genome-wide CRISPR screens, we uncover ILF3 as an RNA binding protein connecting cytoplasmic mRNA decay and transcription during TA and show that it is required for a range of TA substrates. ILF3 is enriched at adapting genes' RNAs, and its artificial recruitment through dCas13 promotes gene expression. Using tiling oligonucleotide screens, we identify trigger RNA fragments that activate adapting genes when introduced into cells. Further functional dissection reveals a critical role for homology between trigger and target sequences. These findings enhance our molecular understanding of TA and inform the design of programmable oligonucleotides for gene expression augmentation.},
}

Humans
CRISPR-Cas Systems
*Cytoplasm/metabolism
*Protein Biosynthesis
*RNA Stability
*RNA, Messenger/metabolism/genetics
*RNA-Binding Proteins/metabolism/genetics
*Transcription, Genetic
HEK293 Cells

@article {pmid41678668,
year = {2026},
author = {Kim, J and Yoon, J and Chen, J and Lee, J and Lee, HJ and Whitworth, K and Redel, B and Prather, RS and Lee, K},
title = {Enhancing the specificity of gene editing outcomes by using Cas9 variants in porcine embryos.},
journal = {Journal of animal science},
volume = {104},
number = {},
pages = {},
pmid = {41678668},
issn = {1525-3163},
support = {R01 OD035561/OD/NIH HHS/United States ; U42 OD011140/OD/NIH HHS/United States ; },
mesh = {Animals ; *Gene Editing/veterinary/methods ; Swine/embryology/genetics ; *CRISPR-Cas Systems ; *CRISPR-Associated Protein 9/genetics/metabolism ; *Embryo, Mammalian ; Female ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {The CRISPR/Cas9 technology has improved the ability to introduce targeted modifications in cells and embryos in diverse species. The use of this technology enables the establishment of genetically modified livestock models to study human diseases or improve food production. However, one of the main concerns with employing this technology is the possibility of introducing unintended genome modifications induced by the Streptococcus pyogenes Cas9 (SpCas9), a commonly used Cas9 protein. Recent advancements in CRISPR/Cas9 technology offer Cas9 variants that are designed to improve gene editing specificity. Here, three high-fidelity SpCas9 variants (eSpCas9, HiFi Cas9, and LZ3 Cas9) were employed to examine their efficacy and specificity in pig embryos. To introduce targeted modifications, mRNA coding for each Cas9 variant was mixed with IGH single guide RNA (sgRNA) and were injected into fertilized pig zygotes. The frequency of on- and off-targeting was calculated by amplifying IGH, AR, and RBFOX1 regions from genomic DNA derived from the injected embryos at the blastocyst stage and sent for Sanger sequencing. The sgRNA targeting IGH locus resulted in a 100% on-target editing rate using SpCas9. However, SpCas9 introduced off-targeting events in AR and RBFOX1 at a high frequency (> 60%) in embryos. Injecting each Cas9 variant at 20 ng/µl could modify the target gene (IGH) at 100% efficiency except for LZ3 Cas9 (59.1%). Importantly, off-target events on AR and RBFOX1 were not detected in any Cas9 variant groups. Gradually reducing the concentration of Cas9 mRNAs lowered the efficacy of on-targeting in all groups; however, the reduction was more dramatic in HiFi Cas9 and LZ3 Cas9 injected embryos. No embryonic toxicity was identified in embryo injected with Cas9 variants and more embryos reached blastocyst stage when injected with either eSpCas9 or HiFiCas9 mRNA. In vivo competency of embryos receiving eSpCas9 was examined by embryo transfer and fetuses recovered from a pregnant sow presented 100% on-target editing efficiency without any detectable off-target events. In summary, among the Cas9 variants examined, eSpCas9 presented the highest specificity with no detectable off-target events and supported the development of gene-edited fetuses. Our findings indicate that the use of Cas9 variants can advance the field of gene editing in livestock models.},
}

Animals
*Gene Editing/veterinary/methods
Swine/embryology/genetics
*CRISPR-Cas Systems
*CRISPR-Associated Protein 9/genetics/metabolism
*Embryo, Mammalian
Female
RNA, Guide, CRISPR-Cas Systems/genetics

@article {pmid41679028,
year = {2026},
author = {Yao, F and Qi, X and Yongli, S and Xiaofen, Z},
title = {Generation of a SV2A knockout human embryonic stem cell line by CRISPR/Cas9 system.},
journal = {Stem cell research},
volume = {91},
number = {},
pages = {103924},
doi = {10.1016/j.scr.2026.103924},
pmid = {41679028},
issn = {1876-7753},
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Human Embryonic Stem Cells/metabolism/cytology ; *Membrane Glycoproteins/genetics/metabolism/deficiency ; *Nerve Tissue Proteins/genetics/metabolism/deficiency ; *Gene Knockout Techniques ; Cell Line ; },
abstract = {Synaptic Vesicle Glycoprotein 2A (SV2A) is a ubiquitously expressed brain glycoprotein, localized to synaptic terminals. It regulates vesicle exocytosis, maintains neurotransmitter release, and serves as a receptor for both botulinum neurotoxins (e.g., BoNT/A) and tetanus neurotoxin (TeNT). It is a target for antiseizure drugs and implicated in epilepsy, Alzheimer's, and Parkinson's diseases. We generated a homozygous SV2A-knockout human embryonic stem cell (hESC) line WAe001-A-3F (H1-SV2A[-/-]), using CRISPR/Cas9 genome editing technology. The SV2A-knockout embryonic stem cell lines provide a precise in vitro model to dissect its roles in synaptic function and disease mechanisms.},
}

Humans
*CRISPR-Cas Systems/genetics
*Human Embryonic Stem Cells/metabolism/cytology
*Membrane Glycoproteins/genetics/metabolism/deficiency
*Nerve Tissue Proteins/genetics/metabolism/deficiency
*Gene Knockout Techniques
Cell Line

@article {pmid41679300,
year = {2026},
author = {Wang, Y and Hu, W and Xia, R and Yang, X and Gu, Y and Ning, Z and Yang, T and Yu, C and Zhang, L and Li, D and Jin, Y and Li, J and Zhang, F and Xu, Y and Xu, C and Wang, Z and Jing, N and Chen, L and Wang, G},
title = {CLIM-TIME identifies metastatic microenvironment modulators for T cell therapy response.},
journal = {Cell},
volume = {189},
number = {5},
pages = {1555-1572.e23},
doi = {10.1016/j.cell.2025.12.042},
pmid = {41679300},
issn = {1097-4172},
mesh = {*Tumor Microenvironment/immunology/genetics ; Animals ; *T-Lymphocytes/immunology ; Mice ; Humans ; Immunotherapy/methods ; Laser Capture Microdissection/methods ; Mice, Inbred C57BL ; Lung Neoplasms/secondary/immunology/therapy ; Cell Line, Tumor ; Extracellular Matrix/metabolism ; CRISPR-Cas Systems ; Neoplasm Metastasis ; Neoplasms/immunology/therapy/pathology ; },
abstract = {The tumor microenvironment (TME) poses a major barrier to effective immunotherapy, yet high-throughput perturbation-mapping approaches to dissect TME spatial complexity and its contextual immune modulators remain lacking. Here, we introduce CRISPR-laser-captured microdissection (LCM) integration mapping of the tumor-immune microenvironment (CLIM-TIME), a scalable platform that integrates CRISPR screening with LCM of metastatic tumors for transcriptomic, deconvolution, and immunofluorescence analyses. CLIM-TIME enables spatially resolved mapping of how tumor suppressor gene (TSG) loss reshapes the TME and modulates immune responses. We identified seven distinct TME subtypes, revealing that DNA repair and Polycomb repressive complex (PRC) TSG loss is linked to immune-infiltrated TMEs sensitive to T cell therapy. In contrast, knockouts of TSGs in the Hippo pathway promoted immune evasion and therapy resistance by fostering myeloid-enriched but T cell-excluded TMEs with elevated extracellular matrix (ECM). Targeting the ECM-crosslinking enzyme LOXL2 effectively remodeled the metastatic TME, enhancing T cell infiltration and improving therapeutic efficacy in lung metastases across multiple cancers.},
}

*Tumor Microenvironment/immunology/genetics
Animals
*T-Lymphocytes/immunology
Mice
Humans
Immunotherapy/methods
Laser Capture Microdissection/methods
Mice, Inbred C57BL
Lung Neoplasms/secondary/immunology/therapy
Cell Line, Tumor
Extracellular Matrix/metabolism
CRISPR-Cas Systems
Neoplasm Metastasis
Neoplasms/immunology/therapy/pathology

@article {pmid41679307,
year = {2026},
author = {Zhao, J and Wang, Z and Lu, L and Bu, G and Miao, Z and Zhang, Y and Guo, Y and Yang, Z and Ma, J and Jiao, J and Ma, X},
title = {An orthogonal CRISPR/Cpf1 platform for precise spatiotemporal gene regulation and osteoporotic fracture repair.},
journal = {Cell reports methods},
volume = {6},
number = {2},
pages = {101299},
pmid = {41679307},
issn = {2667-2375},
mesh = {Animals ; *CRISPR-Cas Systems/genetics ; Mice ; *Fracture Healing/genetics ; *Osteoporotic Fractures/genetics/therapy ; Humans ; Gene Editing/methods ; Osteoblasts/metabolism ; *Gene Expression Regulation ; Osteogenesis/genetics ; Genetic Therapy/methods ; Bone Morphogenetic Protein 2/metabolism/genetics ; Disease Models, Animal ; },
abstract = {CRISPR-Cas systems enable powerful gene editing and regulation, yet single-modality control often fails to achieve orthogonal, spatiotemporally precise regulation of multiple endogenous genes. We engineered OREC, an orthogonal platform integrating chemogenetic and optogenetic modalities for precise, reversible, multiplex gene control. OREC comprises two components: OREC[C] regulated by doxycycline (Dox) and OREC[o] controlled by light. By assembling catalytically dead Cpf1 (dCpf1), gene regulatory elements, and crRNA arrays on single transcripts, OREC enables robust simultaneous manipulation of multiple genes. We demonstrated OREC's therapeutic potential in vitro for osteoblast function modulation and in vivo for osteoporotic fracture repair. OREC effectively activated Bmp2 while inhibiting Dkk1, significantly enhancing bone formation and fracture healing in mouse models. These results establish OREC as a versatile platform for precise multiplex gene regulation, offering significant advancement for CRISPR-based gene therapy applications in complex tissues where coordinated control of multiple therapeutic targets is essential.},
}

Animals
*CRISPR-Cas Systems/genetics
Mice
*Fracture Healing/genetics
*Osteoporotic Fractures/genetics/therapy
Humans
Gene Editing/methods
Osteoblasts/metabolism
*Gene Expression Regulation
Osteogenesis/genetics
Genetic Therapy/methods
Bone Morphogenetic Protein 2/metabolism/genetics
Disease Models, Animal

@article {pmid41679545,
year = {2026},
author = {Bahlmann, N and Alshawabkeh, M and Tsoukas, R and Schröer, K and Schellhorn, S and Sieler, M and Dittmar, T and Ehrke-Schulz, E and Ehrhardt, A and Zhang, W},
title = {Desmoglein 2 (DSG2)-knockout human respiratory epithelial cell model to study species B adenovirus receptor usage.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {172-181},
pmid = {41679545},
issn = {1995-820X},
mesh = {Humans ; *Desmoglein 2/genetics/metabolism ; *Receptors, Virus/genetics/metabolism ; Gene Knockout Techniques ; Membrane Cofactor Protein/genetics/metabolism ; *Adenoviruses, Human/genetics/physiology ; CRISPR-Cas Systems ; *Epithelial Cells/virology/metabolism ; *Coxsackie and Adenovirus Receptor-Like Membrane Protein/genetics/metabolism ; Cell Line ; Cell Proliferation ; },
abstract = {With an increasing number of human adenoviruses identified, the selection of potential therapeutic vectors broadens. For safety reasons, achieving cell-specific gene delivery is crucial to minimize off-target effects. Therefore, it is essential to gain a systematic understanding of adenovirus receptor-usage. Our aim is to establish a human-originated in vitro model for comparative analysis of human adenoviruses receptor usage. Based on our previous work of human CD46 and coxsackievirus and adenovirus receptor (CAR) knockout cell lines, we generated desmoglein 2 (DSG2) knockout cell lines using genome-engineering technology based on Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9 (CRISPR/Cas9). All together, we established a panel of cell lines that carry a single, double, or triple knockout of the three major human adenovirus receptors: CAR, CD46 and DSG2. Notably, cell proliferation speed was affected by the CAR-knockout, but not the DSG2-or CD46-knockouts. In addition, the spheroid formation ability was sharply reduced in CAR- or DSG2-knockout cells, but not the CD46-knockout cells. With this receptor-knockout model, we confirmed the receptor usage of nine species B adenoviruses. Furthermore, adenovirus vectors containing a previously identified DSG2-binding affinity-enhanced mutation showed DSG2-dependent cell entry within this cell model, which indicates that they are de-targeted from CD46 - the ubiquitously expressed receptor on all nucleated cells. Collectively, our findings show that the adenovirus major receptor knockout cell lines can serve as an in vitro model to help select adenovirus types suitable for individual applications and to better understand adenovirus infection biology.},
}

Humans
*Desmoglein 2/genetics/metabolism
*Receptors, Virus/genetics/metabolism
Gene Knockout Techniques
Membrane Cofactor Protein/genetics/metabolism
*Adenoviruses, Human/genetics/physiology
CRISPR-Cas Systems
*Epithelial Cells/virology/metabolism
*Coxsackie and Adenovirus Receptor-Like Membrane Protein/genetics/metabolism
Cell Line
Cell Proliferation

@article {pmid41679604,
year = {2026},
author = {Li, L and Wang, Y and Wang, B and Shen, L and Gao, Y and Lin, W and Li, Z},
title = {A dCas9-integrated iLight9O system enables dynamic regulation for enhanced patchoulol biosynthesis in Saccharomyces cerevisiae.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134195},
doi = {10.1016/j.biortech.2026.134195},
pmid = {41679604},
issn = {1873-2976},
mesh = {*Saccharomyces cerevisiae/metabolism/genetics ; Metabolic Engineering/methods ; *CRISPR-Cas Systems/genetics ; Optogenetics/methods ; Light ; },
abstract = {Numerous organisms have evolved the ability to utilize light through photoreceptor proteins that mediate diverse biological processes. Currently, several optogenetic sensor systems are widely used in yeast. However, when these systems are applied for gene repression to regulate endogenous yeast gene expression, they typically require the insertion of corresponding target sites near the native promoter of the gene of interest to achieve precise modulation. To address these constraints, a novel blue light-inducible optogenetic tool designated iLight9 was developed, a single-component optogenetic biosensor integrated with the CRISPR-dCas9 platform. The stability of the iLight9 system was further enhanced by employing a strategy involving the addition of a protein degradation tag. The resulting system was designated as iLight9O, which facilitated programmable regulation of distinct genes through the introduction of specific sgRNAs. Subsequently, systematic metabolic engineering strategies were employed to construct an efficient patchoulol-producing cell factory in Saccharomyces cerevisiae. Moreover, a two-step isoprenol utilization (IU) pathway was introduced into the recombinant strain to enhance its capacity for patchoulol biosynthesis. Crucially, the iLight9O system was adopted to dynamically downregulate squalene synthase, a key enzyme in the competing squalene biosynthetic pathway. This optogenetic flux control strategy increased patchoulol titers by 66 % in the IU-optimized strain and 24 % in the MVAIU2 strain, demonstrating significant improvements over static engineering approaches.},
}

*Saccharomyces cerevisiae/metabolism/genetics
Metabolic Engineering/methods
*CRISPR-Cas Systems/genetics
Optogenetics/methods
Light

@article {pmid41679990,
year = {2026},
author = {Carota, AG and Spiaggia, F and Poma, N and Palladino, P and Cuffaro, D and Vivaldi, F and Ravelet, C and Di Francesco, F and Minunni, M},
title = {Highly fluorescent copper nanoclusters as programmable reporters for CRISPR/Cas12a-based detection of bacterial DNA.},
journal = {Biosensors & bioelectronics},
volume = {300},
number = {},
pages = {118492},
doi = {10.1016/j.bios.2026.118492},
pmid = {41679990},
issn = {1873-4235},
mesh = {*CRISPR-Cas Systems/genetics ; *Copper/chemistry ; *Biosensing Techniques/methods ; *DNA, Bacterial/isolation & purification/genetics ; Fluorescent Dyes/chemistry ; *Escherichia coli/genetics/isolation & purification ; *Metal Nanoparticles/chemistry ; Humans ; Limit of Detection ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {Early and accessible pathogen detection is crucial for global health security and demands diagnostic assays that are rapid, affordable, and suitable for Point-of-Care use. This study presents a cost-effective, rapid, one-pot fluorescence assay for bacterial DNA detection that exploits the unique optical properties of DNA-templated copper nanoclusters (CuNCs). These nanoclusters offer a sustainable alternative to conventional fluorophores, thanks to their eco-friendly synthesis, high photostability, and large Stokes shift. The assay integrates CuNCs with the CRISPR/Cas12a system to achieve programmable and highly specific target recognition. Upon target binding, activation of the Cas12a/gRNA complex triggers collateral cleavage of rationally designed DNA templates that normally support CuNCs formation, resulting in a marked fluorescence decrease. A panel of hairpin and poly-thymine DNA structures was systematically evaluated to maximize both CuNCs fluorescence and responsiveness to Cas12a/gRNA trans-cleavage, ultimately identifying an AT-rich stem-loop reporter that provided strong signal intensity and complete signal shutdown upon target recognition. The final CRISPR-CuNCs assay achieved picomolar sensitivity, accurately detected E. coli DNA from reference strains, clinical isolates, and serum-spiked samples, and required no fluorophore-quencher probes or multistep procedures. Overall, this work demonstrated that combining the programmability of CRISPR/Cas12a with the versatility and low-cost of DNA-templated CuNCs enables a robust and accessible platform for molecular diagnostics, with strong potential for Point-of-Care deployment.},
}

*CRISPR-Cas Systems/genetics
*Copper/chemistry
*Biosensing Techniques/methods
*DNA, Bacterial/isolation & purification/genetics
Fluorescent Dyes/chemistry
*Escherichia coli/genetics/isolation & purification
*Metal Nanoparticles/chemistry
Humans
Limit of Detection
Bacterial Proteins
Endodeoxyribonucleases
CRISPR-Associated Proteins

@article {pmid41680160,
year = {2026},
author = {Wang, B and Zhou, S and Zhang, X and Wang, R and Huang, S and Li, A and He, H and Zhang, Y and Wei, Y and Yang, Z and Song, F and Li, X and Wan, X and Shen, Y and Ma, C and Mao, H and Ledesma-Amaro, R and Yin, D and Wei, Q and Deng, R and Yang, T and Liu, S and Wan, Y and Mao, C},
title = {PRICE: direct and robust detection of microRNAs at single-nucleotide resolution.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41680160},
issn = {2041-1723},
support = {14208723//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
mesh = {*MicroRNAs/genetics ; Humans ; *CRISPR-Cas Systems/genetics ; *Polymorphism, Single Nucleotide ; *Peptide Nucleic Acids/genetics/metabolism ; },
abstract = {Accurate single-nucleotide discrimination of miRNA is clinically vital because small sequence variations can have significant phenotypic and clinical consequences, yet existing techniques can only detect single nucleotide variations (SNVs) at specific loci. Here, we present a generalized peptide nucleic acid (PNA) mediated CRISPR/Cas13a system (PRICE), enabling detection of SNVs in miRNA sequence without sacrificing the sensitivity. PRICE utilizes PNA blockers fully complementary to non-target miRNAs (e.g., miRNAs containing SNVs at loci of no interest) but not to the target miRNA. These blockers selectively hybridize with and inhibit non-target sequences in samples (serum, cells, or tissues). Only the unhybridized target miRNA then binds to crRNA within the Cas13a complex, activating Cas13a to cleave a fluorescent reporter-quencher linker, generating a detectable signal (~10 fM limit). By designing a panel of PNAs against SNVs, PRICE provides a versatile, amplification-free platform for precise miRNA analysis, advancing cancer diagnosis, prognosis, and biology.},
}

*MicroRNAs/genetics
Humans
*CRISPR-Cas Systems/genetics
*Polymorphism, Single Nucleotide
*Peptide Nucleic Acids/genetics/metabolism

@article {pmid41680202,
year = {2026},
author = {Garmendia-Antoñana, N and Dorado-Morales, P and Gil, C and García, B and Echeverz, M and Solano, C and Penadés, JR and Lasa, I},
title = {Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41680202},
issn = {2055-5008},
support = {PRE2021-097385//Spanish Ministry of Science, Innovation and Universities/ ; PID2020-113494RB-I00/ AEI//Spanish Ministry of Science, Innovation and Universities/ ; BES-2015-07285//the Spanish Ministry of Science, Innovation and Universities/ ; },
mesh = {Animals ; *Staphylococcus aureus/genetics/virology/drug effects/physiology ; *CRISPR-Cas Systems ; *Staphylococcal Infections/therapy/microbiology ; Female ; Mice ; *Mastitis/microbiology/therapy ; Biofilms/growth & development ; Disease Models, Animal ; *Bacteriophages/genetics ; Genomic Islands ; Anti-Bacterial Agents/pharmacology ; *Staphylococcus Phages/genetics ; },
abstract = {Treatment options for Staphylococcus aureus infections are increasingly limited, particularly in livestock, where S. aureus causes mastitis requiring prolonged antibiotic therapy. This study engineered Phage Inducible Chromosomal Islands (ePICIs) to deliver CRISPR-Cas9 modules targeting small RNA genes. ePICIs exhibit bactericidal activity without chromosomal integration, an expanded host range compared to their parental phages, and biofilm-dependent efficacy influenced by the extracellular matrix composition. Biofilms mediated by the Bap protein strongly protect bacteria from ePICIs, whereas PIA/PNAG-based biofilms do not. Despite Bap-mediated protection in vitro, ePICIs achieved bactericidal effects comparable to vancomycin in a mouse mastitis model caused by Bap-producing strains. These findings reveal key factors affecting phage-delivered CRISPR-Cas efficacy and highlight that antibiofilm therapies should not be dismissed based solely on in vitro performance. Non-replicative ePICIs thus represent a promising alternative for treating localized infections such as mastitis.},
}

Animals
*Staphylococcus aureus/genetics/virology/drug effects/physiology
*CRISPR-Cas Systems
*Staphylococcal Infections/therapy/microbiology
Female
Mice
*Mastitis/microbiology/therapy
Biofilms/growth & development
Disease Models, Animal
*Bacteriophages/genetics
Genomic Islands
Anti-Bacterial Agents/pharmacology
*Staphylococcus Phages/genetics

@article {pmid41680487,
year = {2026},
author = {Kroell, AS and Hoffmann, KH and Motzkus, NA and Lemmen, N and Happ, N and Wolf, B and von Bachmann, AL and Southern, N and Vogd, F and Aschenbrenner, S and Niopek, D and Mathony, J},
title = {Modular engineering of thermoresponsive allosteric proteins.},
journal = {Nature chemical biology},
volume = {22},
number = {5},
pages = {751-758},
pmid = {41680487},
issn = {1552-4469},
support = {520612620//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 453202693//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Allosteric Regulation ; *Protein Engineering/methods ; Escherichia coli/genetics/metabolism ; Temperature ; CRISPR-Cas Systems ; Avena/genetics/chemistry ; Gene Editing ; },
abstract = {Thermogenetics enables noninvasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membrane recruitment. Here, we present a generalizable strategy for engineering thermosensitive allosteric proteins through the insertion of optimized Avena sativa LOV2 domain variants. Applying this approach to a diverse set of structurally and functionally unrelated proteins in Escherichia coli, we generated potent, thermoswitchable chimeric variants that can be tightly controlled within narrow temperature ranges (37-41 °C). Extending this strategy to mammalian systems, we engineered CRISPR-Cas genome editors directly modulated by subtle temperature changes within the physiological range. Lastly, we showcase the incorporation of a chemoreceptor domain as an alternative thermosensing module, suggesting thermosensitivity to be a widespread feature in receptor domains. This work expands the toolkit of thermogenetics, providing a blueprint for temperature-dependent control of virtually any protein of interest.},
}

Allosteric Regulation
*Protein Engineering/methods
Escherichia coli/genetics/metabolism
Temperature
CRISPR-Cas Systems
Avena/genetics/chemistry
Gene Editing

@article {pmid41680629,
year = {2026},
author = {Selhorst, P and Van Vyve, E and Falconi-Agapito, F and Mariën, J and Ariën, KK},
title = {Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {188},
pmid = {41680629},
issn = {1471-2164},
support = {U01 AI151378/AI/NIAID NIH HHS/United States ; U01AI151378/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Metagenomic sequencing for pathogen detection has traditionally suffered from low sensitivity due to the overwhelming presence of host nucleic acids. Commercial host-depletion kits are often prohibitively expensive and limited to specific species, hindering adoption in resource-limited settings, where the burden of zoonotic diseases is highest. To address this, we optimized and combined Sequence-Independent Single Primer Amplification (SISPA) with Depletion of Abundant Sequences by Hybridization (DASH), establishing a low-cost metagenomic protocol on the Oxford Nanopore sequencing platform. Our approach can be adapted to any species to detect microbial RNAs in serum samples at PCR-range sensitivity, outperforming existing methods in the field.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12268-4.},
}

@article {pmid41683064,
year = {2026},
author = {Chen, Z and He, D and Yu, W and Fu, X and Zhang, L and Zhang, M and Yu, X and Ye, Z},
title = {Advancing Bongkrekic Acid Detection: From Conventional Instrumental Analysis to Advanced Biosensing for Cross-Toxin Applications.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683064},
issn = {2304-8158},
abstract = {Bongkrekic acid (BKA), a highly lethal toxin, has been implicated in frequent poisoning incidents in recent years, posing a serious threat to global food safety and creating an urgent need for rapid and sensitive detection methods. This review provides a systematic analysis of the entire BKA detection technologies, covering sample pretreatment techniques, instrumental analysis, immunoassays, and biosensing methods. It assesses the merits of key methods and also explores the strategic cross-application of detection paradigms developed for analogous toxins. This review delivers a comprehensive and critical evaluation of BKA detection technologies. First, it discusses sample pretreatment strategies, notably solid-phase extraction (SPE) and QuEChERS. Subsequently, it analyzes the principles, performance, and applications of core detection methods, including high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), high-resolution mass spectrometry (HRMS), time-resolved fluorescence immunoassay (TRFIA), dual-mode immunosensors and nanomaterial-based sensors. Instrumental methods (e.g., HRMS) offer unmatched sensitivity [with a limit of detection (LOD) as low as 0.01 μg/kg], yet remain costly and laboratory-dependent. Immunoassay and biosensor approaches (TRFIA and dual-mode sensors) enable rapid on-site detection with high sensitivity (ng/mL to pg/mL), though challenges in stability and specificity remain. Looking forward, the development of next-generation BKA detection could be accelerated by cross-applying cutting-edge strategies proven for toxins-such as Fumonisin B1 (FB1), Ochratoxin A (OTA), and Aflatoxin B1 (AFB1)-including nanobody technology, CRISPR-Cas-mediated signal amplification, and multimodal integrated platforms. To translate this potential into practical tools, future research should prioritize the synthesis of high-specificity recognition elements, innovative signal amplification strategies, and integrated portable devices, aiming to establish end-to-end biosensing systems capable of on-site rapid detection through multitechnology integration.},
}

@article {pmid41683574,
year = {2026},
author = {Sopel, J and Sarad, K and Kozinska, A and Mokrzyński, K and Szczygieł, D and Murzyn, A and Drzał, A and Słomiński, A and Szczygieł, M and Elas, M},
title = {Pmel17 Deficiency Affects Melanogenesis and Promotes Tumor Vascularization.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683574},
issn = {1422-0067},
mesh = {Animals ; *Melanins/metabolism/biosynthesis ; Mice ; *Neovascularization, Pathologic/metabolism/genetics/pathology ; *Melanoma, Experimental/metabolism/pathology/genetics/blood supply ; Reactive Oxygen Species/metabolism ; Cell Line, Tumor ; *gp100 Melanoma Antigen/genetics/metabolism/deficiency ; CRISPR-Cas Systems ; Cell Movement ; Melanosomes/metabolism ; Cell Cycle ; Melanogenesis ; },
abstract = {Premelanosomal protein (Pmel, also known as Pmel17) is the major component of melanosomal fibrils and plays a key role in melanin polymerization, making it an important factor in melanogenesis. We investigated how the absence of Pmel affects the properties of B16F10 melanoma cells. Pmel-knockout B16F10 cells were generated using CRISPR/Cas9-mediated genome editing. A viability assay revealed no significant differences between wild-type (WT) and Pmel-knockout (KO) sublines; however, melanosome maturation was impaired. In Pmel KO cells, the cell cycle was disrupted, and higher levels of reactive oxygen species (ROS) were observed compared with WT cells. Moreover, the migration capacity and tube formation of melanoma cells were increased. Tumors derived from Pmel KO cells exhibited unchanged growth kinetics but reduced melanin content, along with enhanced vascularization and oxygenation. Thus, knockout of the Pmel17 gene in melanoma cells alters pigmentation, vascularization, and oxygenation of tumors. These parameters are crucial for both tumor progression and therapeutic response.},
}

Animals
*Melanins/metabolism/biosynthesis
Mice
*Neovascularization, Pathologic/metabolism/genetics/pathology
*Melanoma, Experimental/metabolism/pathology/genetics/blood supply
Reactive Oxygen Species/metabolism
Cell Line, Tumor
*gp100 Melanoma Antigen/genetics/metabolism/deficiency
CRISPR-Cas Systems
Cell Movement
Melanosomes/metabolism
Cell Cycle
Melanogenesis

@article {pmid41683605,
year = {2026},
author = {Blazyte, A and Lee, H and Yoon, C and Jeon, S and Lee, J and Bayarsaikhan, D and Kim, J and Park, S and Cho, J and Baek, SA and Byun, G and Lee, B and Bhak, J},
title = {Neurofibromin 1 (NF1) Splicing Mutation c.61-2A>G: From Aberrant mRNA Processing to Therapeutic Implications In Silico.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683605},
issn = {1422-0067},
support = {1.200047.01//Ulsan City Research Fund/ ; RS-2023-00263429//Genome Editing Research Program/ ; KEIT 20018560//Alchemist Project of the Korea Evaluation Institute of Industrial Technology/ ; RS-2024-00435468//Korea Planning & Evaluation Institute of Industrial Technology with support from the Ministry of Trade, Industry and Energy/ ; },
mesh = {*Neurofibromin 1/genetics ; Humans ; *Neurofibromatosis 1/genetics/therapy ; *RNA Splicing/genetics ; *Mutation ; *RNA, Messenger/genetics ; RNA Splice Sites/genetics ; Gene Editing ; Computer Simulation ; DNA Methylation ; CRISPR-Cas Systems ; Male ; },
abstract = {The neurofibromin 1 (NF1) splice-site mutation c.61-2A>G (rs1131691100) is a rare, pathogenic, autosomal dominant variant that disrupts NF1 tumor-suppressor function, causing neurofibromatosis type 1 (NF1). Its pathogenic mechanism is poorly understood, and the potential for personalized therapeutic genome editing remains unknown due to the absence of a standard framework for investigating splicing disorders. Here, we performed a comprehensive multi-omics analysis of a de novo c.61-2A>G case from South Korea, integrating short- and long-read whole genome sequencing, whole transcriptome sequencing, and methylation profiling. We confirm that c.61-2A>G abolishes the canonical splice acceptor site, activating a cryptic splice acceptor 16 nucleotides downstream in exon 2. This splicing shift generates a 16-nucleotide deletion, causing a frameshift and premature stop codon that truncates the protein's N-terminal region. Long-read sequencing further reveals that the mutation creates a novel CpG dinucleotide, which is methylated in the majority of reads. Finally, we assessed therapeutic correction strategies, revealing that CRISPR-Cas9 prime editing is the only viable approach for in vivo correction. This study provides the first comprehensive multi-omics characterization of the NF1 c.61-2A>G mutation and establishes a minimal framework for precision therapeutic development in silico in monogenic splicing disorders.},
}

*Neurofibromin 1/genetics
Humans
*Neurofibromatosis 1/genetics/therapy
*RNA Splicing/genetics
*Mutation
*RNA, Messenger/genetics
RNA Splice Sites/genetics
Gene Editing
Computer Simulation
DNA Methylation
CRISPR-Cas Systems
Male

@article {pmid41683697,
year = {2026},
author = {Kowalik, S and Samoń, M and Przyborowski, M},
title = {Molecular Regulators of In Vitro Regeneration in Wheat: Roles of Morphogenic Factors in Transformation, Genome Editing, and Breeding.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683697},
issn = {1422-0067},
support = {Dotacja Celowa task 4.1//Ministry of Agriculture and Rural Development/ ; },
mesh = {*Triticum/genetics/physiology/growth & development ; *Gene Editing/methods ; *Plant Breeding/methods ; *Regeneration/genetics ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; *Transformation, Genetic ; Transcription Factors/genetics/metabolism ; },
abstract = {Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on extensive transcriptional reprogramming and epigenetic remodeling orchestrated by morphogenic regulators that modulate meristem identity, as well as cellular pluri- and totipotency. In this review, we synthesize current molecular knowledge on key transcription factors (BBM, WUS/WUS2, GRF-GIF, WOX, LAX1, SERK, WIND1/ERF115) and signaling peptides (CLE/CLV-WUS module, phytosulfokine/PSK) that regulate embryogenic competence in monocot cereals, with emphasis on their orthologs and functional relevance in wheat. We highlight how controlled expression of these morphogenic genes, promoter engineering, and transient or excisable induction systems can significantly enhance regeneration capacity, reduce chimerism in CRISPR-Cas-edited plants, and facilitate genotype-independent transformation. We also discuss epigenetic and metabolic constraints underlying wheat recalcitrance and their potential modulation to improve culture responsiveness. By integrating evidence from wheat, rice, maize, and barley, we outline conserved gene-regulatory networks that reinitiate totipotency and propose strategies to accelerate doubled haploid production and speed-breeding pipelines. Collectively, morphogenic factors emerge as central molecular tools for overcoming regeneration bottlenecks and enabling next-generation wheat improvement. The objective of this review is to synthesize and critically evaluate current molecular knowledge on morphogenic regulators controlling in vitro regeneration in wheat (Triticum aestivum L.), with particular emphasis on their roles in genetic transformation and genome editing.},
}

*Triticum/genetics/physiology/growth & development
*Gene Editing/methods
*Plant Breeding/methods
*Regeneration/genetics
Gene Expression Regulation, Plant
Plant Proteins/genetics/metabolism
*Transformation, Genetic
Transcription Factors/genetics/metabolism

@article {pmid41683796,
year = {2026},
author = {Jiang, Y and Chen, Y and Huang, Z and Chen, L and Huang, X},
title = {Tyrosinase-Deficient Skin Melanophore Lineage in Xenopus tropicalis Tadpoles Shows Strong Autofluorescence.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683796},
issn = {1422-0067},
support = {LY20C120003//Zhejiang Provincial Natural Science Foundation/ ; },
mesh = {Animals ; *Monophenol Monooxygenase/genetics/deficiency/metabolism ; *Xenopus/metabolism/genetics ; Larva/metabolism/genetics ; *Melanophores/metabolism ; *Skin/metabolism ; CRISPR-Cas Systems ; Melanins ; Optical Imaging ; Xenopus Proteins/genetics/metabolism ; Skin Pigmentation ; },
abstract = {Tyrosinase, encoded by Tyr, is a key rate-limiting enzyme in melanin biosynthesis. Knockout of Tyr results in a distinct albino phenotype, making it a widely used target for evaluating gene-editing efficiency. Here, we found that the tyrosinase-deficient skin melanophore lineage of Xenopus tropicalis (X. tropicalis) tadpoles shows strong autofluorescence under the GFP filter, which may interfere with in vivo fluorescence imaging. Through spectral scanning analysis, we characterized the emission spectrum of the autofluorescence under commonly used excitation wavelengths for fluorescent proteins. Based on this, we established a reference protocol for identifying and excluding such interference in Tyr-targeted knockin studies. Furthermore, knockout of the GTP cyclohydrolase 2 gene (Gch2) using CRISPR-Cas9 significantly reduced the fluorescence intensity induced by tyrosinase deficiency, indicating an essential role of the enzyme and its mediated pterine biosynthesis in the generation of the autofluorescence. This study systematically characterized these fluorescent mutant melanophores in X. tropicalis tadpoles, providing a practical basis for avoiding fluorescent interference in experimental science and a new perspective on pigment cell development and evolution.},
}

Animals
*Monophenol Monooxygenase/genetics/deficiency/metabolism
*Xenopus/metabolism/genetics
Larva/metabolism/genetics
*Melanophores/metabolism
*Skin/metabolism
CRISPR-Cas Systems
Melanins
Optical Imaging
Xenopus Proteins/genetics/metabolism
Skin Pigmentation

@article {pmid41683905,
year = {2026},
author = {Ortiz-Bueno, M and Zinghirino, F and Serra, PP and Paschoudi, K and Montoliu, L and Atilla, E and Luo, Y and Cavazza, A and Lederer, CW and Benabdellah, K},
title = {From Bench to Bedside: Ethical and Clinical Best Practices for Genome Editing Applications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683905},
issn = {1422-0067},
support = {CA21113//COST (European Cooperation in Science and Technology)./ ; ProyExcel_00875//Consejería de Universidad, Investigación e Innovación/ ; },
mesh = {Humans ; *Gene Editing/ethics/legislation & jurisprudence/methods ; *Genetic Therapy/ethics/methods ; Animals ; CRISPR-Cas Systems ; *Translational Research, Biomedical/ethics ; },
abstract = {Genome editing (GE) has transformed medicine by allowing precise changes to DNA, offering potential treatments for a range of inherited and acquired disorders. Several technologies support these advances, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)-based systems, of which the latter has emerged as the most accessible, versatile, and popular. While GE holds great promise, its clinical use requires careful attention to safety, ethics and regulatory standards. Inadvertent on- and off-target DNA alterations and unintended modification of non-target cells pose major technical challenges, while bioethical considerations and the need for harmonized safety standards create regulatory challenges. The Food and Drug Administration (FDA) and European Medicines Agency (EMA), as regulatory agencies for key advanced therapy markets, provide detailed guidance on these aspects, emphasizing rigorous preclinical testing, patient monitoring, ethical consent, and compliance with legal frameworks. This concise review summarizes what is currently published in the scientific literature and recommended by regulatory agencies, providing an overview of the responsible clinical application of GE, with emphasis on patient safety, adherence to regulatory guidance, and ethical practice.},
}

Humans
*Gene Editing/ethics/legislation & jurisprudence/methods
*Genetic Therapy/ethics/methods
Animals
CRISPR-Cas Systems
*Translational Research, Biomedical/ethics

@article {pmid41683941,
year = {2026},
author = {Skaliter, O and Gura, A and Livneh, Y and Cohen, R and Shklarman, E and Edelbaum, O and Masci, T and Vainstein, A},
title = {Targeted Gene Modification of HMGR Enhances Biosynthesis of Terpenoid and Phenylpropanoid Volatiles in Petunia and Lettuce.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683941},
issn = {1422-0067},
support = {1368/23//Israel Science Foundation/ ; 20-01-0209//Office of the Chief Scientist/ ; },
mesh = {*Petunia/genetics/metabolism ; *Terpenes/metabolism ; *Lactuca/genetics/metabolism ; Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; Gene Editing ; CRISPR-Cas Systems ; Plants, Genetically Modified/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; },
abstract = {Terpenoids constitute the largest class of plant-specialized metabolites, playing essential roles throughout the plants' life cycle and having diverse applications for humans in nutrition, medicine, and flavor. 3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-limiting enzyme of the mevalonate (MVA) pathway, producing sesquiterpenes, saponins, and other terpenoids. HMGR is post-translationally regulated by downstream MVA products through its N-terminal regulatory domain, limiting terpenoid production. To overcome this bottleneck, we employed a virus-based CRISPR/Cas9 system to genetically modify the N-terminal regulatory domain of HMGR in petunia (Petunia × hybrida) and lettuce (Lactuca sativa L.). In petunia, HMGR1-edited lines exhibited vigorous growth, larger flowers, and increased production of sesquiterpenes. Interestingly, they also showed enhanced production of phenylpropanoid volatiles, revealing a connection between these pathways. Transcript analysis revealed altered expression of genes involved in terpenoid biosynthesis, pyruvate metabolism, phenylpropanoid biosynthesis, and gibberellin- and auxin-related pathways, indicating enhanced carbon flux through these metabolic networks. In lettuce, HMGR7-edited plants displayed elevated emission of sesquiterpenes, apocarotenoids, and the phenylpropanoid benzaldehyde. Together, these results establish a transgene-free strategy to enhance the production of terpenoid and phenylpropanoid volatiles, and provide a framework for developing resilient, nutrient-enriched crops.},
}

*Petunia/genetics/metabolism
*Terpenes/metabolism
*Lactuca/genetics/metabolism
Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
Gene Editing
CRISPR-Cas Systems
Plants, Genetically Modified/genetics/metabolism
*Volatile Organic Compounds/metabolism

@article {pmid41683990,
year = {2026},
author = {Psaras, AM and McKay, SJ and Vasquez Vilela, J and Ospina Sanchez, E and Cintrón, MG and Elder, KK and Brooks, TA},
title = {Ovarian Cancer Susceptibility and Chemosensitivity to KRAS Modulation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683990},
issn = {1422-0067},
mesh = {Humans ; Female ; *Proto-Oncogene Proteins p21(ras)/genetics/metabolism/antagonists & inhibitors ; *Ovarian Neoplasms/genetics/drug therapy/pathology/metabolism ; *Drug Resistance, Neoplasm/genetics/drug effects ; Cell Line, Tumor ; Paclitaxel/pharmacology ; Cisplatin/pharmacology ; Antineoplastic Agents/pharmacology ; CRISPR-Cas Systems ; },
abstract = {KRAS is frequently amplified or overexpressed in ovarian cancer and represents a potential therapeutic target for overcoming chemoresistance. We employed complementary approaches-CRISPR/Cas9 gene editing, Tet-ON inducible knockdown, polypurine reverse Hoogsteen hairpin (PPRH) oligonucleotides, and the pan-KRAS inhibitor BI2865-to investigate whether KRAS modulation enhances chemotherapeutic efficacy in ovarian cancer models. CRISPR-mediated KRAS knockdown in SKOV-3 cells dramatically altered three-dimensional spheroid morphology, reducing the average area six-fold, and significantly enhanced sensitivity to both cisplatin and paclitaxel in 3D cultures, where paclitaxel resistance was completely reversed. The Tet-ON system demonstrated dose-dependent chemosensitization with optimal effects at intermediate KRAS knockdown levels (~50-60%). PPRH oligonucleotides at sub-cytotoxic concentrations (50 nM) reduced cisplatin and paclitaxel IC50 values by approximately 50% in 2D cultures. Pharmacological KRAS inhibition with BI2865 produced striking synergy with paclitaxel (several hundred-fold sensitizations in 2D; complete reversal of 3D resistance), and additive effects with cisplatin. In KRAS-amplified Kuramochi cells (representing high-grade serous ovarian carcinoma), BI2865 enhanced paclitaxel efficacy, despite greater baseline chemoresistance. These findings establish KRAS as a promising chemosensitization target in ovarian cancer, with particular potential for taxane-based combination therapies.},
}

Humans
Female
*Proto-Oncogene Proteins p21(ras)/genetics/metabolism/antagonists & inhibitors
*Ovarian Neoplasms/genetics/drug therapy/pathology/metabolism
*Drug Resistance, Neoplasm/genetics/drug effects
Cell Line, Tumor
Paclitaxel/pharmacology
Cisplatin/pharmacology
Antineoplastic Agents/pharmacology
CRISPR-Cas Systems

@article {pmid41685373,
year = {2025},
author = {Hanafiah, A and Sukri, A and Asmawi, MA and Yusoff, H and Mohd Puzi, S and Neoh, HM and Lopes, BS},
title = {Recent Advancements in Development and Characterization of Phages Targeting Helicobacter pylori.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {6},
number = {4},
pages = {282-291},
pmid = {41685373},
issn = {2641-6549},
abstract = {Helicobacter pylori remains a significant global health concern, with rising antibiotic resistance posing challenges for conventional treatments. Bacteriophages, viruses that specifically target and lyse bacterial cells, present a promising alternative therapeutic approach. This review explores the advancements in phage research related to H. pylori, including the isolation, genomic and proteomic characterization, and therapeutic potential of lytic and lysogenic phages. Novel isolation techniques have identified diverse phages from clinical and environmental sources, such as sewage and wastewater, revealing unique genetic and structural adaptations that enhance their effectiveness in targeting H. pylori. Genomic analysis has highlighted the role of prophages in H. pylori evolution, while proteomic studies have uncovered structural features that enable phages to survive the acidic gastric environment. High-throughput technologies, such as next-generation sequencing, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems, and microfluidic platforms, have revolutionized phage discovery and characterization. Furthermore, the potential for phage-antibiotic synergy offers new avenues for combating antibiotic resistance. Despite these advancements, challenges such as H. pylori's genetic diversity, its fastidious growth requirements, and the development of robust delivery mechanisms for gastric application persist. This review highlights the need for further research to optimize phage-based therapies as a viable alternative or adjunct to current treatments for H. pylori infections.},
}

@article {pmid41685943,
year = {2026},
author = {Wang, C and Li, D and Yu, R and Xue, J and Xie, W and Zhang, Q and Gui, X and Wang, L and Guo, S and Xie, Y and Jiang, Y and Liu, G and Wu, J},
title = {A CRISPR/Cas9-regulated dual-ring topological allosteric probe for detection of the EGFR L858R resistance mutation in CTCs.},
journal = {Analytical methods : advancing methods and applications},
volume = {18},
number = {9},
pages = {1815-1825},
doi = {10.1039/d5ay02124c},
pmid = {41685943},
issn = {1759-9679},
mesh = {Humans ; ErbB Receptors/genetics ; *Neoplastic Cells, Circulating/pathology/metabolism ; *CRISPR-Cas Systems/genetics ; *Lung Neoplasms/genetics/blood ; *Carcinoma, Non-Small-Cell Lung/genetics/blood ; Polymorphism, Single Nucleotide ; *Drug Resistance, Neoplasm/genetics ; Mutation ; Fluorescent Dyes/chemistry ; Cell Line, Tumor ; },
abstract = {A single-nucleotide polymorphism (SNP) is a point mutation occurring at a defined genomic locus, and its precise and rapid detection in circulating tumor cells (CTCs) is essential for early diagnosis and therapeutic monitoring of non-small cell lung cancer (NSCLC). In this study, a CRISPR/Cas9-regulated dual-ring topological allosteric probe was developed for ultrasensitive and specific detection of the EGFR L858R mutation. The recognition ring selectively hybridizes with the target sequence and is cleaved by the Cas9-sgRNA complex, triggering the release of the reporter ring. The released reporter ring then serves as a template for rolling circle amplification (RCA), generating products that hybridize with dual-labeled fluorescent probes to yield measurable signals. This assay clearly distinguished L858R from the wild-type sequence and detected mutation frequencies as low as 1.0% with high specificity against other common EGFR variants. Its robustness was further validated using clinical blood samples, enabling sensitive detection of low-abundance L858R mutations. These results demonstrate that the integration of programmable target recognition, efficient signal amplification, and fluorescence readout provides a promising platform for SNP analysis in liquid biopsy, supporting precision diagnosis and treatment monitoring in NSCLC.},
}

Humans
ErbB Receptors/genetics
*Neoplastic Cells, Circulating/pathology/metabolism
*CRISPR-Cas Systems/genetics
*Lung Neoplasms/genetics/blood
*Carcinoma, Non-Small-Cell Lung/genetics/blood
Polymorphism, Single Nucleotide
*Drug Resistance, Neoplasm/genetics
Mutation
Fluorescent Dyes/chemistry
Cell Line, Tumor

@article {pmid41686171,
year = {2026},
author = {Su, M and Lv, MM and Pan, MX and Zha, CJ and Nie, YG and Ying, ZM},
title = {From Self-Processing to Responsive Assembly Enabling an Autocatalytic Cas13a Circuit for Enhanced Biosensing.},
journal = {ACS sensors},
volume = {11},
number = {3},
pages = {2697-2706},
doi = {10.1021/acssensors.5c04673},
pmid = {41686171},
issn = {2379-3694},
mesh = {*Biosensing Techniques/methods ; Humans ; CRISPR-Cas Systems ; Survivin/genetics ; *CRISPR-Associated Proteins/genetics/metabolism ; MicroRNAs/analysis/genetics ; DNA, Viral/analysis/genetics ; RNA, Messenger/analysis/genetics ; DNA-Directed RNA Polymerases ; Viral Proteins ; },
abstract = {Despite the success of non-classical crRNA designs in Cas12a-based biosensing, application to Cas13a systems faces fundamental challenges. Our research discovers that site-specific splitting within the crRNA seed region enables effective activation of Cas13a trans-cleavage. Here, we developed an autocatalytic Cas13a circuit that transitions from self-processing to responsive assembly for enhanced biosensing (PRA-Cas13a). The system employs engineered pre-crRNA as a molecular switch, which undergoes self-processing upon target binding to assemble an active Cas13a complex and activate its trans-cleavage activity. By integrating a dual-UUU site DNA switch template and a T7 RNA polymerase-mediated signal amplification module, a "processing-assembly-amplification" cycle is constructed to enhance the detection signal. Through validation using various targets including miRNA, mRNA, and viral DNA, the PRA-Cas13a system not only achieves an attomolar (aM) level detection limit but also enables visual field detection within 10 min using a lateral flow test strip. Analysis of single-base mutations demonstrated that its sensitivity is significantly superior to conventional CRISPR-based methods. Moreover, the system successfully enabled accurate detection of survivin mRNA in different cell lines and HPV16 in clinical cervical swab samples, showing strong concordance with qPCR gold standard methods. The PRA-Cas13a strategy leverages intrinsic self-processing assembly and autocatalytic signal amplification, addresses the critical issue of off-target cleavage inherent in conventional Cas13a systems while expanding the range of applicable targets, and demonstrates high specificity and point-of-care testing potential in cancer and viral diagnostics.},
}

*Biosensing Techniques/methods
Humans
CRISPR-Cas Systems
Survivin/genetics
*CRISPR-Associated Proteins/genetics/metabolism
MicroRNAs/analysis/genetics
DNA, Viral/analysis/genetics
RNA, Messenger/analysis/genetics
DNA-Directed RNA Polymerases
Viral Proteins

@article {pmid41686483,
year = {2026},
author = {Tanaka, PP and Cotta-Almeida, V and Donadi, EA and Westerberg, L and Passos, GA},
title = {Distinct mutations in the autoimmune regulator gene differentially affect transcriptional and functional properties of medullary thymic epithelial cells.},
journal = {Human molecular genetics},
volume = {35},
number = {4},
pages = {},
doi = {10.1093/hmg/ddag004},
pmid = {41686483},
issn = {1460-2083},
support = {17/10780-4//São Paulo Research Foundation/ ; 311304/2021//National Council for Scientific and Technological Development/ ; 302060/2019-7//National Council for Scientific and Technological Development/ ; 88887.642780/2021-00//CAPES-STINT/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {AIRE Protein ; Animals ; *Epithelial Cells/metabolism/pathology ; Mice ; *Transcription Factors/genetics/metabolism ; *Mutation ; *Thymus Gland/metabolism/pathology ; *Polyendocrinopathies, Autoimmune/genetics/pathology/immunology ; Humans ; CRISPR-Cas Systems ; Gene Expression Regulation ; Transcription, Genetic ; },
abstract = {Autoimmune Polyendocrine Syndrome Type 1 (APS-1) is a rare monogenic disorder caused by mutations in the autoimmune regulator (AIRE) gene. Although AIRE is essential for central immune tolerance, how distinct APS-1-associated mutations differentially affect medullary thymic epithelial cell (mTEC) biology remains incompletely understood. Here, we investigated the molecular and functional consequences of three Aire/AIRE variants using complementary murine mTEC models. To define transcriptional effects, we performed single-cell RNA sequencing (scRNA-seq) on mTECs carrying a heterozygous genomic Aire c.735delG mutation generated by CRISPR-Cas9. This analysis revealed reduced transcriptional heterogeneity, decreased expression of tissue-restricted antigens (TRAs) mRNAs (including Col4a3, Col7a1, and Neto2), and downregulation of key mTEC lineage markers (Epcam, Cldn4, Krt14). Mutant cells also displayed altered expression of mRNAs involved in chemokine-mediated migration (Ccl25, Cxcl16), extracellular matrix and cell adhesion (Fn1, Lama5, Col4a1, Nectin1, Cdh1), and actin cytoskeleton organization (Gsn, Rac1, Wasl, Actn1), indicating broad disruption of pathways governing mTEC identity and cell-cell interactions. Guided by these findings, we assessed mutation-specific functional outcomes using a CRISPR-derived Aire functional knockout and lentiviral expression of the human AIRE missense variants p.G229W and p.C313Y in wild-type mTECs. Functional assays revealed mutation-dependent alterations in mTEC morphology, thymocyte migration, and adhesion, with the p.C313Y variant exerting the strongest effects. Together, these data demonstrate that heterozygous and missense AIRE mutations exert distinct yet convergent effects on mTEC transcriptional programs and cellular behavior, providing mechanistic insight into AIRE-dependent immune tolerance failure in APS-1.},
}

AIRE Protein
Animals
*Epithelial Cells/metabolism/pathology
Mice
*Transcription Factors/genetics/metabolism
*Mutation
*Thymus Gland/metabolism/pathology
*Polyendocrinopathies, Autoimmune/genetics/pathology/immunology
Humans
CRISPR-Cas Systems
Gene Expression Regulation
Transcription, Genetic

@article {pmid41686830,
year = {2026},
author = {Caluianu, M and Owen, KA},
title = {A VPS33B CRISPR knockout study: In vitro evidence of an adhesion defect.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0343240},
pmid = {41686830},
issn = {1932-6203},
mesh = {*Vesicular Transport Proteins/genetics/metabolism ; Humans ; *Cell Adhesion/genetics ; Gene Knockout Techniques ; CRISPR-Cas Systems ; Epithelial Cells/metabolism ; Cell Line ; *Kidney Tubules, Proximal/metabolism/cytology ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {VPS33B is a ubiquitously expressed regulator of vesicular membrane fusion and protein sorting involved in a broad range of cellular functions from organelle biogenesis to the establishment of apicobasal polarity. Loss-of-function mutations in VPS33B cause arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome, a rare autosomal recessive disorder with multi-organ involvement, including a characteristic proximal tubular dysfunction in the kidney. While VPS33B has been studied in several cell types, its role in proximal tubular epithelial cells remains poorly understood. To investigate its function, a proximal tubular cell line (RPTEC-TERT1) was CRISPR-edited to generate VPS33B knockout (KO) cells. These cells were characterised using brightfield imaging, immunostaining, RNA sequencing, and cell detachment assays, revealing a distinct 'peeling' phenotype and altered adhesion properties. Transcriptional profiling indicated changes in genes linked to cell adhesion. Together, these findings offer preliminary evidence that loss of VPS33B impairs cell-matrix attachment and reveal the first insights into the role of VPS33B within proximal tubular epithelial cells.},
}

*Vesicular Transport Proteins/genetics/metabolism
Humans
*Cell Adhesion/genetics
Gene Knockout Techniques
CRISPR-Cas Systems
Epithelial Cells/metabolism
Cell Line
*Kidney Tubules, Proximal/metabolism/cytology
*Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41686849,
year = {2026},
author = {Dueñas, E and Tirado, I and Huaihua, P and Parra Del Riego, A and Cabrera-Sosa, L and Nakamoto, JA and Cruz, M and Restrepo, CM and Arévalo, J and Adaui, V},
title = {LAMP-coupled CRISPR-Cas12a assays: A promising new tool for molecular diagnosis of leishmaniasis.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013456},
pmid = {41686849},
issn = {1935-2735},
mesh = {Humans ; *Molecular Diagnostic Techniques/methods ; *CRISPR-Cas Systems ; *Nucleic Acid Amplification Techniques/methods ; Sensitivity and Specificity ; DNA, Kinetoplast/genetics ; RNA, Ribosomal, 18S/genetics ; DNA, Protozoan/genetics ; *Leishmania/genetics/isolation & purification ; *Leishmaniasis/diagnosis/parasitology ; *Leishmaniasis, Cutaneous/diagnosis/parasitology ; Leishmania braziliensis/genetics/isolation & purification ; },
abstract = {BACKGROUND: Tegumentary leishmaniasis is a parasitic disease endemic in the Americas. Its clinical management and control rely on early and accurate diagnosis and adequate treatment. PCR-based molecular diagnostics offer high sensitivity and specificity over microscopy or culture but are less accessible in low-resource settings. New molecular tools for detecting Leishmania infections are needed in rural endemic regions. A promising tool harnessing CRISPR-Cas technology enables highly specific and sensitive detection of nucleic acid targets, offering an exciting potential for portable molecular diagnostics. Previously, we developed CRISPR-Cas12a-based assays coupled to PCR preamplification for Leishmania detection. Here, we adapted our assays, which target the multicopy 18S rDNA and kinetoplast DNA (kDNA) minicircles, by replacing PCR with loop-mediated isothermal amplification (LAMP).

LAMP-coupled CRISPR assays were optimized for fluorescence-based and lateral flow readouts. The assays could detect as low as 0.2 genome equivalents per reaction using L. braziliensis M2904 strain genomic DNA. The kDNA assay reliably detected all tested species of the L. (Viannia) subgenus, while the 18S assay showed pan-Leishmania detection capability. There was no cross-reactivity with other protozoan (Trypanosoma cruzi and Plasmodium falciparum) and bacterial (Mycobacterium tuberculosis) pathogen DNA, nor with human DNA. When applied to 90 clinical samples (skin lesions) from the Cusco region of Peru and compared to kDNA real-time PCR, LAMP-CRISPR assays with a fluorescence readout achieved a sensitivity of 90.9% (95% CI: 80.1-97.0%) for kDNA and 72.7% (95% CI: 59.0-83.9%) for 18S rDNA, both with 100% (95% CI: 90-100%) specificity. Overall, lateral flow strip results agreed with fluorescence-based detection in 18 tested samples, with one discrepancy observed in the 18S assay associated with low parasite load.

CONCLUSIONS/SIGNIFICANCE: These new proof-of-concept LAMP-CRISPR assays, combining high sensitivity, multiple Leishmania species detection capability, and a portable lateral flow readout, hold promise as next-generation molecular tools to improve leishmaniasis diagnosis and surveillance, supporting One Health strategies for disease control.},
}

Humans
*Molecular Diagnostic Techniques/methods
*CRISPR-Cas Systems
*Nucleic Acid Amplification Techniques/methods
Sensitivity and Specificity
DNA, Kinetoplast/genetics
RNA, Ribosomal, 18S/genetics
DNA, Protozoan/genetics
*Leishmania/genetics/isolation & purification
*Leishmaniasis/diagnosis/parasitology
*Leishmaniasis, Cutaneous/diagnosis/parasitology
Leishmania braziliensis/genetics/isolation & purification

@article {pmid41686883,
year = {2026},
author = {Rathod, BU and Rajyaguru, R and Dhawale, RN and Tomar, RS and Sharma, S and Chaskar, MG and Alsaidan, OA and Hajare, ST},
title = {CRISPR/Cas9-Mediated Editing in FAD2 Gene to Enhance Oil Quality in Soybean [Glycine max (L.) Merrill].},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0342660},
pmid = {41686883},
issn = {1932-6203},
mesh = {*Glycine max/genetics/metabolism ; *Gene Editing/methods ; *Fatty Acid Desaturases/genetics ; *CRISPR-Cas Systems/genetics ; *Soybean Oil/metabolism ; Plants, Genetically Modified/genetics ; Linoleic Acid/metabolism ; *Plant Proteins/genetics ; },
abstract = {Conventional soybean oil contains high levels of linoleic acid, which reduces oxidative stability and necessitates hydrogenation, leading to trans-fat formation. In this study, 40 Indian soybean genotypes were screened for fatty acid composition, and Gujarat Junagadh Soybean-3 (GJS-3) was selected for CRISPR/Cas9-mediated editing of the fatty acid desaturase-2 (FAD2) gene. Agrobacterium-mediated transformation produced 22 regenerated plants, of which 57.1% were PCR-positive for Cas9/sgRNA. Targeted single-nucleotide substitutions were confirmed by Sanger sequencing in three edited lines (T3, T7, and T15), corresponding to an editing efficiency of 13.63%. These lines exhibited a marked increase in oleic acid content (42-45%) compared with the wild type (22%) and a concomitant reduction in linoleic acid (30-32% vs. 54%), resulting in nearly a two-fold improvement in the oleic/linoleic acid ratio. PCR analysis confirmed the absence of Cas9 and U3 sequences, indicating transgene-free edited plants. This study provides the first evidence of CRISPR/Cas9-mediated FAD2 editing in an Indian soybean cultivar and demonstrates its effectiveness in improving oil quality, oxidative stability, and processing efficiency.},
}

*Glycine max/genetics/metabolism
*Gene Editing/methods
*Fatty Acid Desaturases/genetics
*CRISPR-Cas Systems/genetics
*Soybean Oil/metabolism
Plants, Genetically Modified/genetics
Linoleic Acid/metabolism
*Plant Proteins/genetics

@article {pmid41687699,
year = {2026},
author = {García, G and Shapiro, JB and Campbell, ZT},
title = {Efficient genetic perturbation of murine sensory neurons in vivo using CRISPR/Cas9.},
journal = {The journal of pain},
volume = {41},
number = {},
pages = {106217},
pmid = {41687699},
issn = {1528-8447},
support = {R01 NS114018/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; *Sensory Receptor Cells/metabolism ; Ganglia, Spinal/metabolism ; *CRISPR-Cas Systems/genetics ; Mice ; *TRPV Cation Channels/genetics/metabolism ; Mice, Transgenic ; NAV1.7 Voltage-Gated Sodium Channel/genetics/metabolism ; Hyperalgesia/genetics/chemically induced ; Sciatic Nerve/metabolism ; *Gene Editing/methods ; Capsaicin ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; },
abstract = {Gene editing using CRISPR/Cas9 in vivo offers a powerful tool to investigate pain mechanisms. We generated a conditional knock-in mouse model where Streptococcus pyogenes CRISPR-associated protein 9 (Cas9) expression is restricted to cells that express SCN9A. Transgenic markers were detected in key tissues including the dorsal root ganglia (DRG) and sciatic nerve. To assess in vivo editing efficacy, RNA guides targeting TRPV1 were intrathecally administered. Two injections of guide RNAs resulted in a significant reduction of TRPV1 in both the DRG and sciatic nerve without triggering caspase-3-mediated apoptosis or motor deficits. Edited animals exhibited increased withdrawal latencies to heat and reduced nocifensive behaviors following capsaicin injection. Capsaicin-evoked thermal hyperalgesia and mechanical allodynia were diminished. This approach enables rapid and efficient sensory neuron-specific CRISPR/Cas9 gene perturbations for pain research in mice. We envisage that this method can be employed both for the exploration of molecular mechanisms underlying nociception and for the validation of therapeutic targets associated with pain. PERSPECTIVE: There are tremendous opportunities afforded by facile multi-locus genome perturbation of sensory neurons in vivo. This model and approach enables rapid and low-cost genetic depletion experiments in mice.},
}

Animals
*Sensory Receptor Cells/metabolism
Ganglia, Spinal/metabolism
*CRISPR-Cas Systems/genetics
Mice
*TRPV Cation Channels/genetics/metabolism
Mice, Transgenic
NAV1.7 Voltage-Gated Sodium Channel/genetics/metabolism
Hyperalgesia/genetics/chemically induced
Sciatic Nerve/metabolism
*Gene Editing/methods
Capsaicin
Male
Disease Models, Animal
Mice, Inbred C57BL

@article {pmid41687992,
year = {2026},
author = {Bulle, M and Rahman, MM and Kota, S and Islam, MR and Keya, SS and Abbagani, S and Kirti, PB},
title = {Advancing chloroplast bioengineering: Innovations, regulatory challenges, and translational pathways for sustainable agriculture.},
journal = {International journal of biological macromolecules},
volume = {350},
number = {},
pages = {150873},
doi = {10.1016/j.ijbiomac.2026.150873},
pmid = {41687992},
issn = {1879-0003},
mesh = {*Chloroplasts/genetics/metabolism ; *Bioengineering/methods ; *Agriculture/methods ; *Crops, Agricultural/genetics ; },
abstract = {Escalating climate instability and rising global food demand necessitate the development of resilient crop systems underpinned by precise, predictable, and rapidly deployable genetic innovations. Chloroplast bioengineering has emerged as a vanguard strategy, offering a uniquely tractable platform characterized by the organelle's distinct plastome, discrete copy number, and predominantly maternal inheritance. Recent advances in plastid transformation and base editing now enable the high-fidelity, multiplex introduction of photosynthetic, osmoprotective, and redox-regulating pathways across diverse plant lineages. Controlled-environment and field-proximal trials demonstrate that chloroplast-engineered metabolic modules enhance CO2 assimilation, stabilize photochemistry under heat and drought stress, and improve osmotic buffering capacity. Beyond trait improvement, chloroplasts function as high-capacity production organelles capable of accumulating oral or mucosal biologics at levels that reduce reliance on cold-chain logistics. However, challenges such as species-level recalcitrance, prolonged timelines for achieving homoplasmy, and limited scalability of current plastid biomanufacturing pipelines continue to constrain broad agricultural and biopharmaceutical deployment. To overcome these barriers, we propose a standardized, empirically testable framework integrating optimized transformation workflows, quantitative trait benchmarking, multi-location field validation, and techno-economic analyses. This framework embeds long-term stewardship principles, including marker-free selection, proactive resistance management, and FAIR-aligned data transparency, while emphasizing equitable access pathways for resource-limited regions. Collectively, this work positions chloroplast engineering as a mechanistically grounded, field-ready platform poised to reshape crop resilience, sustainable bioproduction, and global biologic accessibility amid accelerating climate stress.},
}

*Chloroplasts/genetics/metabolism
*Bioengineering/methods
*Agriculture/methods
*Crops, Agricultural/genetics

@article {pmid41688137,
year = {2026},
author = {Mathew, AE and Arivarasan, VK},
title = {Cell-free systems for nanobiomaterials assembly.},
journal = {Progress in molecular biology and translational science},
volume = {219},
number = {},
pages = {189-210},
doi = {10.1016/bs.pmbts.2025.11.002},
pmid = {41688137},
issn = {1878-0814},
mesh = {Cell-Free System ; Humans ; Animals ; *Nanostructures/chemistry ; *Biocompatible Materials/chemistry ; },
abstract = {Nanobiomaterials-engineered constructs operating at the 1-100 nm scale-integrate biological macromolecules such as nucleic acids and proteins with synthetic polymers or inorganic nanocomponents to achieve programmable functionality in biomedical and industrial contexts. Representative systems, including DNA origami-based drug carriers, CRISPR-Cas delivery scaffolds, and artificial protein vesicles, demonstrate subcellular targeting precision exceeding 90 % and up to a fivefold enhancement in intratumoral drug accumulation relative to conventional nanocarriers. Despite these advances, in vivo nanomanufacturing remains constrained by cytotoxicity, intracellular metabolic load, and limited spatiotemporal control over synthetic parameters. Cell-free systems (CFS) mitigate these limitations by utilizing crude lysates from prokaryotic or eukaryotic cells that retain functional transcription-translation machinery while eliminating the constraints of cellular viability. Platforms such as the reconstituted PURE system enable high-throughput, template-directed synthesis of nanoscale architectures incorporating noncanonical elements, including synthetic polymers, fluorinated analogs, and unnatural amino acids. This open, tunable environment permits over fivefold increases in yields of cytotoxic or aggregation-prone peptides, accelerates DNA origami prototype fabrication to under 24 h, and supports assembly of hybrid enzyme-polymer conjugates with retained catalytic activity. Distinct CFS sources impart complementary advantages: bacterial extracts offer rapid, cost-effective protein expression; yeast lysates facilitate eukaryote-specific glycosylation for ligand-specific nanocapsules; and mammalian systems enable near-physiological post-translational modification essential for therapeutic nanobiomaterials. Coupling CFS with artificial intelligence-based design optimization and microfluidic automation now underpins a new paradigm of programmable, scalable nanobiomanufacturing. By decoupling molecular construction from living systems, cell-free biofabrication establishes a controllable, high-fidelity platform for the rational engineering of nano-bio hybrid systems in precision medicine, biosensing, and tissue regeneration.},
}

Cell-Free System
Humans
Animals
*Nanostructures/chemistry
*Biocompatible Materials/chemistry

@article {pmid41688147,
year = {2026},
author = {Mu, M and Melms, JC and Ho, P and Izar, B},
title = {Large-scale CRISPR-Cas9 screens to define regulators of immune checkpoints.},
journal = {Methods in cell biology},
volume = {202},
number = {},
pages = {117-132},
doi = {10.1016/bs.mcb.2025.10.011},
pmid = {41688147},
issn = {0091-679X},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; Flow Cytometry/methods ; *Melanoma/genetics/immunology/pathology ; *Immune Checkpoint Proteins/genetics ; Animals ; Cell Line, Tumor ; },
abstract = {Immune checkpoints, which have emerged as potent target for the treatment of a variety of cancers, are central to tumor immunobiology and deciphering their dynamic regulation will continue to enable therapeutic development. CRISPR-Cas9 screening has recently been leveraged as a powerful tool to systematically interrogate regulators of immune checkpoints. Here, we describe a framework for such screens coupled with fluorescence-activated cell sorting (FACS) as a reliable and direct method of isolating and comparing how specific CRISPR perturbations impact the expression and maintenance of immune checkpoints. This approach has provided critical insights into immune checkpoint regulation and interactions in melanoma models and can feasibly be expanded to other systems.},
}

*CRISPR-Cas Systems/genetics
Humans
Flow Cytometry/methods
*Melanoma/genetics/immunology/pathology
*Immune Checkpoint Proteins/genetics
Animals
Cell Line, Tumor

@article {pmid41688767,
year = {2026},
author = {Mansi, M and Danai, P},
title = {The emerging impact of CRISPR and gene editing on global crop improvement.},
journal = {Transgenic research},
volume = {35},
number = {1},
pages = {8},
pmid = {41688767},
issn = {1573-9368},
mesh = {*Gene Editing/methods ; *Crops, Agricultural/genetics/growth & development ; *CRISPR-Cas Systems/genetics ; *Plants, Genetically Modified/genetics/growth & development ; Genome, Plant ; },
abstract = {The advent of CRISPR-based genome editing has revolutionized crop improvement, offering unprecedented precision and efficiency in modifying key agronomic traits. This review comprehensively examines the mechanisms, applications, and future potential of CRISPR technology in enhancing global crop production. CRISPR-Cas systems, originally identified as adaptive immune mechanisms in bacteria and archaea, have been repurposed for targeted genome editing in plants. The CRISPR-Cas9 system, in particular, has emerged as a powerful tool for introducing site-specific double-strand breaks, enabling precise genetic modifications. The three-stage process of adaptation, expression, and interference underlies the CRISPR mechanism, with guide RNAs directing Cas endonucleases to specific genomic loci. Advances in CRISPR technology have expanded its applications beyond gene knockouts, encompassing base editing, prime editing, and epigenome editing. These innovations have facilitated the development of crops with enhanced yield, stress tolerance, disease resistance, nutritional content, and post-harvest quality. However, challenges related to off-target effects, regulatory hurdles, ethical concerns, and public acceptance must be addressed to fully harness the potential of CRISPR in agriculture. Integration of CRISPR with other cutting-edge technologies, such as synthetic biology, artificial intelligence, and high-throughput phenotyping, holds immense promise for accelerating crop improvement efforts. As research continues to refine CRISPR tools and expand their applicability across diverse plant species, this transformative technology is poised to play a pivotal role in shaping a sustainable, resilient, and productive global food system for future generations.},
}

*Gene Editing/methods
*Crops, Agricultural/genetics/growth & development
*CRISPR-Cas Systems/genetics
*Plants, Genetically Modified/genetics/growth & development
Genome, Plant

@article {pmid41689002,
year = {2026},
author = {Zhong, X and Gong, X and Zeng, N and Xie, T and Wang, S and Xia, Q},
title = {Programmable hooded DNA switches for conditional control of CRISPR/Cas12a in multiplexed biosensing.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {41689002},
issn = {1477-3155},
mesh = {*CRISPR-Cas Systems/genetics ; *Biosensing Techniques/methods ; Humans ; MicroRNAs/analysis/genetics ; *DNA/chemistry/genetics ; CRISPR-Associated Proteins/metabolism/genetics ; Bacterial Proteins ; Endodeoxyribonucleases ; },
abstract = {The CRISPR/Cas system has become an indispensable tool for programmable and accurate biosensing, with its performance critically dependent on precise activity control. While most regulatory strategies have focused on engineering Cas proteins or modifying CRISPR RNAs, relatively little attention has been given to the design of substrate probes. Here, we systematically characterize the trans-cleavage activity of split CRISPR/Cas12a on structured substrates and leverage this insight to engineer a tunable "Hooded" probe with switchable properties. This probe architecture confers protection against trans-cleavage, and its activity can be progressively modulated by varying the probe length. Utilizing this design, we constructed a multiplexed logic-gated detection platform for direct and simultaneous analysis of miRNA and PSA, which demonstrated high sensitivity and specificity. Furthermore, we validated the robust performance of this system for logic-operated imaging in diverse cellular models, confirming its reliability in complex biological settings. Overall, our Hooded probe strategy not only broadens the applicability of CRISPR/Cas12a in molecular diagnostics, but also provides a novel design principle for the multiplexed biosensing.},
}

*CRISPR-Cas Systems/genetics
*Biosensing Techniques/methods
Humans
MicroRNAs/analysis/genetics
*DNA/chemistry/genetics
CRISPR-Associated Proteins/metabolism/genetics
Bacterial Proteins
Endodeoxyribonucleases

@article {pmid41689014,
year = {2026},
author = {Lou, C and Wang, J and Dai, C and Wang, J and Yang, J and Fang, Y and Jiang, H and Pan, X and Li, H and Lan, C and Xu, G and Iqbal, S and Bao, J and Cai, L and Zheng, W},
title = {Engineered Cas9 exosome vesicles as a novel gene editing tool for targeted ASPN editing in osteoarthritis.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {165},
pmid = {41689014},
issn = {1477-3155},
support = {LQ24H060008//Basic Public Welfare Research Program of Zhejiang Province/ ; 2025HY0585//Zhejiang Medicine Health Science and Technology Program/ ; GY20250280//Wenzhou Science and Technology Plan Project/ ; },
mesh = {*Osteoarthritis/genetics/therapy ; *Gene Editing/methods ; *Exosomes/metabolism/genetics/chemistry ; Animals ; *CRISPR-Cas Systems/genetics ; Chondrocytes/metabolism ; Humans ; *CRISPR-Associated Protein 9/metabolism/genetics ; Mice ; Male ; Mesenchymal Stem Cells/metabolism ; },
abstract = {CRISPR-Cas9, an innovative genome-editing technique, holds immense promise in therapeutic applications; nevertheless, the lack of effective delivery methods for in vivo gene editing limits its utility in osteoarthritis (OA) treatment. Recently, exosomes, naturally derived nanosized vesicles secreted by cells, have attracted significant attention as potential vehicles for therapeutic cargo delivery. This study proposes a bioinspired engineered exosome-mediated CRISPR/Cas9 delivery platform for targeted editing of the Asporin (ASPN) gene as a potential precision therapy for OA. Specifically, chondrocyte affinity peptide (Cap)-modified MSC-derived exosomes were employed as natural, biocompatible carriers to deliver CRISPR/Cas9 components specifically to OA-affected chondrocytes, thereby achieving precise and efficient ASPN knockout. Flow cytometry analysis confirmed a modification efficiency of 79.1% for Cap, while the encapsulation efficiency of the ASPN-Cas9 plasmid into exosomes reached 9.5% ± 0.6%. Both in vivo and in vitro investigations revealed that this delivery approach markedly improved cellular uptake and gene-editing efficacy, achieving a substantial reduction of ASPN expression by 61.7%. This, in turn, alleviated ferroptosis, improved mitochondrial function, reduced chondrocyte senescence, inhibited inflammation, and enhanced the cartilage microenvironment. Altogether, these findings strongly suggest the promising therapeutic efficacy of this method in OA models, emphasizing its potential as a precise gene-targeting therapeutic intervention for OA.},
}

*Osteoarthritis/genetics/therapy
*Gene Editing/methods
*Exosomes/metabolism/genetics/chemistry
Animals
*CRISPR-Cas Systems/genetics
Chondrocytes/metabolism
Humans
*CRISPR-Associated Protein 9/metabolism/genetics
Mice
Male
Mesenchymal Stem Cells/metabolism

@article {pmid41690121,
year = {2026},
author = {Yin, B and Wu, X and Zhou, H and Meng, Y and Liu, J and Ding, L and Zhu, C and Tai, Z and Zhu, Q and Chen, Z},
title = {Topical ionic liquid-mediated GLUT1 gene editing ameliorates psoriasis and prevents recurrence.},
journal = {Biomaterials},
volume = {330},
number = {},
pages = {124058},
doi = {10.1016/j.biomaterials.2026.124058},
pmid = {41690121},
issn = {1878-5905},
mesh = {Animals ; *Gene Editing/methods ; *Psoriasis/therapy/genetics/pathology ; *Glucose Transporter Type 1/genetics ; Mice ; *Ionic Liquids/chemistry/administration & dosage ; Humans ; CRISPR-Cas Systems/genetics ; Recurrence ; Mice, Inbred C57BL ; Keratinocytes/metabolism ; Disease Models, Animal ; Administration, Topical ; },
abstract = {Psoriasis is a chronic inflammatory skin disorder characterized by immune dysregulation and a high relapse rate. Current therapies seldom achieve lasting remission. Aberrant overexpression of glucose transporter 1 (GLUT1) in keratinocytes enhances glycolysis, fueling inflammation and immune imbalance, thus positioning GLUT1 as a promising therapeutic target. In this work, a composite ionic liquid-mediated transdermal platform was established for the delivery of CRISPR-Cas9 ribonucleoprotein (CIL-RNP), aiming to achieve efficient GLUT1 gene editing in keratinocytes. The CIL-RNP achieved 76.6% editing efficiency, downregulated pyruvate kinase M (PKM) expression, and reduced inflammatory cytokine secretion. In a psoriasis mouse model, topical administration of CIL-RNP decreased lesion severity by 50% PASI (Psoriasis Area and Severity Index) score, alleviating epidermal hyperplasia and immune infiltration. Furthermore, the treatment inhibited M1 macrophage polarization, reduced reactive oxygen species generation, rebalanced Th17/regulatory T cells (Tregs) responses, and diminished the accumulation of tissue-resident memory T cells (TRMs), thereby lowering the risk of relapse. This study establishes ionic liquid-based CRISPR-RNP transdermal editing of GLUT1 as a novel and effective strategy for restoring immune homeostasis in psoriasis, with potential for long-term remission and broader applications in cutaneous immunopathological conditions.},
}

Animals
*Gene Editing/methods
*Psoriasis/therapy/genetics/pathology
*Glucose Transporter Type 1/genetics
Mice
*Ionic Liquids/chemistry/administration & dosage
Humans
CRISPR-Cas Systems/genetics
Recurrence
Mice, Inbred C57BL
Keratinocytes/metabolism
Disease Models, Animal
Administration, Topical

@article {pmid41690142,
year = {2026},
author = {Huang, Z and Ding, Y and Xu, H and Zhang, Q and Wang, X and Ding, H and Zhang, J and Wang, Y and Wang, Y and Jiao, P},
title = {Development of an RT-ERA-CRISPR/Cas12a assay for duck Tembusu virus.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106612},
pmid = {41690142},
issn = {1525-3171},
mesh = {Animals ; *Ducks ; *Flavivirus/isolation & purification/genetics ; *Poultry Diseases/virology/diagnosis ; *Flavivirus Infections/veterinary/diagnosis/virology ; *CRISPR-Cas Systems ; Sensitivity and Specificity ; *Nucleic Acid Amplification Techniques/veterinary/methods ; China ; },
abstract = {Duck Tembusu virus (DTMUV) has continued to threaten the duck industry in China since 2010. Therefore, the establishment of a rapid, specific, and sensitive method for the field detection of DTMUV is urgently needed. Herein, a reverse transcription enzymatic recombinase amplification (RT-ERA) assay was combined with the CRISPR/Cas12a system to target the DTMUV C gene. This assay exhibited high specificity, effectively distinguishing DTMUV from other common avian viruses. Its limit of detection reached 1 copy/μL DTMUV RNA. Moreover, this assay can be completed at 42 °C within 15 min using a thermostatic water bath. Additionally, we tested 30 clinical samples from infected ducks using this assay, and the results showed 100% concordance with SYBR green quantitative PCR results. In summary, this rapid, specific, and sensitive assay shows promising potential for DTMUV detection in the field.},
}

Animals
*Ducks
*Flavivirus/isolation & purification/genetics
*Poultry Diseases/virology/diagnosis
*Flavivirus Infections/veterinary/diagnosis/virology
*CRISPR-Cas Systems
Sensitivity and Specificity
*Nucleic Acid Amplification Techniques/veterinary/methods
China

@article {pmid41690159,
year = {2026},
author = {Ha, E and Shin, D and Ryu, S and Kong, M},
title = {Deciphering the role of endolysin LysCPD7 harboring C. perfringens spore binding domain.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128474},
doi = {10.1016/j.micres.2026.128474},
pmid = {41690159},
issn = {1618-0623},
mesh = {*Clostridium perfringens/virology/drug effects/physiology ; *Endopeptidases/genetics/metabolism/pharmacology/chemistry ; *Spores, Bacterial/drug effects/metabolism ; *Bacteriophages/enzymology/genetics ; Animals ; Milk/microbiology ; Protein Domains ; *Viral Proteins/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Cell Wall/metabolism ; Mutation ; },
abstract = {Due to their potent bactericidal activity, phage-derived endolysins are considered promising alternatives to conventional antibiotics. Although some endolysins from phages infecting spore-forming bacteria contain a spore binding domain (SBD), their biological function remains unclear. LysCPD7, an endolysin from the Clostridium perfringens phage CPD7, showed high antimicrobial activity, effectively reducing C. perfringens contamination in milk and beef broth. Fluorescence assays and immunogold electron microscopy showed that LysCPD7 lacks a C-terminal cell wall binding domain, but contains a SBD that localizes to the spore cortex layer. We found that an E187K mutation in the SBD resulted in reduced spore binding capacity while retaining lytic activity. Infection with the wild-type CPD7 led to a decrease in sporulation efficiency in C. perfringens, whereas the mutant CPD7 carrying the E187K substitution in the SBD had no impact on sporulation, suggesting that the SBD may play a role in the inhibition of sporulation in C. perfringens. Our findings could contribute to the rational design of effective antimicrobials or diagnostic tools for controlling C. perfringens and provide new insights into the interactions between phages and their spore-forming hosts.},
}

*Clostridium perfringens/virology/drug effects/physiology
*Endopeptidases/genetics/metabolism/pharmacology/chemistry
*Spores, Bacterial/drug effects/metabolism
*Bacteriophages/enzymology/genetics
Animals
Milk/microbiology
Protein Domains
*Viral Proteins/genetics/metabolism
Anti-Bacterial Agents/pharmacology
Cell Wall/metabolism
Mutation

@article {pmid41690735,
year = {2026},
author = {Li, G and Su, Z and Li, F and Liu, J and Shi, Y and Chen, J and Wang, P and Wang, R},
title = {Advances in rapid on-site detection techniques for food safety and authenticity.},
journal = {Advances in food and nutrition research},
volume = {118},
number = {},
pages = {43-87},
doi = {10.1016/bs.afnr.2025.08.004},
pmid = {41690735},
issn = {1043-4526},
mesh = {*Food Safety/methods ; *Food Contamination/analysis ; Biosensing Techniques/methods ; *Food Analysis/methods ; Humans ; Food Microbiology ; },
abstract = {Ensuring food safety and authenticity is a pressing global concern. This chapter provides a comprehensive overview of advanced rapid, on-site detection technologies targeting foodborne hazards, including pathogens, toxins, chemical contaminants, and authenticity issues such as adulteration and species fraud. Key aspects of these technologies include signal amplification strategies like catalytic hairpin assembly (CHA) and nanozyme-enhanced systems, as well as signal output platforms encompassing colorimetric, electrochemical, and fluorescence-based methods. The chapter also explores the emerging role of nanopore-based sensing as a novel signal output platform, emphasizing its single-molecule precision and broad applicability. By integrating laboratory innovations with practical field applications, this chapter underscores the potential of these technologies to address challenges in food safety and authenticity monitoring effectively.},
}

*Food Safety/methods
*Food Contamination/analysis
Biosensing Techniques/methods
*Food Analysis/methods
Humans
Food Microbiology

@article {pmid41691189,
year = {2026},
author = {Lv, J and Geng, L and Shi, W and Li, C and Wang, S and Zhang, B and Yu, K and Cui, R and Liu, Y and Xiong, F and Lv, J and Dong, S and Barco, B and Xu, J},
title = {Enhancing heritable genome editing in soybean by optimizing promoter combinations for the LbCas12a system.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41691189},
issn = {1471-2229},
abstract = {UNLABELLED: The CRISPR-Cas system, adapted from prokaryotic immune mechanisms, enables programmable DNA targeting and editing. Recent advancements include base editors and prime editors, expanding genetic research applications. The LbCas12a (Cpf1) system offers unique advantages, including simplified operation and multiplex editing, yet achieving stable heritable edits in soybean remains challenging due to its complex paleo-tetraploid genome and transformation constraints. Here we optimized promoter combinations for the LbCas12a editing system to maximize both editing efficiency in the initial (E0) generation and the frequency of homozygous or biallelic mutants in the subsequent (E1) generation. We identified prAtHSP70-1 (At5G02500), prAtEF1αA4 (At5G60390), and prGmUbi1 (Glyma.10G251900) as an effective promoter set, and demonstrated that LbCas12a–crRNA accumulation needs to exceed a defined threshold to achieve efficient target cleavage. These findings provide a practical strategy for enhancing heritable genome editing in soybean and may be broadly applicable to other crops.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08336-w.},
}

@article {pmid41691442,
year = {2026},
author = {Thevendran, R and Maheswaran, S},
title = {Molecular Genetics as the Leading-Edge Approach in Driving the Development of Live Attenuated Vaccines.},
journal = {Biotechnology journal},
volume = {21},
number = {2},
pages = {e70185},
doi = {10.1002/biot.70185},
pmid = {41691442},
issn = {1860-7314},
support = {//MOHE/ ; },
mesh = {*Vaccines, Attenuated/genetics/immunology ; Humans ; *Vaccine Development/methods ; Gene Editing ; *Molecular Biology/methods ; Animals ; CRISPR-Cas Systems ; Biotechnology ; },
abstract = {Molecular genetics has propelled advancements in scientific instrumentation, yielding transformative discoveries from CRISPR-mediated gene editing and detailed protein identification to sophisticated biosensor fabrications. This profound shift has also reshaped the landscape of live attenuated vaccine (LAV) development in contrast to conventional methods. Here we explore how modern molecular strategies have superseded previous empirical approaches, moving toward deliberate genetic modifications that both enhance and balance the aspects of LAV safety, stability, and potent immunogenicity. By detailing the transition from classical approaches to targeted, molecular-driven attenuation, our work reviews how advanced genetic methods address historical limitations and expand the potential for vaccine design. Hence, the current paper bridges the gap between foundational vaccine practices and cutting-edge biotechnology, offering a comprehensive perspective on the progression of molecular genetic strategies on LAV development and its future trajectory. The paper also elaborates on the key challenges of raising LAVs to clinical standards while describing in tandem the genetic approaches to overcome the limitations. Critical performance factors governing the LAV market and clinical deployment, alongside the pivotal role of artificial intelligence in refining LAV rational design, are also further discussed.},
}

*Vaccines, Attenuated/genetics/immunology
Humans
*Vaccine Development/methods
Gene Editing
*Molecular Biology/methods
Animals
CRISPR-Cas Systems
Biotechnology

@article {pmid41691452,
year = {2026},
author = {Li, T and Zeng, F and Zhang, J and Zhang, Y and Yin, W},
title = {Reversing Antibiotic Resistance: Strategies From Adjuvants to Innovative Therapeutics.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70233},
pmid = {41691452},
issn = {2045-8827},
support = {H2024201044//Natural Science Foundation of Hebei Province/ ; 20231560//The Medical Scientific Research of Hebei Health Commission/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/therapeutic use ; Humans ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/drug effects/genetics ; Gene Editing ; *Bacterial Infections/drug therapy/microbiology ; CRISPR-Cas Systems ; Photochemotherapy ; Nanotechnology ; },
abstract = {The escalating prevalence of antibiotic resistance has become a major threat to the effectiveness of conventional antibiotics. Meanwhile, the development of novel antibiotics faces substantial challenges, including lengthy research cycles, high costs, and the rapid emergence of bacterial tolerance, making it difficult for new drugs to keep pace with bacterial evolution. In this context, molecular reversal strategies targeting antibiotic resistance genes have emerged as a promising avenue to overcome this impasse. Among them, the use of antibiotic adjuvants, agents that enhance the efficacy of existing antibiotics by inhibiting resistance gene function, preventing their horizontal transfer or modulating host defense has gained considerable attention. Furthermore, innovative approaches such as CRISPR-Cas gene editing, photodynamic therapy, nanotechnology, and ecological competition strategies have shown great potential in reversing antimicrobial resistance. Collectively, these strategies offer novel insights into addressing the global crisis of antibiotic resistance, paving the way for more effective clinical interventions and ensuring the sustained efficacy of current antibiotic therapies.},
}

*Anti-Bacterial Agents/pharmacology/therapeutic use
Humans
*Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/drug effects/genetics
Gene Editing
*Bacterial Infections/drug therapy/microbiology
CRISPR-Cas Systems
Photochemotherapy
Nanotechnology

@article {pmid41691970,
year = {2026},
author = {Anders, M and Hoppe, S and Eberl, H and Rebs, S and Seedorf, A and Maurer, W and Schill, T and Zibat, A and Unsöld, JK and Yigit, G and Wollnik, B and Vollmann, D and Sossalla, S and Streckfuss-Bömeke, K},
title = {Generation of pluripotent stem cell line (IPWi001-A) and a corresponding CRISPR/Cas9 modified isogenic rescue control (IPWi001-A-1) from a patient with arrhythmia-induced cardiomyopathy harboring a KCNQ1 truncating mutation.},
journal = {Stem cell research},
volume = {92},
number = {},
pages = {103921},
doi = {10.1016/j.scr.2026.103921},
pmid = {41691970},
issn = {1876-7753},
mesh = {Humans ; *KCNQ1 Potassium Channel/genetics/metabolism ; *CRISPR-Cas Systems/genetics ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Arrhythmias, Cardiac/genetics/complications/pathology ; *Cardiomyopathies/genetics/pathology ; *Mutation/genetics ; Cell Line ; Myocytes, Cardiac/metabolism ; Cell Differentiation ; Male ; },
abstract = {KCNQ1 functions as a slow rectifying potassium channel during the repolarization of the cardiac action potential, with mutations causing long-QT syndrome 1 and arrhythmias. A genetic link between KCNQ1 mutations and arrhythmia-induced cardiomyopathy (AIC) has not been identified, and the underlying pathways remain elusive. We generated human induced pluripotent stem cells (hiPSCs) from an AIC patient harboring the heterozygous truncating mutation p.W15* in KCNQ1 and corrected the mutation to wildtype using CRISPR/Cas9. The hiPSCs retained full pluripotency, genomic integrity, and differentiation ability. They were differentiated into hiPSC-cardiomyocytes (hiPSC-CM), establishing a patient-specific model to explore potential genetic connections to AIC.},
}

Humans
*KCNQ1 Potassium Channel/genetics/metabolism
*CRISPR-Cas Systems/genetics
*Induced Pluripotent Stem Cells/metabolism/cytology
*Arrhythmias, Cardiac/genetics/complications/pathology
*Cardiomyopathies/genetics/pathology
*Mutation/genetics
Cell Line
Myocytes, Cardiac/metabolism
Cell Differentiation
Male

@article {pmid41692169,
year = {2026},
author = {Hu, Y and Wang, Y and Wang, S and Jiao, Y and Tao, R and Yao, S},
title = {Reporter-based screening identifies small-molecule CBL0137 as an enhancer of CRISPR cytosine base editor and prime editor via p53 activation and NF-κB inhibition.},
journal = {New biotechnology},
volume = {93},
number = {},
pages = {54-74},
doi = {10.1016/j.nbt.2026.02.002},
pmid = {41692169},
issn = {1876-4347},
mesh = {*Gene Editing ; *CRISPR-Cas Systems/genetics ; *Cytosine/metabolism ; HEK293 Cells ; Tumor Suppressor Protein p53/metabolism ; *NF-kappa B/antagonists & inhibitors ; Humans ; },
abstract = {Recently developed CRISPR base editors (BEs) and prime editors (PEs) enable precise genome editing without inducing double-strand breaks, making them highly promising tools for therapeutic applications. However, their efficiency remains a major barrier to clinical translation, particularly at difficult-to-target sites. To address this limitation, we used a high-throughput GFP reporter system responsive to cytosine base editor (CBE) activity to screen small molecules involved in DNA damage response, cell cycle, and apoptosis pathways. This screen identified CBL0137 as a candidate that significantly enhanced editing efficiency at both the reporter and endogenous target sites, with up to an 80 % improvement. Mechanistic studies revealed that CBL0137 acts through activation of the p53 pathway and inhibition of NF-κB. Interestingly, the enhancement was largely specific to CBEs, while in PEs, CBL0137 selectively improved multi-site mutations and fragment insertions without affecting single-point edits or deletions. Collectively, these results identify CBL0137 as a selective enhancer of specific genome editing activities, providing a strategy to increase editing efficiency and advancing the translational potential of next-generation genome editing tools for therapeutic applications.},
}

*Gene Editing
*CRISPR-Cas Systems/genetics
*Cytosine/metabolism
HEK293 Cells
Tumor Suppressor Protein p53/metabolism
*NF-kappa B/antagonists & inhibitors
Humans

@article {pmid41693124,
year = {2026},
author = {Xin, W and Tang, Z and Wang, S and Song, ZL and Luo, X},
title = {Scaffold-Proximal DNA Extensions Enhance Cas12a Trans-cleavage for Direct and Broad-Scope Nucleic Acid Detection.},
journal = {Analytical chemistry},
volume = {98},
number = {8},
pages = {6149-6162},
doi = {10.1021/acs.analchem.5c07125},
pmid = {41693124},
issn = {1520-6882},
mesh = {*CRISPR-Associated Proteins/metabolism/chemistry ; CRISPR-Cas Systems ; *DNA/chemistry/metabolism/genetics ; *MicroRNAs/analysis/genetics ; Humans ; *Endodeoxyribonucleases/metabolism/genetics ; Polymorphism, Single Nucleotide ; *RNA, Messenger/analysis ; *Bacterial Proteins/metabolism ; },
abstract = {The CRISPR/Cas12a system has revolutionized nucleic acid diagnostics, but its direct application for RNA detection remains constrained by the requisite reverse transcription step, insufficient sensitivity, and poor compatibility across diverse RNA targets such as microRNAs (miRNAs), long mRNAs, and single nucleotide polymorphisms (SNPs). Here, we introduce a rationally engineered DNA activator architecture that markedly enhances Cas12a trans-cleavage activity and expands its analytical utility. A key mechanistic finding is the strong positional dependence of activator extensions: appending an overhang specifically at the scaffold-proximal end of the DNA activator (termed Proximal-Extended Activator, PEA) potently boosts Cas12a activation through ribonucleoprotein (RNP) stabilization, whereas distal extensions are inhibitory due to steric hindrance of essential interdomain motions. This optimized PEA system facilitates direct, amplification-free RNA detection, achieving exceptional sensitivity with detection limits of 1.3 fM for miRNA and 93 fM for mRNA, all without reverse transcription. Furthermore, a Split-PEA format confers exceptional discriminatory power for SNPs, enabling robust identification of the EGFR T790 M mutation at a 0.1% allelic frequency. This work establishes a facile and versatile platform where simple sequence modification enables highly sensitive and specific analysis of a broad range of nucleic acid targets, effectively overcoming a significant hurdle in CRISPR-based diagnostics.},
}

*CRISPR-Associated Proteins/metabolism/chemistry
CRISPR-Cas Systems
*DNA/chemistry/metabolism/genetics
*MicroRNAs/analysis/genetics
Humans
*Endodeoxyribonucleases/metabolism/genetics
Polymorphism, Single Nucleotide
*RNA, Messenger/analysis
*Bacterial Proteins/metabolism

@article {pmid41693245,
year = {2026},
author = {Kou, S and Chua, LC and Tan, JQ and Lau, OS},
title = {Stomatal XVE: an inducible system for cell-stage-specific gene expression and editing in the stomatal lineage.},
journal = {The New phytologist},
volume = {250},
number = {2},
pages = {1330-1347},
pmid = {41693245},
issn = {1469-8137},
support = {NRF-CRP22-2019-0001//National Research Foundation Singapore/ ; },
mesh = {*Plant Stomata/genetics/cytology ; *Arabidopsis/genetics/cytology ; *Gene Expression Regulation, Plant/drug effects ; *Gene Editing/methods ; *Cell Lineage/genetics ; Arabidopsis Proteins/metabolism/genetics ; Promoter Regions, Genetic/genetics ; CRISPR-Cas Systems/genetics ; Plants, Genetically Modified ; Phenotype ; },
abstract = {Stomatal development has emerged as a valuable model for studying developmental processes. Examining gene function along the stomatal lineage often requires gene perturbation in a controlled and cell-stage-specific manner, but this remains tedious without a dedicated genetic tool. Here, we describe Stomatal XVE, a modular, two-component XVE-based inducible system that enables user-controlled gene overexpression and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based knockout at defined stomatal cell stages in Arabidopsis thaliana. The system consists of a collection of estrogen-responsive XVE driver lines under cell-stage-specific promoters and effector vectors responsive to activated XVE. This design simplifies cloning and allows users to scale their investigation. We validated the cell-stage specificity and inducibility of the XVE driver lines and characterized key induction parameters. To test the system functionally, we employed it to study MAPKKK YODA and a pathogen effector AvrPtoB. While YODA overexpression reproduced known early- and late-stage phenotypes, stage-specific knockouts argued against its late-stage role in guard cell (GC) differentiation. Furthermore, AvrPtoB expression during later stages triggered striking disruptions in GC morphology and viability, revealing cell-type-specific effects of the pathogen protein. Overall, our Stomatal XVE system enables precise functional analysis of genes across defined stages of stomatal development and is particularly well suited for investigating genes with pleiotropic effects.},
}

*Plant Stomata/genetics/cytology
*Arabidopsis/genetics/cytology
*Gene Expression Regulation, Plant/drug effects
*Gene Editing/methods
*Cell Lineage/genetics
Arabidopsis Proteins/metabolism/genetics
Promoter Regions, Genetic/genetics
CRISPR-Cas Systems/genetics
Plants, Genetically Modified
Phenotype

@article {pmid41693565,
year = {2026},
author = {Sinnott, RW and Solanki, A and Govind, AP and Green, WN and Dickinson, BC},
title = {Engineering a human-based translational activator for targeted protein expression restoration.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
pmid = {41693565},
issn = {1362-4962},
support = {R01-EB035016/NH/NIH HHS/United States ; FP106237//G. Harold and Leila Y. Mathers Charitable Foundation/ ; //Bank of America/ ; DGE-2022294368//National Science Foundation/ ; //Dr. Ralph and Marian Falk Medical Research Trust/ ; R01 EB035016/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; *Protein Biosynthesis ; *Epilepsies, Myoclonic/genetics/therapy ; Disease Models, Animal ; RNA, Messenger/genetics/metabolism ; *NAV1.1 Voltage-Gated Sodium Channel/genetics/metabolism ; CRISPR-Cas Systems ; *Protein Engineering/methods ; Haploinsufficiency ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {Therapeutic modalities to programmably increase protein production are in critical need to address diseases caused by deficient gene expression via haploinsufficiency. Restoring physiological protein levels by increasing translation of their cognate messenger RNA (mRNA) would be an advantageous approach to correct gene expression but has not been evaluated in an in vivo disease model. Here, we investigated whether a translational activator could improve phenotype in a Dravet syndrome mouse model, a severe developmental and epileptic encephalopathy caused by SCN1a haploinsufficiency, by increasing translation of the SCN1a mRNA. We identify and engineer human proteins capable of increasing mRNA translation using the CRISPR-Cas-inspired RNA-targeting system (CIRTS) platform to enable programmable, guide RNA-directed translational activation with entirely engineered human proteins. We identify a compact (601 amino acid) CIRTS translational activator (CIRTS-4GT3) that can drive targeted, sustained translation increases up to 100% from three endogenous transcripts relevant to epilepsy and neurodevelopmental disorders. AAV-delivery of CIRTS-4GT3 targeting SCN1a mRNA to a Dravet syndrome mouse model led to increased SCN1a translation and improved survivability and seizure threshold-key phenotypic indicators of Dravet syndrome. This work validates a strategy to address SCN1a haploinsufficiency and emphasizes the preclinical potential of targeted translational activation to address neurological haploinsufficiency.},
}

Animals
Humans
Mice
*Protein Biosynthesis
*Epilepsies, Myoclonic/genetics/therapy
Disease Models, Animal
RNA, Messenger/genetics/metabolism
*NAV1.1 Voltage-Gated Sodium Channel/genetics/metabolism
CRISPR-Cas Systems
*Protein Engineering/methods
Haploinsufficiency
RNA, Guide, CRISPR-Cas Systems/genetics

@article {pmid41695711,
year = {2026},
author = {Browne, TS and Edgell, DR and Gloor, GB},
title = {Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20706},
pmid = {41695711},
issn = {2167-8359},
mesh = {*Deep Learning ; *RNA, Guide, CRISPR-Cas Systems/genetics ; *CRISPR-Cas Systems ; Escherichia coli/genetics ; *CRISPR-Associated Protein 9/genetics/metabolism ; *Gene Editing/methods ; },
abstract = {The Cas9 enzyme along with a single guide RNA molecule is a modular tool for genetic engineering and has shown effectiveness as a species-specific antimicrobial. The ability to accurately predict on-target cleavage is critical as activity varies by target. Using the sgRNA nucleotide sequence and an activity score, predictive models have been developed with the best performance resulting from deep learning architectures. Prior work has emphasized robust and novel architectures to improve predictive performance. Here, we explore the impact of a data-centric approach through optimization of the input target site adjacent nucleotide sequence length and the use of data filtering for read counts in the control conditions to improve input data utility. Using the existing crisprHAL architecture, we develop crisprHAL Tev, a bacterial SpCas9 prediction model with performance that generalizes across related species and across data types. During this process, we also rebuilt two prior Escherichia coli Cas9 datasets, demonstrating the importance of data quality, and resulting in the production of an improved bacterial eSpCas9 prediction model. The crisprHAL models are available through GitHub: https://github.com/tbrowne5/crisprHAL.},
}

*Deep Learning
*RNA, Guide, CRISPR-Cas Systems/genetics
*CRISPR-Cas Systems
Escherichia coli/genetics
*CRISPR-Associated Protein 9/genetics/metabolism
*Gene Editing/methods

@article {pmid41696049,
year = {2026},
author = {Ahmadzadeh, M and Akbarian, F and Sanati, MH and Motaharirad, H and Farrokhi, F},
title = {Computational Optimization of CRISPR-Cas13a sgRNAs Targeting the SARS-CoV-2 Spike Gene for SHERLOCK-Based Diagnostics.},
journal = {Evolutionary bioinformatics online},
volume = {22},
number = {},
pages = {11769343251414318},
pmid = {41696049},
issn = {1176-9343},
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global health crisis, emphasizing the urgent need for accurate and rapid diagnostic tools. Modern molecular biology technologies, including CRISPR-Cas systems, provide highly efficient strategies for viral detection. Bioinformatic pipelines are essential for identifying conserved genomic regions and enabling rational single-guide RNA (sgRNA) design.

METHODS: This study aimed to design specific sgRNAs targeting the spike gene of SARS-CoV-2 isolates from Iranian patients using the SHERLOCK diagnostic platform. Complete genomes of the RefSeq virus and 470 SARS-CoV-2 isolates, representing all variants of concern (VOCs) detected in Iran, were retrieved from the NCBI and GISAID databases. Multiple sequence alignment with ClustalW identified conserved sequences within the receptor-binding domain (RBD) that differ from the RBD of SARS-CoV and MERS-CoV RefSeq genomes. Based on these regions, sgRNAs and isothermal amplification primers were designed using ADAPT, OLIGO7, and the UCSC Genome Browser to maximize diagnostic sensitivity and specificity. Secondary and tertiary structures of sgRNA-target complexes were analyzed via RNAfold and RNAup to select the most efficient sgRNA-amplicon combination.

RESULTS: Twenty-two-nucleotide sgRNA candidates were initially selected based on sequence alignment, showing high similarity to the SARS-CoV-2 RefSeq and low homology to SARS-CoV and MERS-CoV genomes. Analyses of secondary structures, RNA-RNA interactions, and free energy identified 6 sgRNAs with favorable 2-dimensional conformations and strong interaction profiles. Among these, the sgRNA1-Amplicon2 sequence exhibited the most stable 3-dimensional structure and a molecular docking score of -309.67, indicating high sensitivity and specificity for viral detection.

CONCLUSION: This study successfully designed an sgRNA with high sensitivity and specificity for rapid SARS-CoV-2 detection using the CRISPR-Cas13a system, informed by genomic analysis of Iranian isolates. The proposed approach provides an efficient framework for the rapid design and deployment of CRISPR-based diagnostic tools applicable to diverse viral pathogens.},
}

@article {pmid41699287,
year = {2026},
author = {Pindi, C and Palermo, G},
title = {Computation and deep-learning-driven advances in CRISPR genome editing.},
journal = {Nature structural & molecular biology},
volume = {33},
number = {2},
pages = {203-214},
pmid = {41699287},
issn = {1545-9985},
mesh = {*Deep Learning ; *Gene Editing/methods ; *CRISPR-Cas Systems ; Humans ; Neural Networks, Computer ; Algorithms ; },
abstract = {Genome editing with CRISPR-Cas systems is revolutionizing medicine, molecular biology and biotechnology. In this Review, we discuss the contributions of deep learning-based structure prediction algorithms, physics-based simulations, neural networks, graph neural networks and generative models, including diffusion and large language models, in engineering and optimizing CRISPR systems and in understanding their mechanistic basis. We highlight the challenges and limitations to the transformative effects of computational modeling and tools in the context of the development of programmable genome editors for biomedicine and biotechnology.},
}

*Deep Learning
*Gene Editing/methods
*CRISPR-Cas Systems
Humans
Neural Networks, Computer
Algorithms

@article {pmid41699288,
year = {2026},
author = {Hu, C and Tai, H and Zhu, R and Shu, Z and Guo, G and Ma, D and Zuo, S and Tang, L and Zeng, Z},
title = {CRISPR-Cas9 screening identifies ATOX1-driven cisplatin resistance mechanisms in liver cancer and evaluates targeted inhibitor efficacy.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41699288},
issn = {2399-3642},
mesh = {*Cisplatin/pharmacology ; Humans ; *Drug Resistance, Neoplasm/genetics ; *Liver Neoplasms/drug therapy/genetics/metabolism/pathology ; *CRISPR-Cas Systems ; *Antineoplastic Agents/pharmacology ; Animals ; Cell Line, Tumor ; Mice ; *Copper Transport Proteins/genetics/antagonists & inhibitors/metabolism ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Male ; Receptor, Notch1/genetics/metabolism ; },
abstract = {Liver cancer treatment with cisplatin is often hindered by drug resistance. This study aimed to identify key genes associated with cisplatin resistance in liver cancer and develop targeted inhibitors. Using genome-wide CRISPR-Cas9 screening, ATOX1 was identified as a critical gene for cisplatin resistance. ATOX1 was highly expressed in liver cancer tissues and associated with poor prognosis. Knockdown of ATOX1 in liver cancer cells enhanced cisplatin sensitivity in vitro and in vivo. Molecular dynamics simulation and virtual screening identified compound 8 as a potent ATOX1 inhibitor with high affinity (Kd = 12.5 μM) and exhibited synergistic effects with cisplatin on liver cancer cell growth. Mechanistically, compound 8 inhibits the activity of ATOX1, leading to intracellular copper accumulation. The elevated copper levels subsequently promote increased DNA methylation at the NOTCH1 promoter, resulting in suppression of the NOTCH1/HES1 signaling pathway and enhancing the sensitivity of liver cancer cells to cisplatin. In conclusion, ATOX1 is crucial for cisplatin resistance in liver cancer and linked to poor prognosis. Targeting ATOX1 with compound 8 may be a novel therapeutic strategy for overcoming cisplatin resistance.},
}

*Cisplatin/pharmacology
Humans
*Drug Resistance, Neoplasm/genetics
*Liver Neoplasms/drug therapy/genetics/metabolism/pathology
*CRISPR-Cas Systems
*Antineoplastic Agents/pharmacology
Animals
Cell Line, Tumor
Mice
*Copper Transport Proteins/genetics/antagonists & inhibitors/metabolism
Female
Gene Expression Regulation, Neoplastic/drug effects
Male
Receptor, Notch1/genetics/metabolism

@article {pmid41699368,
year = {2026},
author = {Khalid, M and Ishaq, A and Arshad, M and Kaul, H and Majeed, M},
title = {Multiplex CRISPR/Cas9 editing of gliotoxin biosynthesis genes in Aspergillus fumigatus reduces pathogenicity in broilers.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {55},
pmid = {41699368},
issn = {1678-4405},
support = {13224/2020//Higher Education Commision, Pakistan/ ; },
mesh = {Animals ; *Aspergillus fumigatus/genetics/pathogenicity/metabolism ; *Gliotoxin/biosynthesis ; Chickens ; *CRISPR-Cas Systems ; *Gene Editing ; *Aspergillosis/veterinary/microbiology/pathology ; *Poultry Diseases/microbiology/pathology ; Virulence ; Fungal Proteins/genetics/metabolism ; Spores, Fungal/genetics ; },
abstract = {Gliotoxin of Aspergillus fumigatus has been extensively studied for its role in pathogenesis in animals and humans. It triggers pathogenesis by its immunosuppressive and cytotoxic effects. Biosynthetic gene cluster (BGC) consisting of 13 genes regulates its biosynthesis. We targeted gliZ, gliP and gliA genes of this BGC using CRISPR/Cas9 system in a multigene editing approach to check the pathogenesis in broilers. crRNAs were designed using EuPaGDT and 3 single guide RNAs (sgRNA) were commercially synthesized. Each sgRNA was combined with Cas9 to form ribonucleoprotein complexes which were then used for simultaneously transfecting fungal protoplasts. Thin-layer chromatography showed the absence of gliotoxin on silica plate and DNA sequencing showed various indels in target genes. These indels caused amino acid substitutions in all three gene products but, the gliP mutation, since it was synonymous, was likely not functionally relevant. Regenerated protoplasts were matured to form fungal hyphae and spore production was induced. These spores were inoculated intra-air sac in broiler chicks. During one-week infection trial, birds infected with the wild-type spores (group 1) showed morbidity and their mortality rate was 30%. Birds inoculated with RNP-treated spores (group 2) showed mild clinical signs and no mortality. No morbidity or mortality was recorded in birds in negative control group (group 3). Histopathological analysis of lungs showed necrosis and congestion, and presence of mixed population of inflammatory cells in wild-type infected birds, while no such lesions were seen in birds infected with RNP-treated spores. These results show that multigene editing approach was successful in creating indels simultaneously in 3 gliotoxin genes which resulted in amino acid substitution which negatively impacted gliotoxin biosynthesis and export. In vivo experiment results show that RNP-treated fungal spores were unable to cause A. fumigatus pathogenicity in broiler. Targeting gliotoxin biosynthesis could thus be a promising approach to develop antifungal therapy.},
}

Animals
*Aspergillus fumigatus/genetics/pathogenicity/metabolism
*Gliotoxin/biosynthesis
Chickens
*CRISPR-Cas Systems
*Gene Editing
*Aspergillosis/veterinary/microbiology/pathology
*Poultry Diseases/microbiology/pathology
Virulence
Fungal Proteins/genetics/metabolism
Spores, Fungal/genetics

@article {pmid41700332,
year = {2026},
author = {Huang, Y and Zhao, Z and Li, J and Wang, X and Qu, H and Zheng, Y},
title = {An aptamer-CRISPR/Cas12a biosensor for rapid and sensitive detection of florfenicol.},
journal = {Analytical methods : advancing methods and applications},
volume = {18},
number = {9},
pages = {1910-1916},
doi = {10.1039/d5ay01903f},
pmid = {41700332},
issn = {1759-9679},
mesh = {*Biosensing Techniques/methods ; *Thiamphenicol/analogs & derivatives/analysis ; *Aptamers, Nucleotide/chemistry/genetics ; *CRISPR-Cas Systems ; *Anti-Bacterial Agents/analysis ; Limit of Detection ; Animals ; Food Contamination/analysis ; },
abstract = {Florfenicol (FF), a broad-spectrum antibacterial agent widely used in livestock and poultry farming, has raised significant food safety concerns due to the accumulation of its residues in animal-derived products (e.g., eggs), posing potential threats to human health. Herein, we developed a novel aptamer-CRISPR/Cas12a biosensor for the rapid and sensitive detection of FF. The biosensor employs streptavidin-modified magnetic beads (SA-MBs) as a solid carrier to achieve efficient enrichment of FF-specific aptamers (APT), while integrating the dual advantages of the APT's high-specificity target recognition and the CRISPR/Cas12a system's powerful signal amplification capability. The detection mechanism is based on a competitive displacement: APT pre-hybridizes with its complementary strand (APT-c) to form stable duplexes. The presence of FF triggers the release of APT-c from APT, and the liberated APT-c then activates the trans-cleavage activity of the CRISPR/Cas12a system. This process converts the small-molecule FF into a CRISPR/Cas12a-detectable nucleic acid signal and enables quantitative FF detection. Under optimized conditions, the biosensor demonstrated a linear detection range of 10 nM to 100 µM for FF (R[2] = 0.9907) and a limit of detection (LOD) of 1.41 nM. The accuracy and practicality were confirmed through spiked recovery experiments in egg samples, yielding recoveries between 97.1% and 100.8%. Furthermore, the modular design of this platform allows its easy adaptation for detecting other antibiotics simply by replacing the specific APT and its corresponding APT-c, highlighting its considerable potential for broad applications in food safety monitoring.},
}

*Biosensing Techniques/methods
*Thiamphenicol/analogs & derivatives/analysis
*Aptamers, Nucleotide/chemistry/genetics
*CRISPR-Cas Systems
*Anti-Bacterial Agents/analysis
Limit of Detection
Animals
Food Contamination/analysis

@article {pmid41700547,
year = {2026},
author = {Su, T and Zhu, D and Li, X and Qu, Z and Li, F and Zhao, D and Shao, G and Feng, Z and Su, S and Chao, J and Zuo, X and Fan, C and Wang, L},
title = {Accelerated CRISPR/Cas12a-Based Point-of-Care Diagnostics Through Critical Coupling Distance Control.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {38},
number = {16},
pages = {e23381},
doi = {10.1002/adma.202523381},
pmid = {41700547},
issn = {1521-4095},
support = {62071251//National Natural Science Foundation of China/ ; 62235008//National Natural Science Foundation of China/ ; 62227803//National Natural Science Foundation of China/ ; 62288102//National Natural Science Foundation of China/ ; BK20212012//Natural Science Foundation of Jiangsu Province-Major Project/ ; BZ2022011//"Belt and Road" Innovation Cooperation Project of Jiangsu/ ; SKT2306//Project of State Key Laboratory of Transducer Technology/ ; GZR2022010026//Project of State Key Laboratory of Organic Electronics and Information Displays, Nanjing University of Posts and Telecommunications/ ; BK20243057//Basic Research Program of Jiangsu/ ; BK20253006//Basic Research Program of Jiangsu/ ; },
mesh = {*CRISPR-Cas Systems ; *Point-of-Care Systems ; *Endodeoxyribonucleases/metabolism/genetics ; *Bacterial Proteins/metabolism ; *CRISPR-Associated Proteins/metabolism ; DNA/chemistry ; Humans ; },
abstract = {Prompt pathogen detection in resource-limited settings remains constrained by energy-intensive instrumentation and a shortage of trained personnel. The CRISPR/Cas12a-based diagnostic technology, despite its robustness as a promising tool, is constrained by suboptimal detection speed and sensitivity. Here we designed triblock DNA-mediated spherical nucleic acids (tSNA) that acts as a spatially confined reporter with critical coupling distances between substrates, enabling Cas12a protein to rapidly identify concentrated and stretched single-stranded substrates with size-matching intervals. Precise control of distances on tSNA of varying sizes revealed a direct correlation between trans-cleavage efficiency and coupling distance, indicating that only when the distance exceeds the protein size can it offer an appropriate reaction space. It demonstrates a rapid "scooting" reaction model on tSNA, resulting in a trans-cleavage rate of 10 nm A30-tSNA 12 times faster and a sensitivity that is two orders of magnitude higher than that in bulk solution. Furthermore, tSNA can serve as a novel recognition and colorimetric element in lateral-flow strips, thereby reducing the detection time for pathogen nucleic acids to just 3 min. This "size-matching" model of tSNA offers a new perspective on the regulation of Cas12a enzymatic activity, establishing a versatile platform to advance diagnostic development through ultrafast, CRISPR-powered POC systems.},
}

*CRISPR-Cas Systems
*Point-of-Care Systems
*Endodeoxyribonucleases/metabolism/genetics
*Bacterial Proteins/metabolism
*CRISPR-Associated Proteins/metabolism
DNA/chemistry
Humans

@article {pmid41700779,
year = {2026},
author = {Alberio, V and Savy, V and Felipe, MY and Fernandez-Martín, R and Salamone, DF},
title = {Simultaneous CRISPR-on activation of TFAP2C and SMARCA4 promotes development of trophoblast-fate cells in bovine embryos†.},
journal = {Biology of reproduction},
volume = {114},
number = {5},
pages = {1598-1609},
doi = {10.1093/biolre/ioag041},
pmid = {41700779},
issn = {1529-7268},
support = {PICT 2018-04632//ANPCyT from the Ministry of Science and Technology, Argentina/ ; },
mesh = {Animals ; *Trophoblasts/physiology/metabolism/cytology ; Cattle/embryology ; *Transcription Factor AP-2/genetics/metabolism ; Gene Expression Regulation, Developmental ; Female ; *Embryonic Development/genetics ; *Transcription Factors/genetics/metabolism ; *DNA Helicases/genetics/metabolism ; Cell Differentiation/genetics ; *Nuclear Proteins/genetics/metabolism ; Embryo, Mammalian ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Pregnancy ; },
abstract = {Assisted reproductive techniques are widely used to produce domestic animal embryos for commercial or research purposes. In cattle, abnormal trophoblast cell differentiation during embryo development causes pregnancy and placentation failures. The CRISPR-on system has been successfully used in bovine embryos to individually activate early trophoblast lineage genes TFAP2C and SMARCA4. This study evaluates the effect of CRISPR-on activation of early and advanced trophoblast-related genes in bovine zygotes to promote trophectoderm differentiation. In one experiment, RNA was microinjected to simultaneously activate TFAP2C and SMARCA4; in another, circular DNA was microinjected to induce CDX2 or GATA3 expression separately. Controls included groups without small guide RNAs (sgRNAs, SHAM) and non-injected embryos (IVF). RNA microinjection transiently and simultaneously increased TFAP2C, SMARCA4, and downstream gene expression, producing a prolonged effect beyond individual gene activation. This led to a significant increase in trophectoderm cells at the blastocyst stage. Individual activation of CDX2 and GATA3 was effective, also inducing upstream genes without altering trophectoderm cell percentages. Neither RNA nor DNA microinjection affected blastocyst production compared to IVF. This work demonstrates the successful increase of trophoblast cells in bovine embryos using CRISPR-on, offering a useful strategy for IVF or SCNT embryos. The CRISPR-dCas9VP160 system may also aid understanding of trophoblast lineage signaling during development.},
}

Animals
*Trophoblasts/physiology/metabolism/cytology
Cattle/embryology
*Transcription Factor AP-2/genetics/metabolism
Gene Expression Regulation, Developmental
Female
*Embryonic Development/genetics
*Transcription Factors/genetics/metabolism
*DNA Helicases/genetics/metabolism
Cell Differentiation/genetics
*Nuclear Proteins/genetics/metabolism
Embryo, Mammalian
*CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
Pregnancy

@article {pmid41702027,
year = {2026},
author = {Galdikaite-Braziene, E and Krušnauskas, R and Henderson, E and Bujakowska, KM},
title = {CRISPR as a therapeutic tool for inherited retinal degenerations: Advances, challenges, and future directions.},
journal = {Molecular aspects of medicine},
volume = {108},
number = {},
pages = {101462},
doi = {10.1016/j.mam.2026.101462},
pmid = {41702027},
issn = {1872-9452},
mesh = {Humans ; *Gene Editing/methods ; *CRISPR-Cas Systems ; *Genetic Therapy/methods ; *Retinal Degeneration/therapy/genetics ; Animals ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Inherited retinal diseases (IRDs) are a genetically diverse group of disorders characterized by progressive photoreceptor degeneration, leading to vision loss and blindness. With over 320 associated genes and significant phenotypic variability, effective treatment remains challenging. Recent advances in genome editing, particularly CRISPR/Cas-based technologies, have revolutionized therapeutic approaches by enabling precise and customizable DNA and RNA editing. This review explores the application of various CRISPR strategies-such as gene knockout via non-homologous end joining (NHEJ), exon skipping using dual-sgRNAs, homology-directed repair (HDR), base editing (BE), prime editing (PE), RNA editing with Cas13, and epigenetic modulation through CRISPRa/i-in preclinical models of IRDs. Emphasis is placed on allele-specific targeting, gene-agnostic approaches, and mutation-independent strategies to address dominant and recessive forms of disease. We also highlight recent clinical milestones, including the first human trial using CRISPR gene editing for CEP290-associated Leber congenital amaurosis. Finally, we discuss critical challenges, including delivery constraints, immune responses, and off-target effects, along with emerging solutions such as engineered Cas variants, split-intein systems, and advanced off-target detection methods. Together, these advances underscore the transformative potential of CRISPR technologies in treating IRDs and lay the foundation for future clinical translation.},
}

Humans
*Gene Editing/methods
*CRISPR-Cas Systems
*Genetic Therapy/methods
*Retinal Degeneration/therapy/genetics
Animals
*Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41702192,
year = {2026},
author = {Lu, L and Zhang, Y and Liu, B and Zhou, N and Yu, DJ and Wang, Y},
title = {Magnetic Fe3O4-Au@UIO-66-NH2@toehold probe mediated fluorescent sensor for detecting ovarian cancer-specific circRNA coupled with hybridization chain reaction and the CRISPR-Cas12a system.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118535},
doi = {10.1016/j.bios.2026.118535},
pmid = {41702192},
issn = {1873-4235},
mesh = {Humans ; CRISPR-Cas Systems/genetics ; *RNA, Circular/genetics/isolation & purification ; *Biosensing Techniques/methods ; Female ; *Ovarian Neoplasms/genetics/diagnosis ; Gold/chemistry ; Fluorescent Dyes/chemistry ; Nucleic Acid Hybridization ; Limit of Detection ; Magnetite Nanoparticles/chemistry ; Ferrosoferric Oxide/chemistry ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {Circular RNAs (circRNAs) represent an emerging family of noncoding transcripts defined by closed-loop architecture, which are now established as key participants in the etiology of tumorigenesis and malignant progression. While circRNAs show potential as therapeutic targets and biomarkers, the accurate detection of circRNAs remains challenging due to interference from homologous linear RNAs. In this study, an ultrasensitive method for detecting circ_0051240 based on the sulfhydrated toehold capture probe-initiator assembly-mediated hybridization chain reaction (HCR) and the CRISPR-Cas12a system was developed. The capture probe (with a toehold domain)-initiator strand duplex was ingeniously fabricated to identify the back-splice junction (BSJ) of circRNA. After magnetic enrichment and separation by the Fe3O4-Au@UIO-66-NH2 nanocomposite, the initiator strand (H0) was delivered to trigger HCR. The HCR product dsDNA concatemers contained multiply repeated CRISPR-targetable DNA sites that were readily recognized by the CRISPR RNA (crRNA). This specific recognition and binding activated the CRISPR-Cas12a system's collateral endonuclease activity, leading to cleavage of the fluorophore-quencher (FQ) reporters and fluorescence emission at a characteristic wavelength. This design eliminated linear RNA-related interference and enhanced the detection of fluorescence intensity (FI). Under optimal conditions, the proposed HCR/CRISPR-Cas12a method exhibited a wide quantitative measurement range spanning from 45 pM up to 180 nM, achieving a notable limit of detection (LOD) of 0.03 pM. In this study, a novel circRNA sensing strategy capable of accurate and highly sensitive quantification of ovarian cancer-specific circRNA was reported. The proposed method exhibits acceptable performance when compared to present approaches.},
}

Humans
CRISPR-Cas Systems/genetics
*RNA, Circular/genetics/isolation & purification
*Biosensing Techniques/methods
Female
*Ovarian Neoplasms/genetics/diagnosis
Gold/chemistry
Fluorescent Dyes/chemistry
Nucleic Acid Hybridization
Limit of Detection
Magnetite Nanoparticles/chemistry
Ferrosoferric Oxide/chemistry
Bacterial Proteins
Endodeoxyribonucleases
CRISPR-Associated Proteins

@article {pmid41702403,
year = {2026},
author = {Gaizauskaite, U and Tamulaitiene, G and Silanskas, A and Gasiunas, G and Siksnys, V and Sasnauskas, G},
title = {Structural insights into Cas9-mediated prespacer selection in CRISPR-Cas adaptation.},
journal = {Molecular cell},
volume = {86},
number = {5},
pages = {791-804.e9},
doi = {10.1016/j.molcel.2026.01.022},
pmid = {41702403},
issn = {1097-4164},
mesh = {*CRISPR-Cas Systems/genetics ; Cryoelectron Microscopy ; *Streptococcus thermophilus/genetics/enzymology ; *CRISPR-Associated Protein 9/genetics/chemistry/metabolism/ultrastructure ; *Bacterial Proteins/genetics/chemistry/metabolism/ultrastructure ; Models, Molecular ; CRISPR-Associated Proteins/genetics/chemistry/metabolism ; *DNA, Bacterial/genetics/metabolism/chemistry/ultrastructure ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Protein Conformation ; Gene Editing ; },
abstract = {During CRISPR-Cas adaptation, prokaryotic cells become immunized by the insertion of foreign DNA fragments, termed spacers, into the host genome to serve as templates for RNA-guided immunity. Spacer acquisition relies on the Cas1-Cas2 integrase and accessory proteins, which select DNA sequences flanked by the protospacer adjacent motif (PAM) and insert them into the CRISPR array. It has been shown that in type II-A systems, selection of PAM-proximal prespacers is mediated by the effector nuclease Cas9, which forms a "supercomplex" with the Cas1-Cas2 integrase and the Csn2 protein. Here, we present cryo-electron microscopy structures of the Streptococcus thermophilus type II-A prespacer selection supercomplex in the DNA-scanning and two distinct PAM-bound configurations, providing insights into the mechanism of Cas9-mediated prespacer selection in type II-A CRISPR-Cas systems. Repurposing Cas9 by the CRISPR adaptation machinery for prespacer selection, as characterized here, demonstrates Cas9 plasticity and expands our knowledge of Cas9 biology.},
}

*CRISPR-Cas Systems/genetics
Cryoelectron Microscopy
*Streptococcus thermophilus/genetics/enzymology
*CRISPR-Associated Protein 9/genetics/chemistry/metabolism/ultrastructure
*Bacterial Proteins/genetics/chemistry/metabolism/ultrastructure
Models, Molecular
CRISPR-Associated Proteins/genetics/chemistry/metabolism
*DNA, Bacterial/genetics/metabolism/chemistry/ultrastructure
*Clustered Regularly Interspaced Short Palindromic Repeats
Protein Conformation
Gene Editing

@article {pmid41702404,
year = {2026},
author = {Li, Z and Li, Y and Kong, J and Wu, Q and Huang, P and Zhang, Y and Wu, W and Chen, M and Liu, Y and Lin, H and Hou, L and Liu, G and Zeng, T and He, Y and Hu, C and Yang, Z and Lu, M and Luo, M and Xiao, Y},
title = {Structural basis for Cas9-directed spacer acquisition in type II-A CRISPR-Cas systems.},
journal = {Molecular cell},
volume = {86},
number = {5},
pages = {805-816.e4},
doi = {10.1016/j.molcel.2026.01.024},
pmid = {41702404},
issn = {1097-4164},
mesh = {*CRISPR-Cas Systems ; Cryoelectron Microscopy ; *CRISPR-Associated Proteins/genetics/chemistry/metabolism/ultrastructure ; *Enterococcus faecalis/genetics/enzymology ; *Bacterial Proteins/genetics/chemistry/metabolism/ultrastructure ; Models, Molecular ; *CRISPR-Associated Protein 9/chemistry/genetics/metabolism ; Protein Binding ; *DNA, Bacterial/genetics/metabolism/chemistry/ultrastructure ; Binding Sites ; Protein Conformation ; },
abstract = {CRISPR-Cas systems confer prokaryotic immunity by integrating foreign DNA (prespacers) into host arrays. Type II-A systems employ Cas9 for protospacer-adjacent motif (PAM) recognition and coordinate with Csn2 and the Cas1-Cas2 integrase during spacer acquisition, yet their structural basis remains unresolved. Here, we report cryo-electron microscopy (cryo-EM) structures of the Enterococcus faecalis Cas9-Csn2-Cas1-Cas2 supercomplex in apo and DNA-bound states. The apo state (Cas92-Csn28-Cas18-Cas24) is a resting complex, while DNA binding forms a prespacer-catching complex threading DNA through Csn2's channel, enabling Cas9 to interrogate the PAM sequence while sliding along the DNA. Cas9 and Csn2 jointly define a 30-bp DNA segment matching the prespacer length. Cas9 dissociation triggers structural reconfiguration of the Csn2-Cas1-Cas2 assembly. This exposes the PAM-proximal DNA, allowing Cas1-Cas2 to bind the exposed site for subsequent prespacer processing and directional integration. These findings reveal how Cas9, Csn2, and Cas1-Cas2 couple PAM recognition with prespacer selection, ensuring fidelity during adaptation.},
}

*CRISPR-Cas Systems
Cryoelectron Microscopy
*CRISPR-Associated Proteins/genetics/chemistry/metabolism/ultrastructure
*Enterococcus faecalis/genetics/enzymology
*Bacterial Proteins/genetics/chemistry/metabolism/ultrastructure
Models, Molecular
*CRISPR-Associated Protein 9/chemistry/genetics/metabolism
Protein Binding
*DNA, Bacterial/genetics/metabolism/chemistry/ultrastructure
Binding Sites
Protein Conformation

@article {pmid41702797,
year = {2026},
author = {Li, C and Mei, D and Cheng, H and Pan, X and Zhang, B},
title = {CRISPR genome editing in plants without tissue culture.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.12.017},
pmid = {41702797},
issn = {1879-3096},
abstract = {Conventional plant genome editing relies on tissue culture-mediated somatic cell regeneration, a technically demanding process that limits its application across diverse species. Emerging strategies now circumvent this bottleneck by enabling direct genome editing of meristematic or germline cells. Key advances include (i) genome editing via de novo meristem induction or dormant meristem activation; (ii) germline editing facilitated by graft-mobile tRNA-like sequence systems and haploid induction technologies; and (iii) optimized viral delivery platforms that exploit mobile RNA elements and compact editors such as TnpB to achieve efficient, transgene-free, heritable modifications across a broad range of genotypes and species. The development of robust, tissue culture-free editing platforms promises to revolutionize crop improvement pipelines and accelerate trait development for sustainable agriculture.},
}

@article {pmid41702943,
year = {2026},
author = {de Menezes, MN and Chen, AXY and Kulkarni, N and Sampurno, S and Saw, NYL and Yap, KM and Pérez-Núñez, I and Roth, S and Deguit, CDT and Haugen, B and Ramsbottom, KM and Munoz, I and Beavis, PA and Parish, IA},
title = {High efficiency CRISPR knock-in demonstrates that TCF1 is insufficient to reverse T cell exhaustion.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41702943},
issn = {2041-1723},
support = {MCRF21019//Victorian Cancer Agency (VCA)/ ; MCRF20011//Victorian Cancer Agency (VCA)/ ; Lloyd J. Old STAR Grant CRI5578//Cancer Research Institute (CRI)/ ; },
mesh = {Animals ; *Hepatocyte Nuclear Factor 1-alpha/genetics/metabolism ; *Gene Knock-In Techniques/methods ; Mice ; *CD8-Positive T-Lymphocytes/immunology/metabolism/cytology ; Cell Differentiation ; Mice, Inbred C57BL ; CRISPR-Cas Systems ; *T Cell Transcription Factor 1/genetics/metabolism ; Mice, Transgenic ; *Clustered Regularly Interspaced Short Palindromic Repeats ; T-Cell Exhaustion ; },
abstract = {CD8[+] T cell exhaustion is a regulatory state triggered by chronic antigen stimulation in both cancer and persistent infection. The less differentiated stem-like sub-populations of exhausted T cells have been heavily studied given their importance to the efficacy of current immunotherapies. While the transcription factor TCF1 is both necessary and sufficient for formation and maintenance of these stem-like populations, it remains unclear whether TCF1 can actively de-differentiate more terminally exhausted subsets back into a stem-like state. To address this question, here we utilize and optimize a high efficiency CRISPR knock-in methodology, compatible with mouse in vivo exhaustion models, to engineer T cells that either constitutively over-express TCF1, or conditionally over-express TCF1 following differentiation of the cells into a CX3CR1[+] intermediate-exhausted state. Strikingly, we find that only constitutive, and not conditional, TCF1 over-expression can increase the size of the stem-like T cell pool. Thus, while TCF1 can slow stem-like T cell differentiation, it is insufficient to revert more differentiated cells back into a stem-like state.},
}

Animals
*Hepatocyte Nuclear Factor 1-alpha/genetics/metabolism
*Gene Knock-In Techniques/methods
Mice
*CD8-Positive T-Lymphocytes/immunology/metabolism/cytology
Cell Differentiation
Mice, Inbred C57BL
CRISPR-Cas Systems
*T Cell Transcription Factor 1/genetics/metabolism
Mice, Transgenic
*Clustered Regularly Interspaced Short Palindromic Repeats
T-Cell Exhaustion

@article {pmid41703314,
year = {2026},
author = {Rocha, DC and Omoregbee, MO and Luo, W and Fang, H and Ye, Q and Liu, Y and Li, G and Mascoveto, J and de Souza, AA and Coleman, G and Culver, JN and Qi, Y},
title = {Transgene-free genome editing in citrus and poplar meristem tissues via biolistic ribonucleoprotein delivery of CRISPR-Cas9.},
journal = {Plant cell reports},
volume = {45},
number = {3},
pages = {58},
pmid = {41703314},
issn = {1432-203X},
support = {2020/07045-3, 2021/03466-7, and 2023/09068-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; DE-SC0023011//U.S. Department of Energy/ ; IOS-2132693 and IOS-2428015//Directorate for Biological Sciences/ ; 2020-70029-33161, 2021-67013-34554, 2024-33522-42755//National Institute of Food and Agriculture/ ; MD-PSLA-24014//McIntire Stennis Forest Research Program/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; *Meristem/genetics ; *Ribonucleoproteins/genetics/metabolism ; *Populus/genetics ; *Citrus/genetics ; *Biolistics/methods ; Plants, Genetically Modified ; Transgenes/genetics ; },
abstract = {Biolistic particle bombardment was used to deliver CRISPR-Cas9 ribonucleoprotein complexes (RNP) into the shoot apical meristem tissue of citrus and axillary meristem tissue of poplar, generating directed mutations in target genes. The use of meristematic tissues offers a strategic approach to genome editing in woody species, especially those that are recalcitrant to conventional tissue culture, as these regions contain totipotent, highly regenerative cells capable of giving rise to whole plants. Here, we employed biolistic delivery of genome-editing reagents into theshoot apical meristem (SAM) of citrus and the axillary meristems (AXM) of poplar. The system was first validated using a GFP expression construct and subsequently applied for targeted genome editing. In citrus, edited plants were obtained at the CsNPR3 locus exclusively through the delivery of CRISPR/Cas9 ribonucleoproteins (RNPs), whereas plasmid-based vectors were unsuccessful. Similarly, genome editing in poplar was achieved using RNPs targeting the Pt4CL1 gene. Although chimeric events were detected, this approach provides a feasible and innovative framework for producing transgene-free edited perennial plants.},
}

*Gene Editing/methods
*CRISPR-Cas Systems/genetics
*Meristem/genetics
*Ribonucleoproteins/genetics/metabolism
*Populus/genetics
*Citrus/genetics
*Biolistics/methods
Plants, Genetically Modified
Transgenes/genetics

@article {pmid41704216,
year = {2026},
author = {Khweis, SA and Blackburn, MA and Perdigao, CC and Pierce, MO and Lewis, CR and Dunkle, JA},
title = {Cas10 residues lining the target RNA binding channel regulate interference by distinguishing cognate target RNA from mismatched targets.},
journal = {RNA biology},
volume = {23},
number = {1},
pages = {1-18},
pmid = {41704216},
issn = {1555-8584},
support = {R35 GM142966/GM/NIGMS NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; *CRISPR-Associated Proteins/metabolism/genetics/chemistry ; *Staphylococcus epidermidis/genetics/metabolism ; *RNA, Bacterial/metabolism/genetics ; Protein Binding ; *RNA-Binding Proteins/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics/chemistry ; Models, Molecular ; *RNA/metabolism/genetics ; Binding Sites ; Mutation ; },
abstract = {Type III CRISPR systems are defined by the presence of the Cas10 protein and are among the most abundant CRISPR systems in nature. Cas10 forms a complex with crRNA and several Cas proteins that surveils prokaryotic cells for foreign RNA molecules and when they are detected it activates a cascade of interference activities. The synthesis of the cyclic oligoadenylate signalling molecule by Cas10 is a key aspect of the interference cascade. Despite structures of the Cas10 complex bound to target RNAs, the molecular mechanism by which Cas10 senses the bound state to licence interference is lacking. We identified five residues in S. epidermidis Cas10, two in the Cas10 Palm2 domain and three in domain 4, that line the target RNA binding channel. We assessed the contribution of these residues to interference in the context of a cognate or mismatched target RNA. We found that the residues regulate whether a mismatched crRNA-target RNA duplex is able to activate interference in vivo. We purified two site-directed mutants of Cas10-Csm and show with in vitro cOA synthesis assays that they demonstrate enhanced discrimination of cognate versus mismatched target RNAs.},
}

*CRISPR-Cas Systems
*CRISPR-Associated Proteins/metabolism/genetics/chemistry
*Staphylococcus epidermidis/genetics/metabolism
*RNA, Bacterial/metabolism/genetics
Protein Binding
*RNA-Binding Proteins/metabolism/genetics
*Bacterial Proteins/metabolism/genetics/chemistry
Models, Molecular
*RNA/metabolism/genetics
Binding Sites
Mutation

@article {pmid41704956,
year = {2026},
author = {Wang, Y and Diao, Y and Zhang, T and Zhang, F and Wang, W},
title = {Sensitive, specific, and rapid on-site detection of calf diarrhea pathogens using the RPA-CRISPR/Cas 12a assay.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1734185},
pmid = {41704956},
issn = {2235-2988},
mesh = {Animals ; Cattle ; Sensitivity and Specificity ; *Diarrhea/veterinary/diagnosis/virology ; *CRISPR-Cas Systems ; *Cattle Diseases/diagnosis/virology/microbiology ; *Molecular Diagnostic Techniques/methods ; Diarrhea Viruses, Bovine Viral/isolation & purification/genetics ; *Nucleic Acid Amplification Techniques/methods ; Enterotoxigenic Escherichia coli/isolation & purification/genetics ; },
abstract = {Calf diarrhea is a common gastrointestinal disease that usually occurs within one month of birth. The disease causes the greatest economic losses to the cattle industry. Currently, a variety of diagnostic methods have been developed for calf diarrhea infections. However, existing methods are still unsatisfactory in terms of sensitivity, specificity, simplicity, cost, and speed.To provide a more sensitive, specific, simpler, and faster detection method, we recently developed an RPA-CRISPR/Cas12a assay that can detect BVDV, BCoV, BRV, and ETEC infections in cattle on-site. Testing for each pathogen is performed in a single test tube, without the need to open the tube in the middle, and can be completed in under 50 minutes.The RPA-CRISPR/Cas12a assay can detect BVDV, BCoV, BRV, and ETEC at concentrations of at least 10 copies/μL. The RPA-CRISPR/Cas12a assay does not produce false-positive results due to the presence of other pathogens. The sensitivity of BCoV, BRV, and ETEC in the RPA-CRISPR/Cas12a quadruple assay is equivalent to that of single qPCR. The sensitivity of BVDV in the quadruple assay is slightly lower than that of the single qPCR method.Due to its sensitivity, specificity, simplicity, and rapidity, the RPA-CRISPR/Cas12a assay is more practical for on-site detection of cattle diarrhea pathogens than any existing detection method.},
}

Animals
Cattle
Sensitivity and Specificity
*Diarrhea/veterinary/diagnosis/virology
*CRISPR-Cas Systems
*Cattle Diseases/diagnosis/virology/microbiology
*Molecular Diagnostic Techniques/methods
Diarrhea Viruses, Bovine Viral/isolation & purification/genetics
*Nucleic Acid Amplification Techniques/methods
Enterotoxigenic Escherichia coli/isolation & purification/genetics

@article {pmid41705235,
year = {2026},
author = {Li, Z and Ge, L and Yu, T and Lv, S and Fu, Q and Shi, H},
title = {Genome-wide CRISPR/Cas9 screening identifies host factors critical for antiviral defense against equine herpesvirus type 1.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1764863},
pmid = {41705235},
issn = {1664-3224},
mesh = {Animals ; *CRISPR-Cas Systems ; *Herpesvirus 1, Equid/physiology/immunology ; Virus Replication/genetics ; Cell Line ; *Host-Pathogen Interactions/genetics/immunology ; *Herpesviridae Infections/immunology/virology/genetics/veterinary ; Horses ; Gene Knockout Techniques ; *Horse Diseases/virology/immunology/genetics ; Genome-Wide Association Study ; },
abstract = {INTRODUCTION: Equine herpesvirus type 1 (EHV-1) is a major veterinary pathogen causing significant economic losses in the livestock industry. Despite its impact, effective vaccines and targeted antiviral strategies remain limited, largely due to an incomplete understanding of host factors regulating viral replication and pathogenesis.

METHODS: To systematically identify host genes essential for EHV-1 infection, we established a BHK-21 cell line stably expressing Cas9 and performed a genome-wide CRISPR/Cas9 knockout screen using a pooled lentiviral single-guide RNA library. Significantly enriched candidate genes from positive selection were validated by generating knockout cell lines. Viral replication and protein expression were assessed using quantitative polymerase chain reaction and Western blot analysis. Pathway enrichment and protein interaction network analyses were subsequently conducted.

RESULTS: Genome-wide CRISPR/Cas9 screening identified multiple host factors critical for EHV-1 replication. Pathway enrichment analysis revealed that these genes were involved in key cellular signaling and regulatory networks associated with viral infection. Functional validation demonstrated that knockout of selected host genes significantly suppressed EHV-1 replication and viral protein synthesis.

DISCUSSION: These findings highlight essential host determinants required for EHV-1 replication and suggest that targeting host factors may represent a promising strategy for antiviral intervention. This study provides a foundation for the development of host-directed immunotherapeutic and antiviral approaches against EHV-1 infection.},
}

Animals
*CRISPR-Cas Systems
*Herpesvirus 1, Equid/physiology/immunology
Virus Replication/genetics
Cell Line
*Host-Pathogen Interactions/genetics/immunology
*Herpesviridae Infections/immunology/virology/genetics/veterinary
Horses
Gene Knockout Techniques
*Horse Diseases/virology/immunology/genetics
Genome-Wide Association Study

@article {pmid41705504,
year = {2026},
author = {Sun, K and Wu, H},
title = {A highly-efficient isothermal nano-detection platform coupling CRISPR/Cas technology for detection of circRNA.},
journal = {The Analyst},
volume = {151},
number = {5},
pages = {1304-1309},
doi = {10.1039/d6an00107f},
pmid = {41705504},
issn = {1364-5528},
mesh = {Humans ; *Nucleic Acid Amplification Techniques/methods ; *CRISPR-Cas Systems ; *Triple Negative Breast Neoplasms/diagnosis/genetics ; *RNA, Circular/analysis/genetics ; Limit of Detection ; *Biomarkers, Tumor/genetics/analysis ; Female ; Bacterial Proteins/genetics ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {Triple-negative breast cancer (TNBC), an aggressive molecular subtype of breast cancer with poor prognosis, is characterized by a high rate of metastasis and proliferation, which makes early detection particularly challenging. Early diagnosis of TNBC through biomarkers and prompt development of treatment methods can lower its mortality rate. This work has designed a nano-detection platform for TNBC biomarker circRNA based on the CRISPR/Cas system and isothermal amplification strategy. Specifically, this detection system uses functional nucleic acid molecules for recognition of circCD44, as well as dual signal amplification using Klenow(3'-5'exo-) and Cas9n. Furthermore, it combines Cas12a and immunomagnetic beads for an extra signal boost and output. After confirming its feasibility and optimizing the conditions, the detection system achieved a 1.73-fold enhancement in sensitivity, offering a linear detection range of 1 pM to 100 nM, with the limit of detection lowered to 95.1 fM. It also showed good specificity through testing against 5 biomarkers. Therefore, this detection system provides a novel strategy for the early diagnosis of TNBC and other diseases.},
}

Humans
*Nucleic Acid Amplification Techniques/methods
*CRISPR-Cas Systems
*Triple Negative Breast Neoplasms/diagnosis/genetics
*RNA, Circular/analysis/genetics
Limit of Detection
*Biomarkers, Tumor/genetics/analysis
Female
Bacterial Proteins/genetics
Endodeoxyribonucleases
CRISPR-Associated Proteins

@article {pmid41705810,
year = {2026},
author = {Shin, K and Kim, ET},
title = {Viral genome editing methods and applications in the CRISPR era.},
journal = {Journal of virology},
volume = {100},
number = {3},
pages = {e0204825},
pmid = {41705810},
issn = {1098-5514},
support = {RS-2025-02223595//Korea Health Industry Development Institute/ ; RS-2025-25406739//Korea Health Industry Development Institute/ ; RS-2023-00270936//National Research Foundation of Korea/ ; RS-2024-00352590//National Research Foundation of Korea/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems ; Humans ; *Genome, Viral ; Herpesvirus 1, Human/genetics ; Cytomegalovirus/genetics ; *DNA Viruses/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {CRISPR-Cas systems have transformed viral genetics by enabling precise and efficient manipulation of large DNA virus genomes. This review provides a practical framework for applying CRISPR technology to herpesviruses and other large DNA viruses as an alternative and complement to traditional BAC recombination. Key considerations include nuclease choice; sgRNA design that minimizes cut-to-edit distance and prevents re-cutting; donor template configuration and homology arm length; and synchronized delivery of Cas complexes and donor DNA. Strategies to promote HDR efficiency, such as the use of small-molecule modulators, are also summarized. In addition, practical workflows for clone selection, genotypic validation, and phenotypic confirmation are summarized. Case studies in herpes simplex virus type 1 and human cytomegalovirus illustrate how optimized CRISPR designs achieve reproducible, scarless knock-ins and conditional gene manipulation at essential loci without complementing cell lines. Together, these approaches establish CRISPR as a flexible, scalable platform for functional genomics, antiviral target discovery, and translational virology, enabling direct editing of clinical isolates previously inaccessible with bacterial artificial chromosome-based methods.},
}

*Gene Editing/methods
*CRISPR-Cas Systems
Humans
*Genome, Viral
Herpesvirus 1, Human/genetics
Cytomegalovirus/genetics
*DNA Viruses/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41706678,
year = {2026},
author = {Verhezen, T and Van Den Eynde, A and Verstraelen, P and Gehrcken, L and Palmiotto, G and Lau, HW and De Vos, WH and Van Der Heijden, S and Brants, L and Melis, J and Van Audenaerde, J and Rodrigues Fortes, F and Le Compte, M and Roeyen, G and Prenen, H and Campillo-Davo, D and Lion, E and Argüello, RJ and Van Laere, S and Lardon, F and Deben, C and Wouters, A and Smits, E and De Waele, J},
title = {DRP1 depletion protects NK cells from hypoxia-induced dysfunction.},
journal = {Redox report : communications in free radical research},
volume = {31},
number = {1},
pages = {2626181},
pmid = {41706678},
issn = {1743-2928},
mesh = {*Killer Cells, Natural/metabolism ; Humans ; *Dynamins/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Mitochondria/metabolism ; Cell Line, Tumor ; Cell Hypoxia ; Membrane Potential, Mitochondrial ; *Hypoxia/metabolism ; CRISPR-Cas Systems ; Tumor Microenvironment ; },
abstract = {OBJECTIVES: The efficacy of cellular therapies has been disappointing in solid tumors. A major barrier that contributes to the low success rate, is hypoxia within the tumor microenvironment. In this study, we investigated the influence of hypoxia on natural killer (NK) cell function and to evaluated a strategy to restore their activity in hypoxia.

METHODS: Unarmed or CAR NK cells were placed in normoxia (21% O2) or hypoxia (1% O2) prior to experimental readouts. Mitochondrial content and morphology were assessed by confocal microscopy, membrane potential and reactive oxygen species (ROS) by flow cytometry, and global transcriptional changes by RNA sequencing. Cytotoxicity was evaluated against tumor cell lines and patient-derived cancer organoids, which were characterized by RNA sequencing. DRP1 function was inhibited pharmacologically or through CRISPR-Cas9-mediated knockout.

RESULTS: Hypoxia reduced NK cell mitochondrial content and membrane potential, while increasing mitochondrial ROS and inducing broad transcriptional changes in stress response pathways. Their cytotoxic activity was drastically impaired, which could not be prevented by CD70-CAR-IL-15 engineering. Pharmacological inhibition of DRP1 restored mitochondrial content and cytotoxic function. To confirm the role of DRP1, CRISPR-Cas9-mediated DRP1 knockout (KO) NK cells preserved mitochondrial load and membrane potential under hypoxia, and DRP1[KO] CAR NK cells retained cytotoxic activity under hypoxic conditions against cancer cell lines. Patient microtumor models with distinct transcriptomic profiles exhibited divergent responses to DRP1[WT] and DRP1[KO] CAR NK cells.

CONCLUSION: These findings indicate that DRP1 inactivation supports NK cell function in hypoxia and metabolic engineering may enhance CAR-NK efficacy in solid tumors.},
}

*Killer Cells, Natural/metabolism
Humans
*Dynamins/metabolism/genetics
Reactive Oxygen Species/metabolism
Mitochondria/metabolism
Cell Line, Tumor
Cell Hypoxia
Membrane Potential, Mitochondrial
*Hypoxia/metabolism
CRISPR-Cas Systems
Tumor Microenvironment

@article {pmid41707086,
year = {2026},
author = {Banerjee, S and Banerjee, A and Ray, S and Ray, A and Paul, D and Dastidar, SG and Willard, B and Biswas, K},
title = {dCas9 Targeted Proteome Profiling Reveals p300-Mediated Reciprocal Regulation of SMAD and SP1 as a Driver of GM2-synthase Transcription in Renal Cell Carcinoma.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {4},
pages = {e71597},
doi = {10.1096/fj.202502746R},
pmid = {41707086},
issn = {1530-6860},
support = {2019-0137-CMB/adhoc/BMS//MOHFW | DHR | Indian Council of Medical Research (ICMR)/ ; EMR/2016/001983//Department of Science and Technology, Ministry of Science and Technology, India (DST)/ ; CRG/2021/004623//Department of Science and Technology, Ministry of Science and Technology, India (DST)/ ; },
mesh = {Humans ; *Carcinoma, Renal Cell/genetics/metabolism/pathology ; *Sp1 Transcription Factor/metabolism/genetics ; *Kidney Neoplasms/genetics/metabolism/pathology ; *Smad Proteins/metabolism/genetics ; *Sialyltransferases/genetics/metabolism ; Cell Line, Tumor ; *E1A-Associated p300 Protein/metabolism/genetics ; *Proteome/metabolism/genetics ; Gene Expression Regulation, Neoplastic ; Transcription, Genetic ; CRISPR-Cas Systems ; *p300-CBP Transcription Factors/metabolism ; CRISPR-Associated Protein 9/genetics/metabolism ; },
abstract = {Glycolipids constitute an important component of the plasma membrane based on both abundance as well as function. Gangliosides, being a class of structurally diverse and functionally varied glycolipids, can act both as a receptor as well as a ligand and therefore are established as a crucial player in several normal cellular processes. In certain diseases, and in particular cancer, select gangliosides are over-expressed often leading to disease manifestation. GM2-synthase, the enzyme responsible for the formation of a pro-tumorigenic ganglioside, GM2, is well reported to be over-expressed across various cancer tissues and cell lines. This over-expression of GM2-synthase has been linked with increased migration, invasion, and epithelial to mesenchymal transition (1) as well as induction of a local and systemic host immune suppression in cancer. Despite only a handful of studies demonstrating an epigenetic regulation underlying the transcriptional regulation of the GM2-synthase (B4GalNT1) gene, the detailed mechanism still remains unclear. Here we identified the total proteome associated with the GM2-synthase promoter through a two-step CRISPR-dCas9 based proteome profiling approach by categorizing all the identified proteins leading to a detailed elucidation of the molecular drivers behind GM2-synthase transcription. While the previous study identified an acetylation-dependent de-repression of the transcription factor SP1 causing GM2-synthase activation, the underlying molecular mechanism driving its activation wasn't clear. This study demonstrated that the histone acetyl transferase p300, acts as a pivotal factor which on one hand causes acetylation-mediated degradation of SP1, and on the other hand activates SMAD2/4 to have a direct positive impact on GM2-synthase gene transcription. We identified p300 to have an activator role in GM2-synthase gene transcription through knock out, knock down, and over-expression experiments. Furthermore, SP1 degradation, SMAD activation, and their DNA binding patterns show the reciprocal role of p300 on SP1 and SMAD complexes. Altogether we have identified SMAD2/4 as an activator complex, p300 as a positive regulator, and uncovered a critical p300-SMAD-SP1 regulatory axis in GM2-synthase transcriptional regulation.},
}

Humans
*Carcinoma, Renal Cell/genetics/metabolism/pathology
*Sp1 Transcription Factor/metabolism/genetics
*Kidney Neoplasms/genetics/metabolism/pathology
*Smad Proteins/metabolism/genetics
*Sialyltransferases/genetics/metabolism
Cell Line, Tumor
*E1A-Associated p300 Protein/metabolism/genetics
*Proteome/metabolism/genetics
Gene Expression Regulation, Neoplastic
Transcription, Genetic
CRISPR-Cas Systems
*p300-CBP Transcription Factors/metabolism
CRISPR-Associated Protein 9/genetics/metabolism

@article {pmid41707424,
year = {2026},
author = {Zhao, L and Liu, Z and Ding, G and Zhu, Y and Wang, H and Liu, R and Qu, F and Ao, Q and Zhu, X and Zhang, Y and Yang, G and Wang, Z},
title = {Dual-readout aptasensor based on CRISPR/Cas12a and nanozyme for accurate detection of KIM-1 and its application in kidney transplant prognosis.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118533},
doi = {10.1016/j.bios.2026.118533},
pmid = {41707424},
issn = {1873-4235},
mesh = {*Biosensing Techniques/methods ; Humans ; *Hepatitis A Virus Cellular Receptor 1/isolation & purification ; *Aptamers, Nucleotide/chemistry ; CRISPR-Cas Systems ; *Kidney Transplantation ; Limit of Detection ; Prognosis ; Metal Nanoparticles/chemistry ; Silver/chemistry ; Colorimetry/methods ; Metal-Organic Frameworks/chemistry ; SELEX Aptamer Technique ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {Kidney injury molecule-1 (KIM-1) has emerged as a pivotal prognostic biomarker for renal allograft function. However, its detection remains challenging due to sensitivity and accuracy limitations. An innovative biosensing platform synergizing aptamer recognition, CRISPR trans-cleavage and nanozyme amplification for dual-readout KIM-1 detection has been presented in this work. This platform employs a meticulously selected high-affinity aptamer with capillary electrophoresis SELEX for specific target recognition, leverages the CRISPR/Cas12a system for signal transduction and cascade amplification, and utilizes engineered FeNi MOF@AgNPs nanozyme for dual-signal output. With the presence of KIM-1, whose binding with aptamer, effectively inhibits the trans-cleavage activity of the CRISPR/Cas12a system, and uninhibited Cas12a subsequently cleaves nanozyme-conjugated magnetic probes, releasing FeNi MOF@AgNPs nanozymes that catalyze a TMB-based reaction to generate intense colorimetric and fluorescent dual-readout signals. The as developed aptasensor demonstrates satisfied sensitivity achieving detection limits of 58.7 pg/mL (colorimetric) and 34.4 pg/mL (fluorometric), and dependable accuracy achieving average relative deviation of -2.7% (colorimetric) and 3.2% (fluorometric) with commercial ELISA kit in urine samples from patients with acute kidney injury. Moreover, longitudinally track the dynamic changes in urinary KIM-1 concentrations over the first 8 days following renal transplantation was successfully realized. This work not only provides a robust analytical tool for KIM-1 detection but also establishes a generic research approach for extending CRISPR-based systems to the precise detection of proteins.},
}

*Biosensing Techniques/methods
Humans
*Hepatitis A Virus Cellular Receptor 1/isolation & purification
*Aptamers, Nucleotide/chemistry
CRISPR-Cas Systems
*Kidney Transplantation
Limit of Detection
Prognosis
Metal Nanoparticles/chemistry
Silver/chemistry
Colorimetry/methods
Metal-Organic Frameworks/chemistry
SELEX Aptamer Technique
Bacterial Proteins
Endodeoxyribonucleases
CRISPR-Associated Proteins

@article {pmid41707427,
year = {2026},
author = {Tu, Z and Wang, Y and Qian, X and Chen, J and Li, L and Wang, T and Chen, H and Wei, H and Yang, P and Pan, J and Wang, S and Rong, Z},
title = {Plasmonic magnetic nanoparticles-enabled universal enrichment, photothermal lysis, and duplex CRISPR detection of bacteria in urine samples.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118518},
doi = {10.1016/j.bios.2026.118518},
pmid = {41707427},
issn = {1873-4235},
mesh = {Humans ; *Escherichia coli/isolation & purification/genetics ; *Magnetite Nanoparticles/chemistry ; *Enterococcus faecalis/isolation & purification/genetics ; *Biosensing Techniques/methods ; *Urinary Tract Infections/microbiology/urine/diagnosis ; CRISPR-Cas Systems ; Surface Plasmon Resonance/methods ; *Escherichia coli Infections/urine/microbiology/diagnosis ; Limit of Detection ; Boronic Acids/chemistry ; },
abstract = {Urinary tract infections (UTIs), exacerbated by antibiotic resistance and evolving pathogen diversity, demand rapid and sensitive diagnostics. This study introduces an integrated platform combining magnetic enrichment, photothermal lysis, and CRISPR-based detection (ME-CRISPR) for simultaneous identification of Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis) in UTIs. We engineered plasmonic magnetic nanoparticles functionalized with 4-mercaptophenylboronic acid for broad-spectrum bacterial capture within 10 min. Subsequent near-infrared laser irradiation leveraged localized surface plasmon resonance to lyse captured bacteria in situ. The released nucleic acids were directly analyzed in a single-step duplex RPA-CRISPR/Cas12a-Cas13a assay. This 40-min workflow achieved a limit of detection of 10 CFU/mL for both pathogens. Validation with 90 clinical samples (39 E. coli, 26 E. faecalis, and 25 negative controls) demonstrated 100% sensitivity and specificity, matching qPCR performance while significantly reducing turnaround time. The platform overcomes limitations of centrifugation and Gram-class-dependent lysis, offering a rapid and ultrasensitive point-of-care testing tool to curb antibiotic misuse.},
}

Humans
*Escherichia coli/isolation & purification/genetics
*Magnetite Nanoparticles/chemistry
*Enterococcus faecalis/isolation & purification/genetics
*Biosensing Techniques/methods
*Urinary Tract Infections/microbiology/urine/diagnosis
CRISPR-Cas Systems
Surface Plasmon Resonance/methods
*Escherichia coli Infections/urine/microbiology/diagnosis
Limit of Detection
Boronic Acids/chemistry

@article {pmid41707429,
year = {2026},
author = {Nong, J and Pan, Z and Li, Y and Wei, J and Gong, Y and Li, J and Zhang, K and Liao, X},
title = {COF-confined CsPbBr3 nanocomposite with CRISPR/Cas12a-driven DNA walking for ultrasensitive electrochemiluminescent detection of circulating tumor DNA.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118536},
doi = {10.1016/j.bios.2026.118536},
pmid = {41707429},
issn = {1873-4235},
mesh = {*Biosensing Techniques/methods ; Humans ; *Nanocomposites/chemistry ; Luminescent Measurements/methods ; CRISPR-Cas Systems/genetics ; Electrochemical Techniques/methods ; Limit of Detection ; *Circulating Tumor DNA/blood/isolation & purification/genetics ; Endodeoxyribonucleases/chemistry ; DNA Probes/chemistry ; Metal-Organic Frameworks/chemistry ; Bacterial Proteins ; CRISPR-Associated Proteins ; },
abstract = {A highly sensitive electrochemiluminescence biosensor was developed for circulating tumor DNA detection by integrating a covalent organic framework-confined CsPbBr3 nanocomposite with a CRISPR/Cas12a-driven amplification strategy. The covalent organic framework not only stabilizes CsPbBr3 nanocrystals in aqueous environments but also regulates interfacial charge transfer and enables programmable immobilization of DNA probes. Upon recognition of the target sequence, Cas12a is activated and progressively cleaves surface-tethered quencher-modified DNA strands, leading to stepwise restoration of electrochemiluminescence emission. This surface-confined signal amplification eliminates the need for polymerase chain reaction or isothermal preamplification. Under optimized conditions, the biosensor exhibited a linear response over a concentration range from 10 fM to 10 nM, with a detection limit of 5.4 fM. The method demonstrated good selectivity toward single-base mismatches and satisfactory performance in diluted serum and clinical plasma samples. These results highlight a synergistic material-enzyme strategy for sensitive and robust nucleic acid detection and provide a proof-of-concept platform for electrochemiluminescence-based circulating tumor DNA analysis.},
}

*Biosensing Techniques/methods
Humans
*Nanocomposites/chemistry
Luminescent Measurements/methods
CRISPR-Cas Systems/genetics
Electrochemical Techniques/methods
Limit of Detection
*Circulating Tumor DNA/blood/isolation & purification/genetics
Endodeoxyribonucleases/chemistry
DNA Probes/chemistry
Metal-Organic Frameworks/chemistry
Bacterial Proteins
CRISPR-Associated Proteins

@article {pmid41708610,
year = {2026},
author = {Klann, M and Miura, S and Lee, SH and Vianello, SD and Ross, R and Watanabe, M and Gairin, E and Liang, Y and Hutto, HW and McCluskey, BM and Herrera, M and Solnica-Krezel, L and Besseau, L and Pigolotti, S and Parichy, DM and Kinoshita, M and Laudet, V},
title = {Cell-cell communication as underlying principle governing color pattern formation in teleost fishes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41708610},
issn = {2041-1723},
mesh = {Animals ; *Cell Communication/genetics/physiology ; Zebrafish/genetics ; Gap Junctions/metabolism ; *Pigmentation/genetics/physiology ; Mutation, Missense ; Connexins/genetics/metabolism ; Fish Proteins/genetics/metabolism ; CRISPR-Cas Systems ; Genome-Wide Association Study ; Phenotype ; Gene Editing ; *Perciformes/genetics ; },
abstract = {The diverse pigmentation patterns of animals are crucial for predation avoidance and behavioral display. This diversity arises from interactions among distinct pigment cell types, yet mechanisms generating pattern variation across teleost fishes remain incompletely understood. In zebrafish, Turing models have been proposed to explain stripe patterns, but it is unclear if they apply to other fishes. Here, we investigate the Snowflake mutant of the anemonefish Amphiprion ocellaris, which displays enlarged white bars with irregular boundaries. Using genome-wide association mapping and targeted sequencing, we identify a missense mutation (E42K) in gja5b, encoding the gap junction protein Connexin 41.8. CRISPR/Cas9-mediated genome editing recapitulates the Snowflake phenotype, while pharmacological inhibition of gap junctions phenocopies the boundary defects, supporting a causal role for impaired intercellular communication. Expression analyses reveal that, unlike zebrafish, anemonefish gja5b is predominantly expressed in iridophores. With functional in vitro assays we demonstrate that the E42K mutation acts as a dominant negative, strongly reducing gap junctional coupling. Introducing the same mutation in zebrafish reveals context-dependent effects on pigment patterning. Taken together our findings highlighting gap junction-mediated communication as a conserved but flexible mechanism controlling pigment boundary positioning and pattern diversification.},
}

Animals
*Cell Communication/genetics/physiology
Zebrafish/genetics
Gap Junctions/metabolism
*Pigmentation/genetics/physiology
Mutation, Missense
Connexins/genetics/metabolism
Fish Proteins/genetics/metabolism
CRISPR-Cas Systems
Genome-Wide Association Study
Phenotype
Gene Editing
*Perciformes/genetics

@article {pmid41708664,
year = {2026},
author = {Huo, Y and Mei, J and Zhang, D and Yan, B and Zhang, D and Dong, C and Yin, S and Liu, M and Wang, X and Chen, D and Guan, Y and Song, G and Du, B and Wang, Y and Zheng, Z and Liu, H and Li, D and Yang, L and Wang, L},
title = {Engineered Un1Cas12f1 for multiplex genome editing with enhanced activity and targeting scope.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41708664},
issn = {2041-1723},
support = {U24A20677//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025023//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230064//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32311530111//National Natural Science Foundation of China (National Science Foundation of China)/ ; 24J22800400//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Animals ; Humans ; Mice ; HEK293 Cells ; Genome, Human ; Mutation ; Genetic Therapy/methods ; *CRISPR-Associated Proteins/genetics/metabolism ; },
abstract = {The compact CRISPR-Cas12f system is promising for AAV-delivered gene therapy, but its application has been constrained by restrictive PAM recognition (e.g., TTTR) and suboptimal editing efficiency. Through bacterial library screening and mammalian cell validation, we engineer evoCas12f, an optimized variant incorporating five key mutations, that dramatically expands PAM recognition to NTNR/NYTR. This advancement reduces median distance between two neighbouring PAM sites to 2 nucleotides in the human genome. It also demonstrates 1.4-fold enhanced activity at TTTR sites compared to wild-type Un1Cas12f1, achieving up to 91% editing efficiency. Remarkably, evoCas12f enables efficient generation of homozygous mutations in F0 generation mice, even at non-canonical PAM sites. We further adapt this system for robust transcriptional activation and precise base editing with a well-defined editing window. As a compact yet highly efficient platform, evoCas12f represents a significant advance in CRISPR technology, enabling multiplexed editing for high-resolution targeting applications and expanding possibilities for therapeutic genome engineering.},
}

*Gene Editing/methods
*CRISPR-Cas Systems/genetics
Animals
Humans
Mice
HEK293 Cells
Genome, Human
Mutation
Genetic Therapy/methods
*CRISPR-Associated Proteins/genetics/metabolism

@article {pmid41709648,
year = {2026},
author = {Doghish, AS and Ghaiad, HR and Elfar, N and El Said, NH and Radwan, AF and Abd-Elmawla, MA and Mohamed, HH and Mohammed, OA and Rizk, HA},
title = {Unraveling the Function of lncRNAs in Gliomas: Interaction With Signaling Pathways and Therapeutic Opportunities.},
journal = {Journal of biochemical and molecular toxicology},
volume = {40},
number = {3},
pages = {e70756},
doi = {10.1002/jbt.70756},
pmid = {41709648},
issn = {1099-0461},
mesh = {Humans ; *RNA, Long Noncoding/genetics/metabolism ; *Glioma/genetics/metabolism/therapy/pathology ; *Signal Transduction ; *Brain Neoplasms/metabolism/genetics/therapy/pathology ; Animals ; *Gene Expression Regulation, Neoplastic ; *RNA, Neoplasm/metabolism/genetics ; },
abstract = {Brain tumors represent some of the most formidable challenges in neuro-oncology due to their aggressive clinical course, resistance to therapy, and profound molecular heterogeneity. Among the emerging regulatory elements reshaping our understanding of tumor biology are long non-coding RNAs (lncRNAs), a diverse class of RNA transcripts that modulate gene expression and cellular behavior without encoding proteins. This review provides an in-depth and integrative examination of the biogenesis, regulatory mechanisms, and functional roles of lncRNAs in brain tumor development and progression. We systematically explore both canonical and non-canonical pathways of lncRNA biogenesis, detailing how these influence structural specificity and molecular interactions. This review synthesized evidence retrieved from PubMed/MEDLINE, Scopus, and Web of Science, covering publications from January 2010 to June 2025. This analysis highlights key gaps, such as context-dependent therapeutic effects that limit translational applicability. A major focus is placed on the interplay between lncRNAs and core oncogenic signaling pathways, including Phosphoinositide 3-kinase (PI3K)/serine/threonine kinase (AKT), Signal Transducer and Activator of Transcription 3 (STAT3), Wingless/Int-1 (Wnt)/β-catenin, and Transforming Growth Factor-Beta (TGF-β), which drive malignant transformation, invasion, stemness, and therapeutic resistance in gliomas. Furthermore, we dissect the molecular functions of lncRNAs as epigenetic regulators, competitive endogenous RNAs (ceRNAs), and structural scaffolds, and discuss their contribution to the dynamic tumor microenvironment. By synthesizing the latest findings, this review underscores the academic and translational importance of targeting lncRNA-associated networks. It also highlights emerging therapeutic approaches, such as antisense oligonucleotides, RNA interference, CRISPR-Cas systems, and natural lncRNA-modulating compounds, which collectively represent a promising frontier in precision medicine for brain tumors. This work offers a critical framework for future research and therapeutic innovation in the lncRNA landscape of neuro-oncology.},
}

Humans
*RNA, Long Noncoding/genetics/metabolism
*Glioma/genetics/metabolism/therapy/pathology
*Signal Transduction
*Brain Neoplasms/metabolism/genetics/therapy/pathology
Animals
*Gene Expression Regulation, Neoplastic
*RNA, Neoplasm/metabolism/genetics

@article {pmid41709870,
year = {2026},
author = {Feng, L and Yu, P and He, N and Zhang, Q and Tang, Y and Geng, J and Lu, Q and Song, C and Chen, F},
title = {Label-Free MicroRNA Diagnostics: From CRISPR Nucleases to Nanomaterial-Enhanced Transducers.},
journal = {ACS synthetic biology},
volume = {15},
number = {3},
pages = {915-954},
doi = {10.1021/acssynbio.5c00868},
pmid = {41709870},
issn = {2161-5063},
mesh = {*MicroRNAs/genetics/analysis ; *Biosensing Techniques/methods ; Humans ; *CRISPR-Cas Systems/genetics ; *Nanostructures/chemistry ; },
abstract = {Label-free detection of microRNAs (miRNAs) has emerged as a pivotal approach in molecular diagnostics, integrating the programmability of CRISPR systems with the high sensitivity of nanomaterial-based transduction. miRNAs are short, noncoding RNAs that play central roles in gene regulation and disease pathogenesis, serving as valuable biomarkers for early diagnosis and prognosis. Conventional miRNA detection methods rely on labeling and multistep amplification, which hinder their adaptability for rapid and point-of-care applications. In contrast, label-free biosensing translates molecular recognition into intrinsic optical, electrochemical, or mechanical signals, enabling real-time, amplification-free analysis. This review summarizes recent advances in label-free miRNA biosensing, with emphasis on CRISPR/Cas12a, Cas13a, and Cas14a systems that couple target recognition with signal transduction, and nanomaterial-assisted platforms including gold and silver nanoparticles, carbon nanotubes, quantum dots, silica nanostructures, and magnetic composites. Particular attention is given to innovations that achieve attomolar-level sensitivity, single-nucleotide discrimination, and multiplex detection. We also discuss integration into microfluidic and wearable platforms, addressing persistent challenges in repeatability and stability, antifouling performance, and clinical translation. Emerging trends in artificial intelligence-assisted data processing, molecular logic circuits, and digital single-molecule biosensing are highlighted. These advances collectively outline the pathway toward intelligent, amplification-free, and portable miRNA diagnostics, bridging molecular biology and synthetic bioengineering for next-generation healthcare applications.},
}

*MicroRNAs/genetics/analysis
*Biosensing Techniques/methods
Humans
*CRISPR-Cas Systems/genetics
*Nanostructures/chemistry

@article {pmid41710881,
year = {2026},
author = {Karaoglu, IC and Odabas, A and Önder, T and Kizilel, S},
title = {Single-gene knockout of RNLS or HIVEP2 are insufficient to protect β-cell spheroids from allo- and xeno-rejection.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1759835},
pmid = {41710881},
issn = {1664-3224},
mesh = {Animals ; Mice ; *Insulin-Secreting Cells/transplantation/immunology/metabolism ; Humans ; *Graft Rejection/genetics/immunology/prevention & control ; Gene Knockout Techniques ; *Spheroids, Cellular/immunology/transplantation/metabolism ; CRISPR-Cas Systems ; *Islets of Langerhans Transplantation ; Cell Line ; Gene Editing ; Transplantation, Heterologous ; },
abstract = {INTRODUCTION: β-Cell replacement therapy offers a potential cure for type 1 diabetes, but its success is limited by rapid graft rejection. While genome-wide CRISPR screens have recently identified RNLS and HIVEP2 as candidate genes capable of protecting β-cells from autoimmune destruction, their efficacy against the distinct mechanisms of allogeneic and xenogeneic rejection remains unknown. This study aimed to test the hypothesis that single-gene ablation of RNLS or HIVEP2 protects β-cell spheroids from allo- and xenorejection in immunocompetent hosts.

METHODS: Murine β-TC-6 and human EndoC-βH1 β-cell lines were genetically edited using CRISPR-Cas9 to knockout RNLS or HIVEP2. Editing efficiencies were confirmed via T7 endonuclease I assay and Tracking of Indels by Decomposition (TIDE) analysis. Cells were aggregated into uniform, size-controlled spheroids using an optimized agarose suspension culture. Functional integrity was assessed via glucose-stimulated insulin secretion (GSIS). To evaluate immune evasion in vivo, luciferase-labeled spheroids were transplanted subcutaneously into immunocompetent CD-1 mice, modelling allogeneic (murine-to-murine) and xenogeneic (human-to-murine) rejection, with graft survival monitored longitudinally by bioluminescence imaging.

RESULTS: Robust editing efficiencies were achieved for both targets. Functional characterization indicated that Rnls deletion modestly impaired GSIS in murine cells, whereas HIVEP2 deletion showed no functional alterations in either cell line. In vivo assessment revealed no protective effects of RNLS or HIVEP2 deletion; grafts from both knockout groups displayed rejection kinetics indistinguishable from non-targeting controls. While allogeneic grafts survived longer than xenogeneic grafts, both were ultimately cleared by the host immune system regardless of genotype.

DISCUSSION: These data indicate that single-gene deletions of RNLS or HIVEP2 are insufficient to protect β-cell grafts from the barriers of allo- or xenorejection. By defining the limitations of these targets in isolation, our findings highlight the necessity for combinatorial genome editing strategies or complementary integration with immunomodulatory biomaterials to achieve effective and sustained β-cell graft survival.},
}

Animals
Mice
*Insulin-Secreting Cells/transplantation/immunology/metabolism
Humans
*Graft Rejection/genetics/immunology/prevention & control
Gene Knockout Techniques
*Spheroids, Cellular/immunology/transplantation/metabolism
CRISPR-Cas Systems
*Islets of Langerhans Transplantation
Cell Line
Gene Editing
Transplantation, Heterologous

@article {pmid41710969,
year = {2026},
author = {Xu, Z and Wei, M and Jiang, M and Wang, Y and He, K},
title = {Single-step duplex CRISPR coupled with lateral flow assay for point-of-care detection of human immunodeficiency virus and Treponema pallidum.},
journal = {Analytical methods : advancing methods and applications},
volume = {18},
number = {10},
pages = {1996-2004},
doi = {10.1039/d5ay02168e},
pmid = {41710969},
issn = {1759-9679},
mesh = {Humans ; *Treponema pallidum/genetics/isolation & purification ; *Point-of-Care Systems ; *HIV Infections/diagnosis/virology ; *Syphilis/diagnosis/microbiology ; *CRISPR-Cas Systems/genetics ; *HIV/genetics/isolation & purification ; Point-of-Care Testing ; Sensitivity and Specificity ; },
abstract = {Continued acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) and syphilis caused by Treponema pallidum (TP) pose great challenges for global health, highlighting the need for rapid and sensitive diagnostics. Here, we introduced DIAL (Duplex Integrated All-in-one CRISPR Lateral flow assay), a simplified CRISPR-based diagnostic system for simultaneous detection of HIV and TP. We developed a single-step duplex CRISPR assay for dual-target recognition, which incorporated reverse transcription, multiplex recombinase polymerase amplification, transcription, CRISPR/Cas12a detection, and CRISPR/Cas13a detection in one pot. Then, we combined CRISPR detection assay with a "line-elimination" dual-line lateral flow assay for low-cost and equipment-free visual readout. We further developed reagent lyophilization and extraction-free sample lysis techniques to meet the point-of-care testing. The optimized DIAL system detected as low as 100 copies per µL of both HIV RNA and TP DNA within 45 minutes. In a clinical evaluation of 46 samples, it demonstrated 100% sensitivity and 97.5% specificity for HIV and 90% sensitivity and 100% specificity for TP, relative to quantitative PCR. The DIAL provided a scalable, accessible approach for decentralized screening of sexually transmitted infections or other pathogens in resource-limited settings.},
}

Humans
*Treponema pallidum/genetics/isolation & purification
*Point-of-Care Systems
*HIV Infections/diagnosis/virology
*Syphilis/diagnosis/microbiology
*CRISPR-Cas Systems/genetics
*HIV/genetics/isolation & purification
Point-of-Care Testing
Sensitivity and Specificity